Fluorescence spectroscopy using excitation and emission matrix for quantification of tissue native fluorophores and cancer diagnosis

NASA Astrophysics Data System (ADS)

Wu, Binlin; Gayen, S. K.; Xu, M.

2014-03-01

Native fluorescence spectrum of normal and cancerous human prostate tissues is studied to distinguish between normal and cancerous tissues, and cancerous tissues at different cancer grade. The tissue samples were obtained from Cooperative Human Tissue Network (CHTN) and National Disease Research Interchange(NDRI). An excitation and emission matrix (EEM) was generated for each tissue sample by acquiring native fluorescence spectrum of the sample using multiple excitation wavelengths. The non-negative matrix factorization algorithm was used to generate fluorescence EEMs that correspond to the fluorophores in biological tissues, including tryptophan, collagen, elastin, nicotinamide adenine dinucleotide (NADH), flavin adenine dinucleotide (FAD) and the background paraffin. We hypothesize that, as a consequence of metabolic changes associated with the development of cancer, the concentrations of NADH and FAD are different in normal and cancerous tissues, and also different for different cancer grades. We used the ratio of the abundances of FAD and NADH to distinguish between normal and cancerous tissues, and the tissue cancer grade. The FAD-to-NADH ratio was found to be the highest for normal tissue and decreased as the cancer grade increased.

Typical aqueous rare earth element behavior in co-produced Brines, Wyoming

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

Nye, Charles; Quillinan, Scott; McLing, Travis

Normalization of Rare Earth Elements (REEs) is important to remove the distracting effects of the Oddo–Harkins rule and provide a meaningful baseline. Normalizations for rocks are well developed and include chondritic meteorites, UCC, PM, PAAS, and NASC. However normalizations for aqueous REEs are limited to oceanic regions such as the North Pacific Deep Water or North Atlantic Surface Water. This leaves water in contact with continental lithologies without a suitable normalization. We present a preliminary continental aqueous REE normalization derived from 38 deep basin hydrocarbon brines in Wyoming. The REEs in these waters are seven orders of magnitude more dilutemore » than NASC but with significant europium enrichment. Gromet 1984 reports NASC Eu/Eu* is 0.2179, whereas in the normalization offered here, Eu/Eu* is 3.868. These waters also are free from the distracting reduction-oxidation cerium behavior found in ocean normalizations. Because these samples exhibit both the uniform behavior of NASC and the absolute concentration of seawater, a normalization based upon them offers a unique combination of the advantages of both. We used single-peak gaussian analysis to quantify the mean values for each REE and estimate the distribution variability. Additional sample collection during the last year revealed that the Powder River Basin (PRB) is atypical relative to the other sampled basins of Wyoming. Those other basins are the Wind River Basin (WRB) Green River Basin (GRB) and Wamsutter Area (WA). A pre-normalization gadolinium anomaly (Gd/Gd*) of between 4 and 23 with a mean of 11.5, defines the PRB samples. Other basins in this study range from 1 to 7 with a mean of 2.8. Finally, we present a preliminary model for ligand-based behavior of REEs in these samples. This model identifies bicarbonate, bromide, and chloride as forming significant complexes with REEs contributing to REE solubility. The ligand model explains observed REEs in the sampled Cretaceous and Paleocene clastic reservoirs. However, the presence of more REEs than predicted in six samples suggests that there is an additional, unconsidered ligand contributing to REE dissolution. Further work will identify this ligand, which appears to be confined to calcium-cemented and dolostone systems.« less

Sexual self-esteem in mothers of normal and mentally-retarded children.

PubMed

Tavakolizadeh, Jahanshir; Amiri, Mostafa; Nejad, Fahimeh Rastgoo

2017-06-01

Sexual self-esteem is negatively influenced by the stressful experiences in lifetime. This study compared the sexual self-esteem and its components in mothers with normal and mentally-retarded children in Qaen city, in 2014. A total of 120 mothers were selected and assigned into two groups of 60 samples based on convenient sampling method and randomized multiple stage sampling. Both groups completed sexual self-esteem questionnaire. The data were analyzed employing t-test through SPSS software version15. The results showed that the rate of sexual self-esteem in mothers of mentally-retarded children decreased significantly compared with that of mothers with normal children (p<0.05). Moreover, the mean scores of all components of sexual self-esteem including skill and experience, attractiveness, control, moral judgment, and adaptiveness in mothers of mentally-retarded children were significantly less than those of mothers with normal children (p <0.05). Therefore, it is recommended that self-esteem, especially the sexual one, be taught to mothers of mentally-retarded children by specialists.

The Power of Exclusion using Automated Osteometric Sorting: Pair-Matching.

PubMed

Lynch, Jeffrey James; Byrd, John; LeGarde, Carrie B

2018-03-01

This study compares the original pair-matching osteometric sorting model (J Forensic Sci 2003;48:717) against two new models providing validation and performance testing across three samples. The samples include the Forensic Data Bank, USS Oklahoma, and the osteometric sorting reference used within the Defense POW/MIA Accounting Agency. A computer science solution to generating dynamic statistical models across a commingled assemblage is presented. The issue of normality is investigated showing the relative robustness against non-normality and a data transformation to control for normality. A case study is provided showing the relative exclusion power of all three models from an active commingled case within the Defense POW/MIA Accounting Agency. In total, 14,357,220 osteometric t-tests were conducted. The results indicate that osteometric sorting performs as expected despite reference samples deviating from normality. The two new models outperform the original, and one of those is recommended to supersede the original for future osteometric sorting work. © 2017 American Academy of Forensic Sciences.

Highly preserved consensus gene modules in human papilloma virus 16 positive cervical cancer and head and neck cancers.

PubMed

Zhang, Xianglan; Cha, In-Ho; Kim, Ki-Yeol

2017-12-26

In this study, we investigated the consensus gene modules in head and neck cancer (HNC) and cervical cancer (CC). We used a publicly available gene expression dataset, GSE6791, which included 42 HNC, 14 normal head and neck, 20 CC and 8 normal cervical tissue samples. To exclude bias because of different human papilloma virus (HPV) types, we analyzed HPV16-positive samples only. We identified 3824 genes common to HNC and CC samples. Among these, 977 genes showed high connectivity and were used to construct consensus modules. We demonstrated eight consensus gene modules for HNC and CC using the dissimilarity measure and average linkage hierarchical clustering methods. These consensus modules included genes with significant biological functions, including ATP binding and extracellular exosome. Eigengen network analysis revealed the consensus modules were highly preserved with high connectivity. These findings demonstrate that HPV16-positive head and neck and cervical cancers share highly preserved consensus gene modules with common potentially therapeutic targets.

Highly preserved consensus gene modules in human papilloma virus 16 positive cervical cancer and head and neck cancers

PubMed Central

Zhang, Xianglan; Cha, In-Ho; Kim, Ki-Yeol

2017-01-01

In this study, we investigated the consensus gene modules in head and neck cancer (HNC) and cervical cancer (CC). We used a publicly available gene expression dataset, GSE6791, which included 42 HNC, 14 normal head and neck, 20 CC and 8 normal cervical tissue samples. To exclude bias because of different human papilloma virus (HPV) types, we analyzed HPV16-positive samples only. We identified 3824 genes common to HNC and CC samples. Among these, 977 genes showed high connectivity and were used to construct consensus modules. We demonstrated eight consensus gene modules for HNC and CC using the dissimilarity measure and average linkage hierarchical clustering methods. These consensus modules included genes with significant biological functions, including ATP binding and extracellular exosome. Eigengen network analysis revealed the consensus modules were highly preserved with high connectivity. These findings demonstrate that HPV16-positive head and neck and cervical cancers share highly preserved consensus gene modules with common potentially therapeutic targets. PMID:29371966

Self-Regulation during Pretend Play in Children with Intellectual Disability and in Normally Developing Children

ERIC Educational Resources Information Center

Vieillevoye, Sandrine; Nader-Grosbois, Nathalie

2008-01-01

This study investigated the symbolic behavior and the self-regulation in dyads of children with intellectual disability and of normally developing children. Specifically, these processes were studied in link with the children's characteristics (mental age, linguistic level, individual pretend play level). The sample included 80 participants, 40…

Comparing the social skills of students addicted to computer games with normal students.

PubMed

Zamani, Eshrat; Kheradmand, Ali; Cheshmi, Maliheh; Abedi, Ahmad; Hedayati, Nasim

2010-01-01

This study aimed to investigate and compare the social skills of studentsaddicted to computer games with normal students. The dependentvariable in the present study is the social skills. The study population included all the students in the second grade ofpublic secondary school in the city of Isfahan at the educational year of2009-2010. The sample size included 564 students selected using thecluster random sampling method. Data collection was conducted usingQuestionnaire of Addiction to Computer Games and Social SkillsQuestionnaire (The Teenage Inventory of Social Skill or TISS). The results of the study showed that generally, there was a significantdifference between the social skills of students addicted to computer gamesand normal students. In addition, the results indicated that normal studentshad a higher level of social skills in comparison with students addicted tocomputer games. As the study results showed, addiction to computer games may affectthe quality and quantity of social skills. In other words, the higher theaddiction to computer games, the less the social skills. The individualsaddicted to computer games have less social skills.).

Comparing the Social Skills of Students Addicted to Computer Games with Normal Students

PubMed Central

Zamani, Eshrat; Kheradmand, Ali; Cheshmi, Maliheh; Abedi, Ahmad; Hedayati, Nasim

2010-01-01

Background This study aimed to investigate and compare the social skills of studentsaddicted to computer games with normal students. The dependentvariable in the present study is the social skills. Methods The study population included all the students in the second grade ofpublic secondary school in the city of Isfahan at the educational year of2009-2010. The sample size included 564 students selected using thecluster random sampling method. Data collection was conducted usingQuestionnaire of Addiction to Computer Games and Social SkillsQuestionnaire (The Teenage Inventory of Social Skill or TISS). Findings The results of the study showed that generally, there was a significantdifference between the social skills of students addicted to computer gamesand normal students. In addition, the results indicated that normal studentshad a higher level of social skills in comparison with students addicted tocomputer games. Conclusion As the study results showed, addiction to computer games may affectthe quality and quantity of social skills. In other words, the higher theaddiction to computer games, the less the social skills. The individualsaddicted to computer games have less social skills.). PMID:24494102

Human papillomavirus type-16 variants in Quechua aboriginals from Argentina.

PubMed

Picconi, María Alejandra; Alonio, Lidia Virginia; Sichero, Laura; Mbayed, Viviana; Villa, Luisa Lina; Gronda, Jorge; Campos, Rodolfo; Teyssié, Angélica

2003-04-01

Cervical carcinoma is the leading cause of cancer death in Quechua indians from Jujuy (northwestern Argentina). To determine the prevalence of HPV-16 variants, 106 HPV-16 positive cervical samples were studied, including 33 low-grade squamous intraepithelial lesions (LSIL), 28 high-grade squamous intraepithelial lesions (HSIL), 9 invasive cervical cancer (ICC), and 36 samples from women with normal colposcopy and cytology. HPV genome variability was examined in the L1 and E6 genes by PCR-hybridization. In a subset of 20 samples, a LCR fragment was also analyzed by PCR-sequencing. Most variants belonged to the European branch with subtle differences that depended on the viral gene fragment studied. Only about 10% of the specimens had non-European variants, including eight Asian-American, two Asian, and one North-American-1. E6 gene analysis revealed that 43% of the samples were identical to HPV-16 prototype, while 57% corresponded to variants. Interestingly, the majority (87%) of normal smears had HPV-16 prototype, whereas variants were detected mainly in SIL and ICC. LCR sequencing yielded 80% of variants, including 69% of European, 19% Asian-American, and 12% Asian. We identified a new variant, the Argentine Quechua-51 (AQ-51), similar to B-14 plus two additional changes: G7842-->A and A7837-->C; phylogenetic inference allocated it in the Asian-American branch. The high proportion of European variants may reflect Spanish colonial influence on these native Inca descendants. The predominance of HPV-16 variants in pathologic samples when compared to normal controls could have implications for the natural history of cervical lesions. Copyright 2003 Wiley-Liss, Inc.

Differential diagnosis of urothelial carcinoma in situ from non-neoplastic urothelia: Analysis of CK20, CD44, P53 and Ki67

PubMed Central

Asgari, Mojgan; Nabi Maybodi, Mahtab; Abolhasani, Maryam

2016-01-01

Background: Flat urothelial lesions comprise a spectrum of morphologic changes ranging from reactive atypia to carcinoma in situ (CIS). Urothelial dysplasia and CIS are associated with the recurrence and progression of urothelial carcinoma. Distinguishing CIS and dysplasia from reactive atypia based on histolopathogical features alone is often difficult. Using different immunohistochemical markers such as Cytokeratin 20 (CK20), CD44, p53, and Ki-67 is recommended for differential diagnosis. The aim of this study was to evaluate the immunohistochemical pattern of these antibodies to differentiate different flat urothelial lesions. Methods: In this cross- sectional study, three groups of bladder biopsy specimens were evaluated: 20 samples with reactive urothelial lesions, 20 histologically diagnosed as CIS, and 20 morphologically normal samples. Immunohistochemical staining of CK20, p53, CD44 and Ki-67 markers was performed on paraffin-embedded blocks. The groups were compared using chi square test, and the diagnostic value of the markers were evaluated with sensitivity, specificity, positive and negative predictive values. Results: CK20 was full thickness positive in 15 (75%) CIS samples and negative in all samples of the normal and reactive groups (p<0.001); CD44 was positive in 2 (10%) cases of the CIS group and in 17 (85%) of the reactive group; this marker was negative in all the normal samples (p<0.001). P53 was positive in 12 (60%) samples of the CIS group and negative in all samples of the normal and reactive groups (p<0.001). Ki67 was positive in 13 (65%) samples of the CIS group and 1 (5%) sample of the reactive group. This marker was negative in all samples of the normal group (p<0.001). Conclusion: The results of this study revealed that CK20, CD44, P53 and Ki67 are useful in distinguishing CIS from reactive and normal samples. However, they should be used in a panel including at least three markers. Correlation with the morphologic features is necessary. PMID:27579290

[A semimicroquality evaluation method on Panax notoginseng and its application in analysis of continuous cropping obstacles research samples].

PubMed

Cao, Yi; Wang, Chao-Qun; Xu, Feng; Jia, Xiu-Hong; Liu, Guang-Xue; Yang, Sheng-Chao; Long, Guang-Qiang; Chen, Zhong-Jian; Wei, Fu-Zhou; Yang, Shao-Zhou; Fukuda, Kozo; Wang, Xuan; Cai, Shao-Qing

2016-10-01

Panax notoginseng is a commonly used traditional Chinese medicine with blood activating effect while has continuous cropping obstacle problem in planting process. In present study, a semimicroextraction method with water-saturated n-butanol on 0.1 g notoginseng sample was established with good repeatability (RSD<2.5%) and 9.6%-20.6% higher extraction efficiency of seven saponins than the conventional method. A total of 16 characteristic peaks were identified by LC-MS-IT-TOF, including eight 20(S)-protopanaxatriol (PPT) type saponins and eight 20(S)-protopanaxadiol (PPD) type saponins. The established method was utilized to evaluate the quality of notoginseng samples cultivated by manual intervened methods to overcome continuous cropping obstacles.As a result, HPLC fingerprint similarity, content of Fa and ratio of notoginsenoside K and notoginsenoside Fa (N-K/Fa) were found out to be as valuatable markers of the quality of samples in continuous cropping obstacle research, of which N-K/Fa could also be applied to the analysis of notoginseng samples with different growth years.Notoginseng samples with continuous cropping obstacle had HPLC fingerprint similarity lower than 0.87, in consistent with normal sample, and had significant lower content of notoginsenoside Fa and significant higher N-K/Fa (2.35-4.74) than normal group (0.45-1.33). All samples in the first group with manual intervention showed high similarity with normal group (>0.87), similar content of common peaks and N-K/Fa (0.42-2.06). The content of notoginsenoside K in the second group with manual intervention was higher than normal group. All samples except two displayed similarity higher than 0.87 and possessed content of 16 saponins close to normal group. The result showed that notoginseng samples with continuous cropping obstacle had lower quality than normal sample. And manual intervened methods could improve their quality in different levels.The method established in this study was simple, fast and accurate, and the markers may provide new guides for quality control in continuous cropping obstacle research of notoginseng. Copyright© by the Chinese Pharmaceutical Association.

Chemical analysis of water samples and geophysical logs from cored test holes drilled in the central Oklahoma Aquifer, Oklahoma

USGS Publications Warehouse

Schlottmann, Jamie L.; Funkhouser, Ron A.

1991-01-01

Chemical analyses of water from eight test holes and geophysical logs for nine test holes drilled in the Central Oklahoma aquifer are presented. The test holes were drilled to investigate local occurrences of potentially toxic, naturally occurring trace substances in ground water. These trace substances include arsenic, chromium, selenium, residual alpha-particle activities, and uranium. Eight of the nine test holes were drilled near wells known to contain large concentrations of one or more of the naturally occurring trace substances. One test hole was drilled in an area known to have only small concentrations of any of the naturally occurring trace substances.Water samples were collected from one to eight individual sandstone layers within each test hole. A total of 28 water samples, including four duplicate samples, were collected. The temperature, pH, specific conductance, alkalinity, and dissolved-oxygen concentrations were measured at the sample site. Laboratory determinations included major ions, nutrients, dissolved organic carbon, and trace elements (aluminum, arsenic, barium, beryllium, boron, cadmium, chromium, hexavalent chromium, cobalt, copper, iron, lead, lithium, manganese, mercury, molybdenum, nickel, selenium, silver, strontium, vanadium and zinc). Radionuclide activities and stable isotope (5 values also were determined, including: gross-alpha-particle activity, gross-beta-particle activity, radium-226, radium-228, radon-222, uranium-234, uranium-235, uranium-238, total uranium, carbon-13/carbon-12, deuterium/hydrogen-1, oxygen-18/oxygen-16, and sulfur-34/sulfur-32. Additional analyses of arsenic and selenium species are presented for selected samples as well as analyses of density and iodine for two samples, tritium for three samples, and carbon-14 for one sample.Geophysical logs for most test holes include caliper, neutron, gamma-gamma, natural-gamma logs, spontaneous potential, long- and short-normal resistivity, and single-point resistance. Logs for test-hole NOTS 7 do not include long- and short-normal resistivity, spontaneous-potential, or single-point resistivity. Logs for test-hole NOTS 7A include only caliper and natural-gamma logs.

Subtle imitation behaviour in convenience samples of normal, demented, and currently depressed elderly subjects.

PubMed

von Gunten, Armin; Duc, René

2007-06-01

The clinical significance of imitation behaviour (IB) is unclear. The aim of this study was to investigate the prevalence of subtle naïve and obstinate IB in convenience samples of normal elderly, demented, and depressed subjects. Subtle IB was assessed using a protocol constructed ad hoc in 146 patients, consecutively referred to a memory clinic having received an ICD-10 diagnosis of either dementia or depression, and in 241 healthy subjects. The prevalence of IB in the three groups was determined and the association with possible demographic, cognitive, and non-cognitive variables analysed. Subtle naïve IB was frequent in the elderly with dementia, intermediate in the depressed, and rare in the normal elderly except that the latter frequently stretched out their arms. Obstinate IB never occurred in the normal elderly. IB was predicted by none of the variables used. The groups included were convenience samples with the depressed being a small group precluding further distinction of depressive subtypes. Although naïve IB is a frequent clinical feature in the demented, it also accompanies depressive disorders in the elderly. It can be observed as context-specific IB in the normal elderly. Obstinate IB does not occur in the normal elderly. Copyright 2006 John Wiley & Sons, Ltd.

Using Computer Graphics in Statistics.

ERIC Educational Resources Information Center

Kerley, Lyndell M.

1990-01-01

Described is software which allows a student to use simulation to produce analytical output as well as graphical results. The results include a frequency histogram of a selected population distribution, a frequency histogram of the distribution of the sample means, and test the normality distributions of the sample means. (KR)

Mammary stem cell and macrophage markers are enriched in normal tissue adjacent to inflammatory breast cancer.

PubMed

Reddy, Jay P; Atkinson, Rachel L; Larson, Richard; Burks, Jared K; Smith, Daniel; Debeb, Bisrat G; Ruffell, Brian; Creighton, Chad J; Bambhroliya, Arvind; Reuben, James M; Van Laere, Steven J; Krishnamurthy, Savitri; Symmans, William F; Brewster, Abenaa M; Woodward, Wendy A

2018-06-01

We hypothesized that breast tissue not involved by tumor in inflammatory breast cancer (IBC) patients contains intrinsic differences, including increased mammary stem cells and macrophage infiltration, which may promote the IBC phenotype. Normal breast parenchyma ≥ 5 cm away from primary tumors was obtained from mastectomy specimens. This included an initial cohort of 8 IBC patients and 60 non-IBC patients followed by a validation cohort of 19 IBC patients and 25 non-IBC patients. Samples were immunostained for either CD44 + CD49f + CD133/2 + mammary stem cell markers or the CD68 macrophage marker and correlated with IBC status. Quantitation of positive cells was determined using inForm software from PerkinElmer. We also examined the association between IBC status and previously published tumorigenic stem cell and IBC tumor signatures in the validation cohort samples. 8 of 8 IBC samples expressed isolated CD44 + CD49f + CD133/2 + stem cell marked cells in the initial cohort as opposed to 0/60 non-IBC samples (p = 0.001). Similarly, the median number of CD44 + CD49f + CD133/2 + cells was significantly higher in the IBC validation cohort as opposed to the non-IBC validation cohort (25.7 vs. 14.2, p = 0.007). 7 of 8 IBC samples expressed CD68 + histologically confirmed macrophages in initial cohort as opposed to 12/48 non-IBC samples (p = 0.001). In the validation cohort, the median number of CD68 + cells in IBC was 3.7 versus 1.0 in the non-IBC cohort (p = 0.06). IBC normal tissue was positively associated with a tumorigenic stem cell signature (p = 0.02) and with a 79-gene IBC signature (p < 0.001). Normal tissue from IBC patients is enriched for both mammary stem cells and macrophages and has higher association with both a tumorigenic stem cell signature and IBC-specific tumor signature. Collectively, these data suggest that IBC normal tissue differs from non-IBC tissue. Whether these changes occur before the tumor develops or is induced by tumor warrants further investigation.

Optimal Scaling of Digital Transcriptomes

PubMed Central

Glusman, Gustavo; Caballero, Juan; Robinson, Max; Kutlu, Burak; Hood, Leroy

2013-01-01

Deep sequencing of transcriptomes has become an indispensable tool for biology, enabling expression levels for thousands of genes to be compared across multiple samples. Since transcript counts scale with sequencing depth, counts from different samples must be normalized to a common scale prior to comparison. We analyzed fifteen existing and novel algorithms for normalizing transcript counts, and evaluated the effectiveness of the resulting normalizations. For this purpose we defined two novel and mutually independent metrics: (1) the number of “uniform” genes (genes whose normalized expression levels have a sufficiently low coefficient of variation), and (2) low Spearman correlation between normalized expression profiles of gene pairs. We also define four novel algorithms, one of which explicitly maximizes the number of uniform genes, and compared the performance of all fifteen algorithms. The two most commonly used methods (scaling to a fixed total value, or equalizing the expression of certain ‘housekeeping’ genes) yielded particularly poor results, surpassed even by normalization based on randomly selected gene sets. Conversely, seven of the algorithms approached what appears to be optimal normalization. Three of these algorithms rely on the identification of “ubiquitous” genes: genes expressed in all the samples studied, but never at very high or very low levels. We demonstrate that these include a “core” of genes expressed in many tissues in a mutually consistent pattern, which is suitable for use as an internal normalization guide. The new methods yield robustly normalized expression values, which is a prerequisite for the identification of differentially expressed and tissue-specific genes as potential biomarkers. PMID:24223126

Optimal consistency in microRNA expression analysis using reference-gene-based normalization.

PubMed

Wang, Xi; Gardiner, Erin J; Cairns, Murray J

2015-05-01

Normalization of high-throughput molecular expression profiles secures differential expression analysis between samples of different phenotypes or biological conditions, and facilitates comparison between experimental batches. While the same general principles apply to microRNA (miRNA) normalization, there is mounting evidence that global shifts in their expression patterns occur in specific circumstances, which pose a challenge for normalizing miRNA expression data. As an alternative to global normalization, which has the propensity to flatten large trends, normalization against constitutively expressed reference genes presents an advantage through their relative independence. Here we investigated the performance of reference-gene-based (RGB) normalization for differential miRNA expression analysis of microarray expression data, and compared the results with other normalization methods, including: quantile, variance stabilization, robust spline, simple scaling, rank invariant, and Loess regression. The comparative analyses were executed using miRNA expression in tissue samples derived from subjects with schizophrenia and non-psychiatric controls. We proposed a consistency criterion for evaluating methods by examining the overlapping of differentially expressed miRNAs detected using different partitions of the whole data. Based on this criterion, we found that RGB normalization generally outperformed global normalization methods. Thus we recommend the application of RGB normalization for miRNA expression data sets, and believe that this will yield a more consistent and useful readout of differentially expressed miRNAs, particularly in biological conditions characterized by large shifts in miRNA expression.

Confidence intervals for correlations when data are not normal.

PubMed

Bishara, Anthony J; Hittner, James B

2017-02-01

With nonnormal data, the typical confidence interval of the correlation (Fisher z') may be inaccurate. The literature has been unclear as to which of several alternative methods should be used instead, and how extreme a violation of normality is needed to justify an alternative. Through Monte Carlo simulation, 11 confidence interval methods were compared, including Fisher z', two Spearman rank-order methods, the Box-Cox transformation, rank-based inverse normal (RIN) transformation, and various bootstrap methods. Nonnormality often distorted the Fisher z' confidence interval-for example, leading to a 95 % confidence interval that had actual coverage as low as 68 %. Increasing the sample size sometimes worsened this problem. Inaccurate Fisher z' intervals could be predicted by a sample kurtosis of at least 2, an absolute sample skewness of at least 1, or significant violations of normality hypothesis tests. Only the Spearman rank-order and RIN transformation methods were universally robust to nonnormality. Among the bootstrap methods, an observed imposed bootstrap came closest to accurate coverage, though it often resulted in an overly long interval. The results suggest that sample nonnormality can justify avoidance of the Fisher z' interval in favor of a more robust alternative. R code for the relevant methods is provided in supplementary materials.

Is Season of Birth Related to Developmental Dyslexia?

ERIC Educational Resources Information Center

Donfrancesco, Renato; Iozzino, Roberto; Caruso, Barbara; Ferrante, Laura; Mugnaini, Daniele; Talamo, Alessandra; Miano, Silvia; Dimitri, Andrea; Masi, Gabriele

2010-01-01

Different moderators/mediators of risk are involved in developmental dyslexia (DD), but data are inconsistent. We explored the prevalence of season of birth and its association with gender and age of school entry in an Italian sample of dyslexic children compared to an Italian normal control group. The clinical sample included 498 children (345…

Anomalous waveforms observed in laboratory-formed gas hydrate-bearing and ice-bearing sediments

PubMed Central

Lee, Myung W.; Waite, William F.

2011-01-01

Acoustic transmission measurements of compressional, P, and shear, S, wave velocities rely on correctly identifying the P- and S-body wave arrivals in the measured waveform. In cylindrical samples for which the sample is much longer than the acoustic wavelength, these body waves can be obscured by high-amplitude waveform features arriving just after the relatively small-amplitude P-body wave. In this study, a normal mode approach is used to analyze this type of waveform, observed in sediment containing gas hydrate or ice. This analysis extends an existing normal-mode waveform propagation theory by including the effects of the confining medium surrounding the sample, and provides guidelines for estimating S-wave velocities from waveforms containing multiple large-amplitude arrivals. PMID:21476628

Fragile X protein in newborn dried blood spots.

PubMed

Adayev, Tatyana; LaFauci, Giuseppe; Dobkin, Carl; Caggana, Michele; Wiley, Veronica; Field, Michael; Wotton, Tiffany; Kascsak, Richard; Nolin, Sarah L; Glicksman, Anne; Hosmer, Nicole; Brown, W Ted

2014-10-28

The fragile X syndrome (FXS) results from mutation of the FMR1 gene that prevents expression of its gene product, FMRP. We previously characterized 215 dried blood spots (DBS) representing different FMR1 genotypes and ages with a Luminex-based immunoassay (qFMRP). We found variable FMRP levels in the normal samples and identified affected males by the drastic reduction of FMRP. Here, to establish the variability of expression of FMRP in a larger random population we quantified FMRP in 2,000 anonymous fresh newborn DBS. We also evaluated the effect of long term storage on qFMRP by retrospectively assaying 74 aged newborn DBS that had been stored for 7-84 months that included normal and full mutation individuals. These analyses were performed on 3 mm DBS disks. To identify the alleles associated with the lowest FMRP levels in the fresh DBS, we analyzed the DNA in the samples that were more than two standard deviations below the mean. Analysis of the fresh newborn DBS revealed a broad distribution of FMRP with a mean approximately 7-fold higher than that we previously reported for fresh DBS in normal adults and no samples whose FMRP level indicated FXS. DNA analysis of the lowest FMRP DBS showed that this was the low extreme of the normal range and included a female carrying a 165 CGG repeat premutation. In the retrospective study of aged newborn DBS, the FMRP mean of the normal samples was less than 30% of the mean of the fresh DBS. Despite the degraded signal from these aged DBS, qFMRP identified the FXS individuals. The assay showed that newborn DBS contain high levels of FMRP that will allow identification of males and potentially females, affected by FXS. The assay is also an effective screening tool for aged DBS stored for up to four years.

Differential Expression of c-fos Proto-Oncogene in Normal Oral Mucosa versus Squamous Cell Carcinoma

PubMed Central

Krishna, Akhilesh; Bhatt, Madan Lal Brahma; Singh, Vineeta; Singh, Shraddha; Gangwar, Pravin Kumar; Singh, Uma Shankar; Kumar, Vijay; Mehrotra, Divya

2018-01-01

Background: The c-Fos nuclear protein dimerizes with Jun family proteins to form the transcription factor AP-1 complex which participates in signal transduction and regulation of normal cellular processes. In tumorigenesis, c-Fos promotes invasive growth through down-regulation of tumor suppressor genes but its role in oral carcinogenesis is not clear. Objectives: This study concerned c-fos gene expression in normal and malignant tissues of the oral cavity, with attention to associations between expression status and clinico-pathological profiles of OSCC patients. Method: A total of 65 histopathologically confirmed OSCC tissue samples were included in case group along with an equal number of age and sex-matched normal tissue samples of oral cavity for the control group. c-Fos protein and m-RNA expressions were analyzed using immunohistochemistry and qRT-PCR, respectively. Results: A significant low expression of c-Fos protein was observed in OSCC cases than normal control subjects (p= <0.001). The mean percent positivity of c-Fos protein in cases vs. controls was 24.91± 2.7 vs. 49.68± 2.2 (p= <0.001). Most OSCC tissue samples showed weak or moderate c-Fos expression whereas 53.8% of normal tissue sections presented with strong immunostaining. Moreover, the relative m-RNA expression for the c-fos gene was significantly decreased in case group (0.93± 0.48) as compared to the control group (1.22± 0.87). Majority of c-Fos positive cases were diagnosed with well developed tumor. The mean percent positivity of c-Fos protein was significantly lower in higher grade tumor as compared with normal oral mucosa (p= < 0.001). Conclusion: The present study suggested that the c-fos gene is downregulated in oral carcinomas. The disparity of c-Fos protein levels in different pathological grades of tumor and normal oral tissue samples may indicate that loss of c-Fos expression is related with the progression of OSCC. PMID:29582647

The Classification Accuracy of the Minnesota Multiphasic Personality Inventory--Adolescent: Effects of Modifying the Normative Sample

ERIC Educational Resources Information Center

Hand, Cynthia G.; Archer, Robert P.; Handel, Richard W.; Forbey, Johnathan D.

2007-01-01

Numerous studies have reported that the Minnesota Multiphasic Personality Inventory-Adolescent (MMPI-A) produces a high frequency of within-normal-limits basic scale profiles for adolescents with significant clinical pathology (e.g., Archer, 2005). The current study builds on the observation that the MMPI-A normative sample included participants…

Testing Response-Stimulus Equivalence Relations Using Differential Responses as a Sample

ERIC Educational Resources Information Center

Shimizu, Hirofumi

2006-01-01

This study tested the notion that an equivalence relation may include a response when differential responses are paired with stimuli presented during training. Eight normal adults learned three kinds of computer mouse movements as differential response topographies (R1, R2, and R3). Next, in matching-to-sample training, one of the response…

77 FR 76458 - Fisheries of the Caribbean, Gulf of Mexico, and South Atlantic; Spiny Lobster Fishery of Puerto...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-12-28

... the Caribbean, Gulf of Mexico, and South Atlantic; Spiny Lobster Fishery of Puerto Rico and the U.S... berried Caribbean spiny lobster for non-lethal sampling (tagging) during the course of their normal fishing activities. This non-lethal sampling would include implanting a tag on each spiny lobster before...

NHEXAS PHASE I MARYLAND STUDY--STANDARD OPERATING PROCEDURE FOR CHAIN-OF-CUSTODY AND SAMPLE TRACKING (G04)

EPA Science Inventory

The purpose of the SOP is to establish the normal procedures for ensuring data chain-of-custody and data tracking. The chain-of-custody form included in this SOP is the standard form to be used for all data collected in the field. Keywords: samples; custody; records.

The Nat...

[The value of alpha-methylacyl-CoA racemase expression in the progression of colonic carcinoma].

PubMed

López-Valdivia, Cecilia M; González-Matea, Manuel; Mayordomo, Empar; Hervás, David; Ramos, David

Alpha-methylacyl-CoA racemase (AMACR) expression has been demonstrated in several normal tissues and in diverse types of carcinoma. Our aim was to analyze the immunohistochemical expression of AMACR in the sequence-progression of colonic cancer. We studied 237 cases, including samples of normal mucosa of the colon, adenomas with different degrees of dysplasia, colonic carcinomas, lymph nodes and liver metastases of colonic carcinomas. A scale of intensity and percentage of expression was used to analyze the AMACR immunohistochemical profile. The expression was nearly absent in samples of normal mucosa, increased in both adenomas and carcinomas, decreased in lymph node metastases but was significantly increased in liver metastases. Copyright © 2016 Sociedad Española de Anatomía Patológica. Publicado por Elsevier España, S.L.U. All rights reserved.

Reducing Bias and Error in the Correlation Coefficient Due to Nonnormality.

PubMed

Bishara, Anthony J; Hittner, James B

2015-10-01

It is more common for educational and psychological data to be nonnormal than to be approximately normal. This tendency may lead to bias and error in point estimates of the Pearson correlation coefficient. In a series of Monte Carlo simulations, the Pearson correlation was examined under conditions of normal and nonnormal data, and it was compared with its major alternatives, including the Spearman rank-order correlation, the bootstrap estimate, the Box-Cox transformation family, and a general normalizing transformation (i.e., rankit), as well as to various bias adjustments. Nonnormality caused the correlation coefficient to be inflated by up to +.14, particularly when the nonnormality involved heavy-tailed distributions. Traditional bias adjustments worsened this problem, further inflating the estimate. The Spearman and rankit correlations eliminated this inflation and provided conservative estimates. Rankit also minimized random error for most sample sizes, except for the smallest samples ( n = 10), where bootstrapping was more effective. Overall, results justify the use of carefully chosen alternatives to the Pearson correlation when normality is violated.

Gene expression profiling of human breast tissue samples using SAGE-Seq.

PubMed

Wu, Zhenhua Jeremy; Meyer, Clifford A; Choudhury, Sibgat; Shipitsin, Michail; Maruyama, Reo; Bessarabova, Marina; Nikolskaya, Tatiana; Sukumar, Saraswati; Schwartzman, Armin; Liu, Jun S; Polyak, Kornelia; Liu, X Shirley

2010-12-01

We present a powerful application of ultra high-throughput sequencing, SAGE-Seq, for the accurate quantification of normal and neoplastic mammary epithelial cell transcriptomes. We develop data analysis pipelines that allow the mapping of sense and antisense strands of mitochondrial and RefSeq genes, the normalization between libraries, and the identification of differentially expressed genes. We find that the diversity of cancer transcriptomes is significantly higher than that of normal cells. Our analysis indicates that transcript discovery plateaus at 10 million reads/sample, and suggests a minimum desired sequencing depth around five million reads. Comparison of SAGE-Seq and traditional SAGE on normal and cancerous breast tissues reveals higher sensitivity of SAGE-Seq to detect less-abundant genes, including those encoding for known breast cancer-related transcription factors and G protein-coupled receptors (GPCRs). SAGE-Seq is able to identify genes and pathways abnormally activated in breast cancer that traditional SAGE failed to call. SAGE-Seq is a powerful method for the identification of biomarkers and therapeutic targets in human disease.

Reducing Bias and Error in the Correlation Coefficient Due to Nonnormality

PubMed Central

Hittner, James B.

2014-01-01

It is more common for educational and psychological data to be nonnormal than to be approximately normal. This tendency may lead to bias and error in point estimates of the Pearson correlation coefficient. In a series of Monte Carlo simulations, the Pearson correlation was examined under conditions of normal and nonnormal data, and it was compared with its major alternatives, including the Spearman rank-order correlation, the bootstrap estimate, the Box–Cox transformation family, and a general normalizing transformation (i.e., rankit), as well as to various bias adjustments. Nonnormality caused the correlation coefficient to be inflated by up to +.14, particularly when the nonnormality involved heavy-tailed distributions. Traditional bias adjustments worsened this problem, further inflating the estimate. The Spearman and rankit correlations eliminated this inflation and provided conservative estimates. Rankit also minimized random error for most sample sizes, except for the smallest samples (n = 10), where bootstrapping was more effective. Overall, results justify the use of carefully chosen alternatives to the Pearson correlation when normality is violated. PMID:29795841

Establishment of a cervical cancer bio-bank for the Chinese population: from project-based sample collection to routine management.

PubMed

Yang, Ru; Li, Xiong; Zhou, Hang; Jia, Yao; Zhou, Jin; Huang, Kecheng; Tang, Fangxu; Hu, Ting; Shen, Jian; Chen, Zhilan; Wang, Shaoshuai; Sun, Haiying; Guo, Lili; Wang, Lin; Wang, Hui; Ma, Ding; Li, Shuang

2015-08-01

There is an increasing need for the establishment of a cervical cancer bio-bank that will facilitate both clinical and basic research. The cervical cancer bio-bank was first established in January 1999 and included two stages. First, a GWAS-based sample collection was conducted with special emphasis on the diagnosis and the retrieval of the corresponding bio-specimens, especially blood samples. Second, clinical data and their corresponding bio-specimens were routinely collected and handled. Notably, these bio-specimens also included samples from Wufeng Tujia Autonomous County, which has the highest incidence of cervical cancer in China. The specimens were collected from patients with cervical cancer and those with cervical intraepithelial neoplasia, while the control samples were collected from normal individuals. With special emphasis on clinical data and blood samples for the GWAS analysis, the collection of other bio-specimens was slow, and the pairing of specimens and clinical data was poor during the first stage. However, in the second stage, the pairing of the clinical data and its corresponding bio-specimens improved. At present, the samples procured and preserved in the bio-bank cover most regions of China and different ethnic groups for both the normal controls and cervical cancer patients of different pathological categories. This bio-bank of cervical cancer specimens from the Chinese population will greatly promote the studies of cervical cancer in China.

Composition, toxicity, and mutagenicity of particulate and semivolatile emissions from heavy-duty compressed natural gas-powered vehicles.

PubMed

Seagrave, JeanClare; Gigliotti, Andrew; McDonald, Jacob D; Seilkop, Steven K; Whitney, Kevin A; Zielinska, Barbara; Mauderly, Joe L

2005-09-01

Particulate matter (PM) and vapor-phase semivolatile organic compounds (SVOC) were collected from three buses fueled by compressed natural gas. The bus engines included a well-functioning, conventional engine; a "high emitter" engine; and a new technology engine with an oxidation catalyst. Chemical analysis of the emissions showed differences among these samples, with the high emitter sample containing markers of engine oil constituents. PM + SVOC samples were also collected for mutagenicity and toxicity testing. Extraction efficiencies from the collection media were lower than for similarly collected samples from gasoline or diesel vehicles. Responses to the recovered samples were compared on the basis of exhaust volume, to incorporate the emission rates into the potency factors. Mutagenicity was assessed by Salmonella reverse mutation assay. Mutagenicity was greatest for the high emitter sample and lowest for the new technology sample. Metabolic activation reduced mutagenicity in strain TA100, but not TA98. Toxicity, including inflammation, cytotoxicity, and parenchymal changes, was assessed 24 h after intratracheal instillation into rat lungs. Lung responses were generally mild, with little difference between the responses to equivalent volumes of emissions from the normal emitter and the new technology, but greater responses for the high emitter. These emission sample potencies are further compared on the basis of recovered mass with previously reported samples from normal and high-emitter gasoline and diesel vehicles. While mutagenic potencies for the CNG emission samples were similar to the range observed in the gasoline and diesel emission samples, lung toxicity potency factors were generally lower than those for the gasoline and diesel samples.

Anomalous waveforms observed in laboratory-formed gas hydrate-bearing and ice-bearing sediments

USGS Publications Warehouse

Lee, M.W.; Waite, W.F.

2011-01-01

Acoustic transmission measurements of compressional, P, and shear, S, wave velocities rely on correctly identifying the P- and S-body wave arrivals in the measured waveform. In cylindrical samples for which the sample is much longer than the acoustic wavelength, these body waves can be obscured by high-amplitude waveform features arriving just after the relatively small-amplitude P-body wave. In this study, a normal mode approach is used to analyze this type of waveform, observed in sediment containing gas hydrate or ice. This analysis extends an existing normal-mode waveform propagation theory by including the effects of the confining medium surrounding the sample, and provides guidelines for estimating S-wave velocities from waveforms containing multiple large-amplitude arrivals. ?? 2011 Acoustical Society of America.

Clinical flow cytometric screening of SAP and XIAP expression accurately identifies patients with SH2D1A and XIAP/BIRC4 mutations.

PubMed

Gifford, Carrie E; Weingartner, Elizabeth; Villanueva, Joyce; Johnson, Judith; Zhang, Kejian; Filipovich, Alexandra H; Bleesing, Jack J; Marsh, Rebecca A

2014-07-01

X-linked lymphoproliferative disease is caused by mutations in two genes, SH2D1A and XIAP/BIRC4. Flow cytometric methods have been developed to detect the gene products, SAP and XIAP. However, there is no literature describing the accuracy of flow cytometric screening performed in a clinical lab setting. We reviewed the clinical flow cytometric testing results for 656 SAP and 586 XIAP samples tested during a 3-year period. Genetic testing was clinically performed as directed by the managing physician in 137 SAP (21%) and 115 XIAP (20%) samples. We included these samples for analyses of flow cytometric test accuracy. SH2D1A mutations were detected in 15/137 samples. SAP expression was low in 13/15 (sensitivity 87%, CI 61-97%). Of the 122 samples with normal sequencing, SAP was normal in 109 (specificity 89%, CI 82-94%). The positive predictive values (PPVs) and the negative predictive values (NPVs) were 50% and 98%, respectively. XIAP/BIRC4 mutations were detected in 19/115 samples. XIAP expression was low in 18/19 (sensitivity 95%, CI 73-100%). Of the 96 samples with normal sequencing, 59 had normal XIAP expression (specificity 61%, CI 51-71%). The PPVs and NPVs were 33% and 98%, respectively. Receiver-operating characteristic analysis was able to improve the specificity to 75%. Clinical flow cytometric screening tests for SAP and XIAP deficiencies offer good sensitivity and specificity for detecting genetic mutations, and are characterized by high NPVs. We recommend these tests for patients suspected of having X-linked lymphoproliferative disease type 1 (XLP1) or XLP2. © 2014 Clinical Cytometry Society.

Changes in Abundance of Oral Microbiota Associated with Oral Cancer

PubMed Central

Schmidt, Brian L.; Kuczynski, Justin; Bhattacharya, Aditi; Huey, Bing; Corby, Patricia M.; Queiroz, Erica L. S.; Nightingale, Kira; Kerr, A. Ross; DeLacure, Mark D.; Veeramachaneni, Ratna; Olshen, Adam B.; Albertson, Donna G.

2014-01-01

Individual bacteria and shifts in the composition of the microbiome have been associated with human diseases including cancer. To investigate changes in the microbiome associated with oral cancers, we profiled cancers and anatomically matched contralateral normal tissue from the same patient by sequencing 16S rDNA hypervariable region amplicons. In cancer samples from both a discovery and a subsequent confirmation cohort, abundance of Firmicutes (especially Streptococcus) and Actinobacteria (especially Rothia) was significantly decreased relative to contralateral normal samples from the same patient. Significant decreases in abundance of these phyla were observed for pre-cancers, but not when comparing samples from contralateral sites (tongue and floor of mouth) from healthy individuals. Weighted UniFrac principal coordinates analysis based on 12 taxa separated most cancers from other samples with greatest separation of node positive cases. These studies begin to develop a framework for exploiting the oral microbiome for monitoring oral cancer development, progression and recurrence. PMID:24887397

Concentration trends for lead and calcium-normalized lead in fish fillets from the Big River, a mining-contaminated stream in southeastern Missouri USA

USGS Publications Warehouse

Schmitt, Christopher J.; McKee, Michael J.

2016-01-01

Lead (Pb) and calcium (Ca) concentrations were measured in fillet samples of longear sunfish (Lepomis megalotis) and redhorse suckers (Moxostoma spp.) collected in 2005–2012 from the Big River, which drains a historical mining area in southeastern Missouri and where a consumption advisory is in effect due to elevated Pb concentrations in fish. Lead tends to accumulated in Ca-rich tissues such as bone and scale. Concentrations of Pb in fish muscle are typically low, but can become elevated in fillets from Pb-contaminated sites depending in part on how much bone, scale, and skin is included in the sample. We used analysis-of-covariance to normalize Pb concentration to the geometric mean Ca concentration (415 ug/g wet weight, ww), which reduced variation between taxa, sites, and years, as was the number of samples that exceeded Missouri consumption advisory threshold (300 ng/g ww). Concentrations of Pb in 2005–2012 were lower than in the past, especially after Ca-normalization, but the consumption advisory is still warranted because concentrations were >300 ng/g ww in samples of both taxa from contaminated sites. For monitoring purposes, a simple linear regression model is proposed for estimating Ca-normalized Pb concentrations in fillets from Pb:Ca molar ratios as a way of reducing the effects of differing preparation methods on fillet Pb variation.

Concentration Trends for Lead and Calcium-Normalized Lead in Fish Fillets from the Big River, a Mining-Contaminated Stream in Southeastern Missouri USA.

PubMed

Schmitt, Christopher J; McKee, Michael J

2016-11-01

Lead (Pb) and calcium (Ca) concentrations were measured in fillet samples of longear sunfish (Lepomis megalotis) and redhorse suckers (Moxostoma spp.) collected in 2005-2012 from the Big River, which drains a historical mining area in southeastern Missouri and where a consumption advisory is in effect due to elevated Pb concentrations in fish. Lead tends to accumulated in Ca-rich tissues such as bone and scale. Concentrations of Pb in fish muscle are typically low, but can become elevated in fillets from Pb-contaminated sites depending in part on how much bone, scale, and skin is included in the sample. We used analysis-of-covariance to normalize Pb concentration to the geometric mean Ca concentration (415 ug/g wet weight, ww), which reduced variation between taxa, sites, and years, as was the number of samples that exceeded Missouri consumption advisory threshold (300 ng/g ww). Concentrations of Pb in 2005-2012 were lower than in the past, especially after Ca-normalization, but the consumption advisory is still warranted because concentrations were >300 ng/g ww in samples of both taxa from contaminated sites. For monitoring purposes, a simple linear regression model is proposed for estimating Ca-normalized Pb concentrations in fillets from Pb:Ca molar ratios as a way of reducing the effects of differing preparation methods on fillet Pb variation.

Vaginal lactobacilli profile in pregnant women with normal & abnormal vaginal flora.

PubMed

Yeruva, Thirupathaiah; Rajkumar, Hemalatha; Donugama, Vasundhara

2017-10-01

Lactobacilli species that are better adapted to vaginal environment of women may colonize better and offer protection against vaginal pathogenic bacteria. In this study, the distribution of common Lactobacillus species was investigated in pregnant women. Sixty seven pregnant women were included in the study and vaginal samples were collected for Gram staining. Women were classified as normal vaginal flora, intermediate flora and bacterial vaginosis (BV) based on Nugent's score. Vaginal samples were also collected for the identification of Lactobacillus spp. by multiplex polymerase chain reaction (PCR) profiling of 16S rDNA amplification method. Lactobacillus crispatus (100%) was the most predominant Lactobacillus spp. present in pregnant women with normal flora, followed by L. iners (77%), L. jensenii (74%) and L. helveticus (60%). While, L. iners was commonly present across groups in women with normal, intermediate or BV flora, L. crispatus, L. jensenii and L. helveticus decreased significantly as the vaginal flora changed to intermediate and BV. In women with BV, except L. iners other species of lactobacilli was less frequently prevalent. Species such as L. rhamnosus, L. fermentum, L. paracasei and L. casei were not detected in any vaginal sample. L. crispatus, L. jensinii and L. helveticus were predominant species in women with normal flora. L. crispatus alone or in combination with L. jensinii and L. helveticus may be evaluated for probiotic properties for the prevention and treatment of BV.

Asymptotic confidence intervals for the Pearson correlation via skewness and kurtosis.

PubMed

Bishara, Anthony J; Li, Jiexiang; Nash, Thomas

2018-02-01

When bivariate normality is violated, the default confidence interval of the Pearson correlation can be inaccurate. Two new methods were developed based on the asymptotic sampling distribution of Fisher's z' under the general case where bivariate normality need not be assumed. In Monte Carlo simulations, the most successful of these methods relied on the (Vale & Maurelli, 1983, Psychometrika, 48, 465) family to approximate a distribution via the marginal skewness and kurtosis of the sample data. In Simulation 1, this method provided more accurate confidence intervals of the correlation in non-normal data, at least as compared to no adjustment of the Fisher z' interval, or to adjustment via the sample joint moments. In Simulation 2, this approximate distribution method performed favourably relative to common non-parametric bootstrap methods, but its performance was mixed relative to an observed imposed bootstrap and two other robust methods (PM1 and HC4). No method was completely satisfactory. An advantage of the approximate distribution method, though, is that it can be implemented even without access to raw data if sample skewness and kurtosis are reported, making the method particularly useful for meta-analysis. Supporting information includes R code. © 2017 The British Psychological Society.

User's Guide to the Stand Prognosis Model

Treesearch

William R. Wykoff; Nicholas L. Crookston; Albert R. Stage

1982-01-01

The Stand Prognosis Model is a computer program that projects the development of forest stands in the Northern Rocky Mountains. Thinning options allow for simulation of a variety of management strategies. Input consists of a stand inventory, including sample tree records, and a set of option selection instructions. Output includes data normally found in stand, stock,...

Testing the significance of a correlation with nonnormal data: comparison of Pearson, Spearman, transformation, and resampling approaches.

PubMed

Bishara, Anthony J; Hittner, James B

2012-09-01

It is well known that when data are nonnormally distributed, a test of the significance of Pearson's r may inflate Type I error rates and reduce power. Statistics textbooks and the simulation literature provide several alternatives to Pearson's correlation. However, the relative performance of these alternatives has been unclear. Two simulation studies were conducted to compare 12 methods, including Pearson, Spearman's rank-order, transformation, and resampling approaches. With most sample sizes (n ≥ 20), Type I and Type II error rates were minimized by transforming the data to a normal shape prior to assessing the Pearson correlation. Among transformation approaches, a general purpose rank-based inverse normal transformation (i.e., transformation to rankit scores) was most beneficial. However, when samples were both small (n ≤ 10) and extremely nonnormal, the permutation test often outperformed other alternatives, including various bootstrap tests.

Power of tests of normality for detecting contaminated normal samples

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

Thode, H.C. Jr.; Smith, L.A.; Finch, S.J.

1981-01-01

Seventeen tests of normality or goodness of fit were evaluated for power at detecting a contaminated normal sample. This study used 1000 replications each of samples of size 12, 17, 25, 33, 50, and 100 from six different contaminated normal distributions. The kurtosis test was the most powerful over all sample sizes and contaminations. The Hogg and weighted Kolmogorov-Smirnov tests were second. The Kolmogorov-Smirnov, chi-squared, Anderson-Darling, and Cramer-von-Mises tests had very low power at detecting contaminated normal random variables. Tables of the power of the tests and the power curves of certain tests are given.

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

PubMed

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

2012-07-15

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

Effects of Moisture and Particle Size on Quantitative Determination of Total Organic Carbon (TOC) in Soils Using Near-Infrared Spectroscopy.

PubMed

Tamburini, Elena; Vincenzi, Fabio; Costa, Stefania; Mantovi, Paolo; Pedrini, Paola; Castaldelli, Giuseppe

2017-10-17

Near-Infrared Spectroscopy is a cost-effective and environmentally friendly technique that could represent an alternative to conventional soil analysis methods, including total organic carbon (TOC). Soil fertility and quality are usually measured by traditional methods that involve the use of hazardous and strong chemicals. The effects of physical soil characteristics, such as moisture content and particle size, on spectral signals could be of great interest in order to understand and optimize prediction capability and set up a robust and reliable calibration model, with the future perspective of being applied in the field. Spectra of 46 soil samples were collected. Soil samples were divided into three data sets: unprocessed, only dried and dried, ground and sieved, in order to evaluate the effects of moisture and particle size on spectral signals. Both separate and combined normalization methods including standard normal variate (SNV), multiplicative scatter correction (MSC) and normalization by closure (NCL), as well as smoothing using first and second derivatives (DV1 and DV2), were applied to a total of seven cases. Pretreatments for model optimization were designed and compared for each data set. The best combination of pretreatments was achieved by applying SNV and DV2 on partial least squares (PLS) modelling. There were no significant differences between the predictions using the three different data sets ( p < 0.05). Finally, a unique database including all three data sets was built to include all the sources of sample variability that were tested and used for final prediction. External validation of TOC was carried out on 16 unknown soil samples to evaluate the predictive ability of the final combined calibration model. Hence, we demonstrate that sample preprocessing has minor influence on the quality of near infrared spectroscopy (NIR) predictions, laying the ground for a direct and fast in situ application of the method. Data can be acquired outside the laboratory since the method is simple and does not need more than a simple band ratio of the spectra.

A rapid method for the simultaneous quantification of the major tocopherols, carotenoids, free and esterified sterols in canola (Brassica napus) oil using normal phase liquid chromatography.

PubMed

Flakelar, Clare L; Prenzler, Paul D; Luckett, David J; Howitt, Julia A; Doran, Gregory

2017-01-01

A normal phase high performance liquid chromatography (HPLC) method was developed to simultaneously quantify several prominent bioactive compounds in canola oil vis. α-tocopherol, γ-tocopherol, δ-tocopherol, β-carotene, lutein, β-sitosterol, campesterol and brassicasterol. The use of sequential diode array detection (DAD) and tandem mass spectrometry (MS/MS) allowed direct injection of oils, diluted in hexane without derivatisation or saponification, greatly reducing sample preparation time, and permitting the quantification of both free sterols and intact sterol esters. Further advantages over existing methods included increased analytical selectivity, and a chromatographic run time substantially less than other reported normal phase methods. The HPLC-DAD-MS/MS method was applied to freshly extracted canola oil samples as well as commercially available canola, palm fruit, sunflower and olive oils. Copyright © 2016 Elsevier Ltd. All rights reserved.

Anisotropic analysis of trabecular architecture in human femur bone radiographs using quaternion wavelet transforms.

PubMed

Sangeetha, S; Sujatha, C M; Manamalli, D

2014-01-01

In this work, anisotropy of compressive and tensile strength regions of femur trabecular bone are analysed using quaternion wavelet transforms. The normal and abnormal femur trabecular bone radiographic images are considered for this study. The sub-anatomic regions, which include compressive and tensile regions, are delineated using pre-processing procedures. These delineated regions are subjected to quaternion wavelet transforms and statistical parameters are derived from the transformed images. These parameters are correlated with apparent porosity, which is derived from the strength regions. Further, anisotropy is also calculated from the transformed images and is analyzed. Results show that the anisotropy values derived from second and third phase components of quaternion wavelet transform are found to be distinct for normal and abnormal samples with high statistical significance for both compressive and tensile regions. These investigations demonstrate that architectural anisotropy derived from QWT analysis is able to differentiate normal and abnormal samples.

Mutagenicity and in vivo toxicity of combined particulate and semivolatile organic fractions of gasoline and diesel engine emissions.

PubMed

Seagrave, JeanClare; McDonald, Jacob D; Gigliotti, Andrew P; Nikula, Kristen J; Seilkop, Steven K; Gurevich, Michael; Mauderly, Joe L

2002-12-01

Exposure to engine emissions is associated with adverse health effects. However, little is known about the relative effects of emissions produced by different operating conditions, fuels, or technologies. Rapid screening techniques are needed to compare the biological effects of emissions with different characteristics. Here, we examined a set of engine emission samples using conventional bioassays. The samples included combined particulate material and semivolatile organic compound fractions of emissions collected from normal- and high-emitter gasoline and diesel vehicles collected at 72 degrees F, and from normal-emitter groups collected at 30 degrees F. The relative potency of the samples was determined by statistical analysis of the dose-response curves. All samples induced bacterial mutagenicity, with a 10-fold range of potency among the samples. Responses to intratracheal instillation in rats indicated generally parallel rankings of the samples by multiple endpoints reflecting cytotoxic, inflammatory, and lung parenchymal changes, allowing selection of a more limited set of parameters for future studies. The parameters selected to assess oxidative stress and macrophage function yielded little useful information. Responses to instillation indicated little difference in potency per unit of combined particulate material and semivolatile organic compound mass between normal-emitter gasoline and diesel vehicles, or between emissions collected at different temperatures. However, equivalent masses of emissions from high-emitter vehicles of both types were more potent than those from normal-emitters. While preliminary in terms of assessing contributions of different emissions to health hazards, the results indicate that a subset of this panel of assays will be useful in providing rapid, cost-effective feedback on the biological impact of modified technology.

The great importance of normalization of LC-MS data for highly-accurate non-targeted metabolomics.

PubMed

Mizuno, Hajime; Ueda, Kazuki; Kobayashi, Yuta; Tsuyama, Naohiro; Todoroki, Kenichiro; Min, Jun Zhe; Toyo'oka, Toshimasa

2017-01-01

The non-targeted metabolomics analysis of biological samples is very important to understand biological functions and diseases. LC combined with electrospray ionization-based MS has been a powerful tool and widely used for metabolomic analyses. However, the ionization efficiency of electrospray ionization fluctuates for various unexpected reasons such as matrix effects and intraday variations of the instrument performances. To remove these fluctuations, normalization methods have been developed. Such techniques include increasing the sensitivity, separating co-eluting components and normalizing the ionization efficiencies. Normalization techniques allow simultaneously correcting of the ionization efficiencies of the detected metabolite peaks and achieving quantitative non-targeted metabolomics. In this review paper, we focused on these normalization methods for non-targeted metabolomics by LC-MS. Copyright © 2016 John Wiley & Sons, Ltd.

Illustrated field guide for assessing external and internal anomalies in fish

USGS Publications Warehouse

Smith, Stephen B.; Donahue, Anne P.; Lipkin, Robin J.; Blazer, Vicki; Schmitt, Christopher J.; Goede, Ronald W.

2002-01-01

Procedures are described for processing fish for examination of external and internal anomalies and pathologies indicative of exposure to environmental contaminants and other peturbations. For the procedures described here, fish are captured (preferably by electrofishing) and held alive until processing (generally < 1 h). Fish are weighed, measured, and necropsied, and a scale sample is obtained from for age determination. Information is given for the collection and preservation of tissue samples for histopathological analysis. Photographs of most abnormalities are included along with normal conditions for easier identification of external (oral, head, eye, gill, opercula, and fin) and internal (liver, spleen, gonad, and kidney) anomalies. The report also includes recommendations for record keeping, sample labeling, and shipping records, equipment, supplies,and samples. A list of suggested equipment and supplies for field processing is included as are instructions for cleaning equipment.

Differential expression of glucose transporters in normal and pathologic thyroid tissue.

PubMed

Matsuzu, Kenichi; Segade, Fernando; Matsuzu, Utako; Carter, Aaron; Bowden, Donald W; Perrier, Nancy D

2004-10-01

Malignant cells demonstrate increased glucose uptake and utilization. Immunohistochemical studies have suggested that enhanced glucose uptake in cancer cells may be caused by the overexpression of glucose transporters (GLUTs), in most cases GLUT1 and/or GLUT3. The aim of this study was to examine in detail the expression pattern and levels of GLUT genes in normal and pathologic thyroid tissues and to evaluate the clinical significance of GLUT mRNA levels. One hundred fifty-two surgically resected thyroid tissue samples from 103 patients were evaluated. Samples included: normal thyroid tissue (n = 58), benign thyroid disease (n = 61), and thyroid carcinoma (n = 33). Expression of the GLUT1, GLUT2, GLUT3, GLUT4, and GLUT10 genes were examined by reverse transcription-polymerase chain reaction (RT-PCR) and mRNA levels were quantitated by real-time RT-PCR. All thyroid parenchymal cells expressed GLUT1, GLUT3, GLUT4, and GLUT10. GLUT1 showed increased expression in carcinoma cases (p < 0.0001) and also in comparison with paired normal tissue samples from the same patient (p < 0.0001). Other GLUTs were statistically unchanged in pathologic tissues. These results are consistent with the theory that GLUT1 is upregulated during carcinogenesis and may play a major role in enhanced glucose uptake in thyroid cancer cells.

Increased Steady-State Mutant Huntingtin mRNA in Huntington's Disease Brain.

PubMed

Liu, Wanzhao; Chaurette, Joanna; Pfister, Edith L; Kennington, Lori A; Chase, Kathryn O; Bullock, Jocelyn; Vonsattel, Jean Paul G; Faull, Richard L M; Macdonald, Douglas; DiFiglia, Marian; Zamore, Phillip D; Aronin, Neil

2013-01-01

Huntington's disease is caused by expansion of CAG trinucleotide repeats in the first exon of the huntingtin gene, which is essential for both development and neurogenesis. Huntington's disease is autosomal dominant. The normal allele contains 6 to 35 CAG triplets (average, 18) and the mutant, disease-causing allele contains >36 CAG triplets (average, 42). We examined 279 postmortem brain samples, including 148 HD and 131 non-HD controls. A total of 108 samples from 87 HD patients that are heterozygous at SNP rs362307, with a normal allele (18 to 27 CAG repeats) and a mutant allele (39 to 73 CAG repeats) were used to measure relative abundance of mutant and wild-type huntingtin mRNA. We used allele-specific, quantitative RT-PCR based on SNP heterozygosity to estimate the relative amount of mutant versus normal huntingtin mRNA in postmortem brain samples from patients with Huntington's disease. In the cortex and striatum, the amount of mRNA from the mutant allele exceeds that from the normal allele in 75% of patients. In the cerebellum, no significant difference between the two alleles was evident. Brain tissues from non-HD controls show no significant difference between two alleles of huntingtin mRNAs. Allelic differences were more pronounced at early neuropathological grades (grades 1 and 2) than at late grades (grades 3 and 4). More mutant HTT than normal could arise from increased transcription of mutant HTT allele, or decreased clearance of mutant HTT mRNA, or both. An implication is that equimolar silencing of both alleles would increase the mutant HTT to normal HTT ratio.

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.

Language Sampling for Preschoolers With Severe Speech Impairments

PubMed Central

Ragsdale, Jamie; Bustos, Aimee

2016-01-01

Purpose The purposes of this investigation were to determine if measures such as mean length of utterance (MLU) and percentage of comprehensible words can be derived reliably from language samples of children with severe speech impairments and if such measures correlate with tools that measure constructs assumed to be related. Method Language samples of 15 preschoolers with severe speech impairments (but receptive language within normal limits) were transcribed independently by 2 transcribers. Nonparametric statistics were used to determine which measures, if any, could be transcribed reliably and to determine if correlations existed between language sample measures and standardized measures of speech, language, and cognition. Results Reliable measures were extracted from the majority of the language samples, including MLU in words, mean number of syllables per utterance, and percentage of comprehensible words. Language sample comprehensibility measures were correlated with a single word comprehensibility task. Also, language sample MLUs and mean length of the participants' 3 longest sentences from the MacArthur–Bates Communicative Development Inventory (Fenson et al., 2006) were correlated. Conclusion Language sampling, given certain modifications, may be used for some 3-to 5-year-old children with normal receptive language who have severe speech impairments to provide reliable expressive language and comprehensibility information. PMID:27552110

Language Sampling for Preschoolers With Severe Speech Impairments.

PubMed

Binger, Cathy; Ragsdale, Jamie; Bustos, Aimee

2016-11-01

The purposes of this investigation were to determine if measures such as mean length of utterance (MLU) and percentage of comprehensible words can be derived reliably from language samples of children with severe speech impairments and if such measures correlate with tools that measure constructs assumed to be related. Language samples of 15 preschoolers with severe speech impairments (but receptive language within normal limits) were transcribed independently by 2 transcribers. Nonparametric statistics were used to determine which measures, if any, could be transcribed reliably and to determine if correlations existed between language sample measures and standardized measures of speech, language, and cognition. Reliable measures were extracted from the majority of the language samples, including MLU in words, mean number of syllables per utterance, and percentage of comprehensible words. Language sample comprehensibility measures were correlated with a single word comprehensibility task. Also, language sample MLUs and mean length of the participants' 3 longest sentences from the MacArthur-Bates Communicative Development Inventory (Fenson et al., 2006) were correlated. Language sampling, given certain modifications, may be used for some 3-to 5-year-old children with normal receptive language who have severe speech impairments to provide reliable expressive language and comprehensibility information.

Coexpression patterns of vimentin and glial filament protein with cytokeratins in the normal, hyperplastic, and neoplastic breast.

PubMed Central

Gould, V. E.; Koukoulis, G. K.; Jansson, D. S.; Nagle, R. B.; Franke, W. W.; Moll, R.

1990-01-01

The authors studied by immunohistochemistry the intermediate filament (IF) protein profile of 66 frozen samples of breast tissue, including normal parenchyma, all variants of fibrocystic disease (FCD), fibroadenomas, cystosarcoma phylloides, and ductal and lobular carcinomas. Monoclonal antibodies (MAbs) to cytokeratins included MAb KA 1, which binds to polypeptide 5 in a complex with polypeptide 14 and recognizes preferentially myoepithelial cells; MAb KA4, which binds to polypeptides 14, 15, 16 and 19; individual MAbs to polypeptides 7, 13, and 16, 17, 18, and 19, and the MAb mixture AE1/AE3. The authors also applied three MAbs to vimentin (Vim), and three MAbs to glial filament protein (GFP). Selected samples were studied by double-label immunofluorescence microscopy and by staining sequential sections with some of the said MAbs, an MAb to alpha-smooth muscle actin, and well-characterized polyclonal antibodies for the possible coexpression of diverse types of cytoskeletal proteins. Gel electrophoresis and immunoblot analysis also were performed. All samples reacted for cytokeratins with MAbs AE1/AE3, although the reaction did not involve all cells. Monoclonal antibody KA4 stained preferentially the luminal-secretory cells in the normal breast and in FCD, whereas it stained the vast majority of cells in all carcinomas. Monoclonal antibody KA1 stained preferentially the basal-myoepithelial cells of the normal breast and FCD while staining tumor cell subpopulations in 4 of 31 carcinomas. Vimentin-positive cells were found in 8 of 12 normal breasts and in 12 of 20 FCD; in most cases, Vim-reactive cells appeared to be myoepithelial, but occasional luminal cells were also stained. Variable subpopulations of Vim-positive cells were noted in 9 of 20 ductal and in 1 of 7 lobular carcinomas. Glial filament protein-reactive cells were found in normal breast lobules and ducts and in 15 of 20 cases of FCD; with rare exceptions, GFP-reactivity was restricted to basally located, myoepithelial-appearing cells. Occasional GFP-reactive cells were found in 3 of 31 carcinomas. Evaluation of sequential sections and double-label immunofluorescence microscopy showed the coexpression of certain cytokeratins (possibly including polypeptides 14 and 17) with vimentin and alpha-smooth muscle actin together with GFP in some myoepithelial cells. The presence of GFP in myoepithelial cells was confirmed by gel electrophoresis and immunoblotting. Our results indicate that coexpression of cytokeratin with vimentin and/or GFP is comparatively frequent in normal basal-myoepithelial cells of the breast.(ABSTRACT TRUNCATED AT 400 WORDS) Images Figure 1 Figure 2 Figure 3 Figure 4 PMID:1700618

Association between dental caries and body mass in preschool children.

PubMed

Pikramenou, V; Dimitraki, D; Zoumpoulakis, M; Verykouki, E; Kotsanos, N

2016-06-01

This was to explore the association between dental caries and body mass index (BMI) by conducting a cross-sectional study of a sample of preschool children from a major Greek city. The sample consisted of 2180 children aged 2.5-5.9 years from 33 private day care centres of Thessaloniki. The examinations were performed on site in ample day light by one examiner using disposable dental mirrors and a penlight. Oral examinations included recording of dental caries by dmfs index. Subject's height and weight were measured using a portable measuring unit and a digital scale, respectively. The overall prevalence of underweight, normal weight, overweight and obese children in each BMI-based weight category was 11.8, 72.2, 12.8, and 3.2 %, respectively. The mean age of the total sample was 50.09 (±10.28) months, mean dmfs was 0.36 (±1.9) and the caries-free children were 90.0 %. Overweight children were 1.36 times and obese children 1.99 times more likely to have higher dmfs than normal weight children. The mean dmfs values of underweight children did not significantly differ than that of children with normal weight. The relatively higher dmfs of the obese and overweight children was mostly evident in the older (60-71 months) age group. Caries prevalence in this sample of Greek children attending private day care centres was low. Overweight and obese preschool children were at higher risk of dental caries than normal- and underweight children.

Normalization of mass cytometry data with bead standards

PubMed Central

Finck, Rachel; Simonds, Erin F.; Jager, Astraea; Krishnaswamy, Smita; Sachs, Karen; Fantl, Wendy; Pe’er, Dana; Nolan, Garry P.; Bendall, Sean C.

2013-01-01

Mass cytometry uses atomic mass spectrometry combined with isotopically pure reporter elements to currently measure as many as 40 parameters per single cell. As with any quantitative technology, there is a fundamental need for quality assurance and normalization protocols. In the case of mass cytometry, the signal variation over time due to changes in instrument performance combined with intervals between scheduled maintenance must be accounted for and then normalized. Here, samples were mixed with polystyrene beads embedded with metal lanthanides, allowing monitoring of mass cytometry instrument performance over multiple days of data acquisition. The protocol described here includes simultaneous measurements of beads and cells on the mass cytometer, subsequent extraction of the bead-based signature, and the application of an algorithm enabling correction of both short- and long-term signal fluctuations. The variation in the intensity of the beads that remains after normalization may also be used to determine data quality. Application of the algorithm to a one-month longitudinal analysis of a human peripheral blood sample reduced the range of median signal fluctuation from 4.9-fold to 1.3-fold. PMID:23512433

Subtelomeric multiplex ligation-dependent probe amplification as a supplement for rapid prenatal detection of fetal chromosomal aberrations.

PubMed

Chen, Xiangnan; Li, Huanzheng; Mao, Yijian; Xu, Xueqin; Lv, Jiaojiao; Zhou, Lili; Lin, Xiaoling; Tang, Shaohua

2014-01-01

Pregnant women with high-risk indications are highly suspected of fetal chromosomal aberrations. To determine whether Multiplex Ligation-dependent Probe Amplification (MLPA) using subtelomeric probe mixes (P036-E2 and P070-B2) is a reliable method for rapid detection of fetal chromosomal aberrations. The subtelomeric MLPA probe mixes were used to evaluate 50 blood samples from healthy individuals. 168 amniocytes and 182 umbilical cord blood samples from high-risk fetuses were analyzed using the same subtelomeric MLPA probe sets. Karyotyping was also performed in all cases of high-risk pregnancies, and single nucleotide polymorphism array analysis was used to confirm submicroscopic and ambiguous results from MLPA/karyotyping. Subtelomeric MLPA analysis of normal samples showed normal result in all cases by use of P036-E2 probe mix, while P070-B2 probe mix gave normal results for all but one case. In one normal control case P070-B2 produced a duplicated signal of probe for 13q34. In the high-risk group, totally 44 chromosomal abnormalities were found by karyotyping and MLPA, including 23 aneuploidies and 21 rearrangements or mosaics. MLPA detected all 23 aneuploidies, 12 rearrangements and 1 mosaic. Importantly, MLPA revealed 4 chromosomal translocations, 2 small supernumerary marker chromosomes (sSMCs), and 3 subtelomeric imbalances that were not well characterized or not detectable by karyotyping. However, MLPA showed negetive results for the remaining 8 rearrangements or mosaics, including 3 low mosaic aneuploidies, 1 inherited sSMC, and 4 paracentric inversions. Results suggest that combined use of subtelomeric MLPA and karyotyping may be an alternative method for using karyotype analyses alone in rapid detection of aneuploidies, rearrangements, and sSMCs.

Average of delta: a new quality control tool for clinical laboratories.

PubMed

Jones, Graham R D

2016-01-01

Average of normals is a tool used to control assay performance using the average of a series of results from patients' samples. Delta checking is a process of identifying errors in individual patient results by reviewing the difference from previous results of the same patient. This paper introduces a novel alternate approach, average of delta, which combines these concepts to use the average of a number of sequential delta values to identify changes in assay performance. Models for average of delta and average of normals were developed in a spreadsheet application. The model assessed the expected scatter of average of delta and average of normals functions and the effect of assay bias for different values of analytical imprecision and within- and between-subject biological variation and the number of samples included in the calculations. The final assessment was the number of patients' samples required to identify an added bias with 90% certainty. The model demonstrated that with larger numbers of delta values, the average of delta function was tighter (lower coefficient of variation). The optimal number of samples for bias detection with average of delta was likely to be between 5 and 20 for most settings and that average of delta outperformed average of normals when the within-subject biological variation was small relative to the between-subject variation. Average of delta provides a possible additional assay quality control tool which theoretical modelling predicts may be more valuable than average of normals for analytes where the group biological variation is wide compared with within-subject variation and where there is a high rate of repeat testing in the laboratory patient population. © The Author(s) 2015.

Metabolomic Profiling of Extracellular Vesicles and Alternative Normalization Methods Reveal Enriched Metabolites and Strategies to Study Prostate Cancer-Related Changes

PubMed Central

Puhka, Maija; Takatalo, Maarit; Nordberg, Maria-Elisa; Valkonen, Sami; Nandania, Jatin; Aatonen, Maria; Yliperttula, Marjo; Laitinen, Saara; Velagapudi, Vidya; Mirtti, Tuomas; Kallioniemi, Olli; Rannikko, Antti; Siljander, Pia R-M; af Hällström, Taija Maria

2017-01-01

Body fluids are a rich source of extracellular vesicles (EVs), which carry cargo derived from the secreting cells. So far, biomarkers for pathological conditions have been mainly searched from their protein, (mi)RNA, DNA and lipid cargo. Here, we explored the small molecule metabolites from urinary and platelet EVs relative to their matched source samples. As a proof-of-concept study of intra-EV metabolites, we compared alternative normalization methods to profile urinary EVs from prostate cancer patients before and after prostatectomy and from healthy controls. Methods: We employed targeted ultra-performance liquid chromatography-tandem mass spectrometry to profile over 100 metabolites in the isolated EVs, original urine samples and platelets. We determined the enrichment of the metabolites in the EVs and analyzed their subcellular origin, pathways and relevant enzymes or transporters through data base searches. EV- and urine-derived factors and ratios between metabolites were tested for normalization of the metabolomics data. Results: Approximately 1 x 1010 EVs were sufficient for detection of metabolite profiles from EVs. The profiles of the urinary and platelet EVs overlapped with each other and with those of the source materials, but they also contained unique metabolites. The EVs enriched a selection of cytosolic metabolites including members from the nucleotide and spermidine pathways, which linked to a number of EV-resident enzymes or transporters. Analysis of the urinary EVs from the patients indicated that the levels of glucuronate, D-ribose 5-phosphate and isobutyryl-L-carnitine were 2-26-fold lower in all pre-prostatectomy samples compared to the healthy control and post-prostatectomy samples (p < 0.05). These changes were only detected from EVs by normalization to EV-derived factors or with metabolite ratios, and not from the original urine samples. Conclusions: Our results suggest that metabolite analysis of EVs from different samples is feasible using a high-throughput platform and relatively small amount of sample material. With the knowledge about the specific enrichment of metabolites and normalization methods, EV metabolomics could be used to gain novel biomarker data not revealed by the analysis of the original EV source materials. PMID:29109780

Performance of statistical models to predict mental health and substance abuse cost.

PubMed

Montez-Rath, Maria; Christiansen, Cindy L; Ettner, Susan L; Loveland, Susan; Rosen, Amy K

2006-10-26

Providers use risk-adjustment systems to help manage healthcare costs. Typically, ordinary least squares (OLS) models on either untransformed or log-transformed cost are used. We examine the predictive ability of several statistical models, demonstrate how model choice depends on the goal for the predictive model, and examine whether building models on samples of the data affects model choice. Our sample consisted of 525,620 Veterans Health Administration patients with mental health (MH) or substance abuse (SA) diagnoses who incurred costs during fiscal year 1999. We tested two models on a transformation of cost: a Log Normal model and a Square-root Normal model, and three generalized linear models on untransformed cost, defined by distributional assumption and link function: Normal with identity link (OLS); Gamma with log link; and Gamma with square-root link. Risk-adjusters included age, sex, and 12 MH/SA categories. To determine the best model among the entire dataset, predictive ability was evaluated using root mean square error (RMSE), mean absolute prediction error (MAPE), and predictive ratios of predicted to observed cost (PR) among deciles of predicted cost, by comparing point estimates and 95% bias-corrected bootstrap confidence intervals. To study the effect of analyzing a random sample of the population on model choice, we re-computed these statistics using random samples beginning with 5,000 patients and ending with the entire sample. The Square-root Normal model had the lowest estimates of the RMSE and MAPE, with bootstrap confidence intervals that were always lower than those for the other models. The Gamma with square-root link was best as measured by the PRs. The choice of best model could vary if smaller samples were used and the Gamma with square-root link model had convergence problems with small samples. Models with square-root transformation or link fit the data best. This function (whether used as transformation or as a link) seems to help deal with the high comorbidity of this population by introducing a form of interaction. The Gamma distribution helps with the long tail of the distribution. However, the Normal distribution is suitable if the correct transformation of the outcome is used.

Upregulation of Poly (ADP-Ribose) Polymerase-1 (PARP1) in Triple-Negative Breast Cancer and Other Primary Human Tumor Types

PubMed Central

Ossovskaya, Valeria; Koo, Ingrid Chou; Kaldjian, Eric P.; Alvares, Christopher; Sherman, Barry M.

2010-01-01

Poly (ADP-ribose) polymerase-1 (PARP1) is a key facilitator of DNA repair and is implicated in pathways of tumorigenesis. PARP inhibitors have gained recent attention as rationally designed therapeutics for the treatment of several malignancies, particularly those associated with dysfunctional DNA repair pathways, including triple-negative breast cancer (TNBC). We investigated the PARP1 gene expression profile in surgical samples from more than 8,000 primary malignant and normal human tissues. PARP1 expression was found to be significantly increased in several malignant tissues, including those isolated from patients with breast, uterine, lung, ovarian, and skin cancers, and non-Hodgkin’s lymphoma. Within breast infiltrating ductal carcinoma (IDC) samples tested, mean PARP1 expression was significantly higher relative to normal breast tissue, with over 30% of IDC samples demonstrating upregulation of PARP1, compared with 2.9% of normal tissues. Because of known DNA repair defects, including BRCA1 dysfunction, associated with TNBC, exploration of PARP1 expression in breast cancers related to expression of estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2) led to the observation that negative expression of any of the 3 receptors was associated with upregulation of PARP1 expression, compared with receptor-positive tissues. To validate these observations, an independent set of breast adenocarcinomas was evaluated and demonstrated >2-fold upregulation of PARP1 in approximately 70% of primary breast adenocarcinomas, including TNBC, compared with syngeneic nonmalignant breast tissues. Immunohistochemistry (IHC) showed that upregulation of the PARP1 gene was consistent with increased protein expression in TNBC. These analyses suggest a potential biological role for PARP1 in several distinct malignancies, including TNBC. Further investigation of PARP1 as a biomarker for the therapeutic activity of PARP inhibitor-based therapy is warranted. PMID:21779467

Basal-like Breast Cancers: From Pathology to Biology and Back Again.

PubMed

Gusterson, Barry; Eaves, Connie J

2018-06-05

Human breast cancers referred to as "basal-like" are of interest because they lack effective therapies and their biology is poorly understood. The term basal-like derives from studies demonstrating tumor gene expression profiles that include some transcripts characteristic of the basal cells of the normal adult human mammary gland and others associated with a subset of normal luminal cells. Elucidating the mechanisms responsible for the profiles of basal-like tumors is an active area of investigation. More refined molecular analysis of patients' samples and genetic strategies to produce breast cancers de novo from defined populations of normal mouse mammary cells have served as complementary approaches to identify relevant pathway alterations. However, both also have limitations. Here, we review some of the underlying reasons, including the unifying concept that some normal luminal cells have both luminal and basal features, as well as some emerging new avenues of investigation. Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved.

Usual normalization strategies for gene expression studies impair the detection and analysis of circadian patterns.

PubMed

Figueredo, Diego de Siqueira; Barbosa, Mayara Rodrigues; Coimbra, Daniel Gomes; Dos Santos, José Luiz Araújo; Costa, Ellyda Fernanda Lopes; Koike, Bruna Del Vechio; Alexandre Moreira, Magna Suzana; de Andrade, Tiago Gomes

2018-03-01

Recent studies have shown that transcriptomes from different tissues present circadian oscillations. Therefore, the endogenous variation of total RNA should be considered as a potential bias in circadian studies of gene expression. However, normalization strategies generally include the equalization of total RNA concentration between samples prior to cDNA synthesis. Moreover, endogenous housekeeping genes (HKGs) frequently used for data normalization may exhibit circadian variation and distort experimental results if not detected or considered. In this study, we controlled experimental conditions from the amount of initial brain tissue samples through extraction steps, cDNA synthesis, and quantitative real time PCR (qPCR) to demonstrate a circadian oscillation of total RNA concentration. We also identified that the normalization of the RNA's yield affected the rhythmic profiles of different genes, including Per1-2 and Bmal1. Five widely used HKGs (Actb, Eif2a, Gapdh, Hprt1, and B2m) also presented rhythmic variations not detected by geNorm algorithm. In addition, the analysis of exogenous microRNAs (Cel-miR-54 and Cel-miR-39) spiked during RNA extraction suggests that the yield was affected by total RNA concentration, which may impact circadian studies of small RNAs. The results indicate that the approach of tissue normalization without total RNA equalization prior to cDNA synthesis can avoid bias from endogenous broad variations in transcript levels. Also, the circadian analysis of 2 -Cycle threshold (Ct) data, without HKGs, may be an alternative for chronobiological studies under controlled experimental conditions.

A survey of FRAXE allele sizes in three populations

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

Zhong, N.; Ju, W.; Curley, D.

1996-08-09

FRAXE is a fragile site located at Xq27-8, which contains polymorphic triplet GCC repeats associated with a CpG island. Similar to FRAXA, expansion of the GCC repeats results in an abnormal methylation of the CpG island and is associated with a mild mental retardation syndrome (FRAXE-MR). We surveyed the GCC repeat alleles of FRAXE from 3 populations. A total of 665 X chromosomes including 416 from a New York Euro-American sample (259 normal and 157 with FRAXA mutations), 157 from a Chinese sample (144 normal and 13 FRAXA), and 92 from a Finnish sample (56 normal and 36 FRAXA) weremore » analyzed by polymerase chain reaction. Twenty-seven alleles, ranging from 4 to 39 GCC repeats, were observed. The modal repeat number was 16 in the New York and Finnish samples and accounted for 24% of all the chromosomes tested (162/665). The modal repeat number in the Chinese sample was 18. A founder effect for FRAXA was suggested among the Finnish FRAXA samples in that 75% had the FRAXE 16 repeat allele versus only 30% of controls. Sequencing of the FRAXE region showed no imperfections within the GCC repeat region, such as those commonly seen in FRAXA. The smaller size and limited range of repeats and the lack of imperfections suggests the molecular mechanisms underlying FRAXE triplet mutations may be different from those underlying FRAXA. 27 refs., 4 figs., 1 tab.« less

Perceived health status and cardiometabolic risk among a sample of youth in Mexico

PubMed Central

Flores, Yvonne N.; Shaibi, Gabriel Q.; Morales, Leo S.; Salmerón, Jorge; Skalicky, Anne M.; Edwards, Todd C.; Gallegos-Carrillo, Katia; Patrick, Donald L.

2015-01-01

Purpose To examine differences in self-reported perceived mental and physical health status (PHS), as well as known cardiometabolic risk factors in a sample of normal weight, overweight, and obese Mexican youths. Methods Cross-sectional analysis of 164 youths aged 11-18 years recruited in Cuernavaca, Mexico. Participants completed a self-administered questionnaire that included measures of generic and weight-specific quality of life (QoL), perceived health, physical function, depressive symptoms, and body shape satisfaction. Height, weight and waist circumference were measured and body mass index (BMI) was determined. Fasting blood samples from participants yielded levels of glucose, triglycerides, and cholesterol (total, HDL and LDL). Results Nearly 50% of participants were female, 21% had a normal BMI, 39% were overweight, and 40% were obese. Obese youths reported significantly lower measures of PHS and showed an increase in cardiometabolic risk, compared to normal weight youths. Physical functioning, generic and weight-specific QoL were inversely associated with BMI, waist circumference and glucose. Depressive symptoms were positively correlated with BMI, waist circumference, glucose levels and HDL cholesterol. No correlation was found between PHS and cardiometabolic risk measures after controlling for BMI. Conclusions In this sample of Mexican youths, obesity was associated with a significantly lower PHS and increased cardiometabolic risk. PMID:25648756

Getting DNA copy numbers without control samples

PubMed Central

2012-01-01

Background The selection of the reference to scale the data in a copy number analysis has paramount importance to achieve accurate estimates. Usually this reference is generated using control samples included in the study. However, these control samples are not always available and in these cases, an artificial reference must be created. A proper generation of this signal is crucial in terms of both noise and bias. We propose NSA (Normality Search Algorithm), a scaling method that works with and without control samples. It is based on the assumption that genomic regions enriched in SNPs with identical copy numbers in both alleles are likely to be normal. These normal regions are predicted for each sample individually and used to calculate the final reference signal. NSA can be applied to any CN data regardless the microarray technology and preprocessing method. It also finds an optimal weighting of the samples minimizing possible batch effects. Results Five human datasets (a subset of HapMap samples, Glioblastoma Multiforme (GBM), Ovarian, Prostate and Lung Cancer experiments) have been analyzed. It is shown that using only tumoral samples, NSA is able to remove the bias in the copy number estimation, to reduce the noise and therefore, to increase the ability to detect copy number aberrations (CNAs). These improvements allow NSA to also detect recurrent aberrations more accurately than other state of the art methods. Conclusions NSA provides a robust and accurate reference for scaling probe signals data to CN values without the need of control samples. It minimizes the problems of bias, noise and batch effects in the estimation of CNs. Therefore, NSA scaling approach helps to better detect recurrent CNAs than current methods. The automatic selection of references makes it useful to perform bulk analysis of many GEO or ArrayExpress experiments without the need of developing a parser to find the normal samples or possible batches within the data. The method is available in the open-source R package NSA, which is an add-on to the aroma.cn framework. http://www.aroma-project.org/addons. PMID:22898240

Getting DNA copy numbers without control samples.

PubMed

Ortiz-Estevez, Maria; Aramburu, Ander; Rubio, Angel

2012-08-16

The selection of the reference to scale the data in a copy number analysis has paramount importance to achieve accurate estimates. Usually this reference is generated using control samples included in the study. However, these control samples are not always available and in these cases, an artificial reference must be created. A proper generation of this signal is crucial in terms of both noise and bias.We propose NSA (Normality Search Algorithm), a scaling method that works with and without control samples. It is based on the assumption that genomic regions enriched in SNPs with identical copy numbers in both alleles are likely to be normal. These normal regions are predicted for each sample individually and used to calculate the final reference signal. NSA can be applied to any CN data regardless the microarray technology and preprocessing method. It also finds an optimal weighting of the samples minimizing possible batch effects. Five human datasets (a subset of HapMap samples, Glioblastoma Multiforme (GBM), Ovarian, Prostate and Lung Cancer experiments) have been analyzed. It is shown that using only tumoral samples, NSA is able to remove the bias in the copy number estimation, to reduce the noise and therefore, to increase the ability to detect copy number aberrations (CNAs). These improvements allow NSA to also detect recurrent aberrations more accurately than other state of the art methods. NSA provides a robust and accurate reference for scaling probe signals data to CN values without the need of control samples. It minimizes the problems of bias, noise and batch effects in the estimation of CNs. Therefore, NSA scaling approach helps to better detect recurrent CNAs than current methods. The automatic selection of references makes it useful to perform bulk analysis of many GEO or ArrayExpress experiments without the need of developing a parser to find the normal samples or possible batches within the data. The method is available in the open-source R package NSA, which is an add-on to the aroma.cn framework. http://www.aroma-project.org/addons.

A menu-driven software package of Bayesian nonparametric (and parametric) mixed models for regression analysis and density estimation.

PubMed

Karabatsos, George

2017-02-01

Most of applied statistics involves regression analysis of data. In practice, it is important to specify a regression model that has minimal assumptions which are not violated by data, to ensure that statistical inferences from the model are informative and not misleading. This paper presents a stand-alone and menu-driven software package, Bayesian Regression: Nonparametric and Parametric Models, constructed from MATLAB Compiler. Currently, this package gives the user a choice from 83 Bayesian models for data analysis. They include 47 Bayesian nonparametric (BNP) infinite-mixture regression models; 5 BNP infinite-mixture models for density estimation; and 31 normal random effects models (HLMs), including normal linear models. Each of the 78 regression models handles either a continuous, binary, or ordinal dependent variable, and can handle multi-level (grouped) data. All 83 Bayesian models can handle the analysis of weighted observations (e.g., for meta-analysis), and the analysis of left-censored, right-censored, and/or interval-censored data. Each BNP infinite-mixture model has a mixture distribution assigned one of various BNP prior distributions, including priors defined by either the Dirichlet process, Pitman-Yor process (including the normalized stable process), beta (two-parameter) process, normalized inverse-Gaussian process, geometric weights prior, dependent Dirichlet process, or the dependent infinite-probits prior. The software user can mouse-click to select a Bayesian model and perform data analysis via Markov chain Monte Carlo (MCMC) sampling. After the sampling completes, the software automatically opens text output that reports MCMC-based estimates of the model's posterior distribution and model predictive fit to the data. Additional text and/or graphical output can be generated by mouse-clicking other menu options. This includes output of MCMC convergence analyses, and estimates of the model's posterior predictive distribution, for selected functionals and values of covariates. The software is illustrated through the BNP regression analysis of real data.

Validity of the WISC-IV Spanish for a clinically referred sample of Hispanic children.

PubMed

San Miguel Montes, Liza E; Allen, Daniel N; Puente, Antonio E; Neblina, Cris

2010-06-01

The Wechsler Intelligence Scale for Children (WISC) is the most commonly used intelligence test for children. Five years ago, a Spanish version of the WISC-IV was published (WISC-IV Spanish; Wechsler, 2005), but a limited amount of published information is available regarding its utility when assessing clinical samples. The current study included 107 children who were Spanish speaking and of Puerto Rican descent that had been administered the WISC-IV Spanish. They were subdivided into a clinical sample of 35 children with diagnoses of various forms of brain dysfunction (primarily learning disability, attention-deficit/hyperactivity disorder, and epilepsy) and a comparison group made up of 72 normal children who were part of the WISC-IV Spanish version standardization sample. Comparisons between these groups and the standardization sample were performed for the WISC-IV Spanish index and subtest scores. Results indicated that the clinical sample performed worse than the comparison samples on the Working Memory and Processing Speed Indexes, although findings varied to some extent depending on whether the clinical group was compared with the normal comparison group or the standardization sample. These findings provide support for the criterion validity of the WISC-IV Spanish when it is used to assess a clinically referred sample with brain dysfunction.

TRAM (Transcriptome Mapper): database-driven creation and analysis of transcriptome maps from multiple sources

PubMed Central

2011-01-01

Background Several tools have been developed to perform global gene expression profile data analysis, to search for specific chromosomal regions whose features meet defined criteria as well as to study neighbouring gene expression. However, most of these tools are tailored for a specific use in a particular context (e.g. they are species-specific, or limited to a particular data format) and they typically accept only gene lists as input. Results TRAM (Transcriptome Mapper) is a new general tool that allows the simple generation and analysis of quantitative transcriptome maps, starting from any source listing gene expression values for a given gene set (e.g. expression microarrays), implemented as a relational database. It includes a parser able to assign univocal and updated gene symbols to gene identifiers from different data sources. Moreover, TRAM is able to perform intra-sample and inter-sample data normalization, including an original variant of quantile normalization (scaled quantile), useful to normalize data from platforms with highly different numbers of investigated genes. When in 'Map' mode, the software generates a quantitative representation of the transcriptome of a sample (or of a pool of samples) and identifies if segments of defined lengths are over/under-expressed compared to the desired threshold. When in 'Cluster' mode, the software searches for a set of over/under-expressed consecutive genes. Statistical significance for all results is calculated with respect to genes localized on the same chromosome or to all genome genes. Transcriptome maps, showing differential expression between two sample groups, relative to two different biological conditions, may be easily generated. We present the results of a biological model test, based on a meta-analysis comparison between a sample pool of human CD34+ hematopoietic progenitor cells and a sample pool of megakaryocytic cells. Biologically relevant chromosomal segments and gene clusters with differential expression during the differentiation toward megakaryocyte were identified. Conclusions TRAM is designed to create, and statistically analyze, quantitative transcriptome maps, based on gene expression data from multiple sources. The release includes FileMaker Pro database management runtime application and it is freely available at http://apollo11.isto.unibo.it/software/, along with preconfigured implementations for mapping of human, mouse and zebrafish transcriptomes. PMID:21333005

Viability and Burden of Leishmania in Extralesional Sites during Human Dermal Leishmaniasis

PubMed Central

Romero, Ibeth; Téllez, Jair; Suárez, Yazmín; Cardona, Maria; Figueroa, Roger; Zelazny, Adrian; Gore Saravia, Nancy

2010-01-01

Background The clinical and epidemiological significance of Leishmania DNA in extralesional sites is obscured by uncertainty of whether the DNA derives from viable parasites. To examine dissemination of Leishmania during active disease and the potential participation of human infection in transmission, Leishmania 7SLRNA was exploited to establish viability and estimate parasite burden in extralesional sites of dermal leishmaniasis patients. Methods The feasibility of discriminating parasite viability by PCR of Leishmania 7SLRNA was evaluated in relation with luciferase activity of luc transfected intracellular amastigotes in dose-response assays of Glucantime cytotoxicity. Monocytes, tonsil swabs, aspirates of normal skin and lesions of 28 cutaneous and 2 mucocutaneous leishmaniasis patients were screened by kDNA amplification/Southern blot. Positive samples were analyzed by quantitative PCR of Leishmania 7SLRNA genes and transcripts. Results 7SLRNA amplification coincided with luciferase activity, confirming discrimination of parasite viability. Of 22 patients presenting kDNA in extralesional samples, Leishmania 7SLRNA genes or transcripts were detected in one or more kDNA positive samples in 100% and 73% of patients, respectively. Gene and transcript copy number amplified from extralesional tissues were comparable to lesions. 7SLRNA transcripts were detected in 13/19 (68%) monocyte samples, 5/12 (42%) tonsil swabs, 4/11 (36%) normal skin aspirates, and 22/25 (88%) lesions; genes were quantifiable in 15/19 (79%) monocyte samples, 12/13 (92%) tonsil swabs, 8/11 (73%) normal skin aspirates. Conclusion Viable parasites are present in extralesional sites, including blood monocytes, tonsils and normal skin of dermal leishmaniasis patients. Leishmania 7SLRNA is an informative target for clinical and epidemiologic investigations of human leishmaniasis. PMID:20856851

Molecular Survey of Bacterial Communities Associated with Bacterial Chondronecrosis with Osteomyelitis (BCO) in Broilers

PubMed Central

Jiang, Tieshan; Mandal, Rabindra K.; Wideman, Robert F.; Khatiwara, Anita; Pevzner, Igal; Min Kwon, Young

2015-01-01

Bacterial chondronecrosis with osteomyelitis (BCO) is recognized as an important cause of lameness in commercial broiler chickens (meat-type chickens). Relatively little is known about the microbial communities associated with BCO. This study was conducted to increase our understanding of the microbial factors associated with BCO using a culture-independent approach. Using Illumina sequencing of the hyper-variable region V6 in the 16S rRNA gene, we characterized the bacterial communities in 97 femoral or tibial heads from normal and lame broilers carefully selected to represent diverse variations in age, line, lesion type, floor type, clinical status and bone type. Our in-depth survey based on 14 million assembled sequence reads revealed that complex bacterial communities exist in all samples, including macroscopically normal bones from clinically healthy birds. Overall, Proteobacteria (mean 90.9%) comprised the most common phylum, followed by Firmicutes (6.1%) and Actinobacteria (2.6%), accounting for more than 99% of all reads. Statistical analyses demonstrated that there are differences in bacterial communities in different types of bones (femur vs. tibia), lesion types (macroscopically normal femora or tibiae vs. those with pathognomonic BCO lesions), and among individual birds. This analysis also showed that BCO samples overrepresented genera Staphylococcus, whose species have been frequently isolated in BCO samples in previous studies. Rarefaction analysis demonstrated the general tendency that increased severities of BCO lesions were associated with reduced species diversity in both femoral and tibial samples when compared to macroscopically normal samples. These observations suggest that certain bacterial subgroups are preferentially selected in association with the development of BCO lesions. Understanding the microbial species associated with BCO will identify opportunities for understanding and modulating the pathogenesis of this form of lameness in broilers. PMID:25881241

Human respiratory syncytial virus load normalized by cell quantification as predictor of acute respiratory tract infection.

PubMed

Gómez-Novo, Miriam; Boga, José A; Álvarez-Argüelles, Marta E; Rojo-Alba, Susana; Fernández, Ana; Menéndez, María J; de Oña, María; Melón, Santiago

2018-05-01

Human respiratory syncytial virus (HRSV) is a common cause of respiratory infections. The main objective is to analyze the prediction ability of viral load of HRSV normalized by cell number in respiratory symptoms. A prospective, descriptive, and analytical study was performed. From 7307 respiratory samples processed between December 2014 to April 2016, 1019 HRSV-positive samples, were included in this study. Low respiratory tract infection was present in 729 patients (71.54%). Normalized HRSV load was calculated by quantification of HRSV genome and human β-globin gene and expressed as log10 copies/1000 cells. HRSV mean loads were 4.09 ± 2.08 and 4.82 ± 2.09 log10 copies/1000 cells in the 549 pharyngeal and 470 nasopharyngeal samples, respectively (P < 0.001). The viral mean load was 4.81 ± 1.98 log10 copies/1000 cells for patients under the age of 4-year-old (P < 0.001). The viral mean loads were 4.51 ± 2.04 cells in patients with low respiratory tract infection and 4.22 ± 2.28 log10 copies/1000 cells with upper respiratory tract infection or febrile syndrome (P < 0.05). A possible cut off value to predict LRTI evolution was tentatively established. Normalization of viral load by cell number in the samples is essential to ensure an optimal virological molecular diagnosis avoiding that the quality of samples affects the results. A high viral load can be a useful marker to predict disease progression. © 2018 Wiley Periodicals, Inc.

Improving CSF biomarker accuracy in predicting prevalent and incident Alzheimer disease

PubMed Central

Fagan, A.M.; Williams, M.M.; Ghoshal, N.; Aeschleman, M.; Grant, E.A.; Marcus, D.S.; Mintun, M.A.; Holtzman, D.M.; Morris, J.C.

2011-01-01

Objective: To investigate factors, including cognitive and brain reserve, which may independently predict prevalent and incident dementia of the Alzheimer type (DAT) and to determine whether inclusion of identified factors increases the predictive accuracy of the CSF biomarkers Aβ42, tau, ptau181, tau/Aβ42, and ptau181/Aβ42. Methods: Logistic regression identified variables that predicted prevalent DAT when considered together with each CSF biomarker in a cross-sectional sample of 201 participants with normal cognition and 46 with DAT. The area under the receiver operating characteristic curve (AUC) from the resulting model was compared with the AUC generated using the biomarker alone. In a second sample with normal cognition at baseline and longitudinal data available (n = 213), Cox proportional hazards models identified variables that predicted incident DAT together with each biomarker, and the models' concordance probability estimate (CPE), which was compared to the CPE generated using the biomarker alone. Results: APOE genotype including an ε4 allele, male gender, and smaller normalized whole brain volumes (nWBV) were cross-sectionally associated with DAT when considered together with every biomarker. In the longitudinal sample (mean follow-up = 3.2 years), 14 participants (6.6%) developed DAT. Older age predicted a faster time to DAT in every model, and greater education predicted a slower time in 4 of 5 models. Inclusion of ancillary variables resulted in better cross-sectional prediction of DAT for all biomarkers (p < 0.0021), and better longitudinal prediction for 4 of 5 biomarkers (p < 0.0022). Conclusions: The predictive accuracy of CSF biomarkers is improved by including age, education, and nWBV in analyses. PMID:21228296

MR morphology of triangular fibrocartilage complex: correlation with quantitative MR and biomechanical properties.

PubMed

Bae, Won C; Ruangchaijatuporn, Thumanoon; Chang, Eric Y; Biswas, Reni; Du, Jiang; Statum, Sheronda; Chung, Christine B

2016-04-01

To evaluate pathology of the triangular fibrocartilage complex (TFCC) using high-resolution morphologic magnetic resonance (MR) imaging, and compare with quantitative MR and biomechanical properties. Five cadaveric wrists (22-70 years) were imaged at 3 T using morphologic (proton density weighted spin echo, PD FS, and 3D spoiled gradient echo, 3D SPGR) and quantitative MR sequences to determine T2 and T1rho properties. In eight geographic regions, morphology of TFC disc and laminae were evaluated for pathology and quantitative MR values. Samples were disarticulated and biomechanical indentation testing was performed on the distal surface of the TFC disc. On morphologic PD SE images, TFC disc pathology included degeneration and tears, while that of the laminae included degeneration, degeneration with superimposed tear, mucinous transformation, and globular calcification. Punctate calcifications were highly visible on 3D SPGR images and found only in pathologic regions. Disc pathology occurred more frequently in proximal regions of the disc than distal regions. Quantitative MR values were lowest in normal samples, and generally higher in pathologic regions. Biomechanical testing demonstrated an inverse relationship, with indentation modulus being high in normal regions with low MR values. The laminae studied were mostly pathologic, and additional normal samples are needed to discern quantitative changes. These results show technical feasibility of morphologic MR, quantitative MR, and biomechanical techniques to characterize pathology of the TFCC. Quantitative MRI may be a suitable surrogate marker of soft tissue mechanical properties, and a useful adjunct to conventional morphologic MR techniques.

Experimental investigation of the tip based micro/nano machining

NASA Astrophysics Data System (ADS)

Guo, Z.; Tian, Y.; Liu, X.; Wang, F.; Zhou, C.; Zhang, D.

2017-12-01

Based on the self-developed three dimensional micro/nano machining system, the effects of machining parameters and sample material on micro/nano machining are investigated. The micro/nano machining system is mainly composed of the probe system and micro/nano positioning stage. The former is applied to control the normal load and the latter is utilized to realize high precision motion in the xy plane. A sample examination method is firstly introduced to estimate whether the sample is placed horizontally. The machining parameters include scratching direction, speed, cycles, normal load and feed. According to the experimental results, the scratching depth is significantly affected by the normal load in all four defined scratching directions but is rarely influenced by the scratching speed. The increase of scratching cycle number can increase the scratching depth as well as smooth the groove wall. In addition, the scratching tests of silicon and copper attest that the harder material is easier to be removed. In the scratching with different feed amount, the machining results indicate that the machined depth increases as the feed reduces. Further, a cubic polynomial is used to fit the experimental results to predict the scratching depth. With the selected machining parameters of scratching direction d3/d4, scratching speed 5 μm/s and feed 0.06 μm, some more micro structures including stair, sinusoidal groove, Chinese character '田', 'TJU' and Chinese panda have been fabricated on the silicon substrate.

Magnetic measurements on human erythrocytes: Normal, beta thalassemia major, and sickle

NASA Astrophysics Data System (ADS)

Sakhnini, Lama

2003-05-01

In this article magnetic measurements were made on human erythrocytes at different hemoglobin states (normal and reduced hemoglobin). Different blood samples: normal, beta thalassemia major, and sickle were studied. Beta thalassemia major and sickle samples were taken from patients receiving lifelong blood transfusion treatment. All samples examined exhibited diamagnetic behavior. Beta thalassemia major and sickle samples showed higher diamagnetic susceptibilities than that for the normal, which was attributed to the increase of membrane to hemoglobin volume ratio of the abnormal cells. Magnetic measurements showed that the erythrocytes in the reduced state showed less diamagnetic response in comparison with erythrocytes in the normal state. Analysis of the paramagnetic component of magnetization curves gave an effective magnetic moment of μeff=7.6 μB per reduced hemoglobin molecule. The same procedure was applied to sickle and beta thalassemia major samples and values for μeff were found to be comparable to that of the normal erythrocytes.

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.

Sialidase activity in aerobic vaginitis is equal to levels during bacterial vaginosis.

PubMed

Marconi, C; Donders, G G G; Bellen, G; Brown, D R; Parada, C M G L; Silva, M G

2013-04-01

To evaluate levels of proinflammatory cytokines and sialidase activity in aerobic vaginitis (AV) in relation to normal vaginal flora and bacterial vaginosis (BV). In this cross-sectional study, a total of 682 consecutive non-pregnant women attending the gynecology service were assessed and 408 women were included. Vaginal rinsing samples were collected from 223 women with microscopic finding of BV (n=98), aerobic vaginitis (n=25) and normal flora (n=100). Samples were tested for interleukin (IL)-1β, IL-6, IL-8, tumor necrosis factor (TNF)-α, and sialidase activity. Compared to women with normal flora, vaginal levels of IL-1β were highly increased in both BV and AV (p<0.0001). Significantly higher vaginal IL-6 was detected in AV (p<0.0001) but not in BV, in relation to normal flora. Women with AV also presented increased IL-8 levels (p<0.001), while those with BV presented levels similar to normal flora. Sialidase was increased in BV and AV compared with the normal group (p<0.0001) but no difference in sialidase activity was observed between BV and AV. A more intense inflammatory host response occurs for AV than for BV when compared with normal flora. Furthermore, the increased sialidase activity in AV and BV indicates that both abnormal vaginal flora types can be harmful to the maintenance of a healthy vaginal environment. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

Bayesian Normalization Model for Label-Free Quantitative Analysis by LC-MS

PubMed Central

Nezami Ranjbar, Mohammad R.; Tadesse, Mahlet G.; Wang, Yue; Ressom, Habtom W.

2016-01-01

We introduce a new method for normalization of data acquired by liquid chromatography coupled with mass spectrometry (LC-MS) in label-free differential expression analysis. Normalization of LC-MS data is desired prior to subsequent statistical analysis to adjust variabilities in ion intensities that are not caused by biological differences but experimental bias. There are different sources of bias including variabilities during sample collection and sample storage, poor experimental design, noise, etc. In addition, instrument variability in experiments involving a large number of LC-MS runs leads to a significant drift in intensity measurements. Although various methods have been proposed for normalization of LC-MS data, there is no universally applicable approach. In this paper, we propose a Bayesian normalization model (BNM) that utilizes scan-level information from LC-MS data. Specifically, the proposed method uses peak shapes to model the scan-level data acquired from extracted ion chromatograms (EIC) with parameters considered as a linear mixed effects model. We extended the model into BNM with drift (BNMD) to compensate for the variability in intensity measurements due to long LC-MS runs. We evaluated the performance of our method using synthetic and experimental data. In comparison with several existing methods, the proposed BNM and BNMD yielded significant improvement. PMID:26357332

Copy Number Variations of TBK1 in Australian Patients With Primary Open-Angle Glaucoma

PubMed Central

AWADALLA, MONA S.; FINGERT, JOHN H.; ROOS, BENJAMIN E.; CHEN, SIMON; HOLMES, RICHARD; GRAHAM, STUART L.; CHEHADE, MARK; GALANOPOLOUS, ANNA; RIDGE, BRONWYN; SOUZEAU, EMMANUELLE; ZHOU, TIGER; SIGGS, OWEN M.; HEWITT, ALEX W.; MACKEY, DAVID A.; BURDON, KATHRYN P.; CRAIG, JAMIE E.

2015-01-01

PURPOSE To investigate the presence of TBK1 copy number variations in a large, well-characterized Australian cohort of patients with glaucoma comprising both normal-tension glaucoma and high-tension glaucoma cases. DESIGN A retrospective cohort study. METHODS DNA samples from patients with normal-tension glaucoma and high-tension glaucoma and unaffected controls were screened for TBK1 copy number variations using real-time quantitative polymerase chain reaction. Samples with additional copies of the TBK1 gene were further tested using custom comparative genomic hybridization arrays. RESULTS Four out of 334 normal-tension glaucoma cases (1.2%) were found to carry TBK1 copy number variations using quantitative polymerase chain reaction. One extra dose of the TBK1 gene (duplication) was detected in 3 normal-tension glaucoma patients, while 2 extra doses of the gene (triplication) were detected in a fourth normal-tension glaucoma patient. The results were further confirmed by custom comparative genomic hybridization arrays. Further, the TBK1 copy number variation segregated with normal-tension glaucoma in the family members of the probands, showing an autosomal dominant pattern of inheritance. No TBK1 copy number variations were detected in 1045 Australian patients with high-tension glaucoma or in 254 unaffected controls. CONCLUSION We report the presence of TBK1 copy number variations in our Australian normal-tension glaucoma cohort, including the first example of more than 1 extra copy of this gene in glaucoma patients (gene triplication). These results confirm TBK1 to be an important cause of normal-tension glaucoma, but do not suggest common involvement in high-tension glaucoma. PMID:25284765

Effect of a single intra-articular injection of bupivacaine on synovial fluid prostaglandin E2 concentrations in normal canine stifles.

PubMed

Giangarra, Jenna E; Barry, Sabrina L; Dahlgren, Linda A; Lanz, Otto I; Benitez, Marian E; Werre, Stephen R

2018-04-25

To identify if synovial fluid prostaglandin E 2 increases in response to a single intra-articular dose of bupivacaine in the normal canine stifle. There were no significant differences in synovial fluid prostaglandin E 2 (PGE 2 ) concentrations between treatment groups or over time within bupivacaine or saline groups. Samples requiring ≥ 3 arthrocentesis attempts had significantly higher PGE 2 concentrations compared to samples requiring 1 or 2 attempts. Following correction for number of arthrocentesis attempts, PGE 2 concentrations were significantly higher than baseline at 24 and 48 h in the bupivacaine group; however there were no significant differences between the bupivacaine and saline groups. In normal dogs, a single bupivacaine injection did not cause significant synovial inflammation, as measured by PGE 2 concentrations, compared to saline controls. Future research should minimize aspiration attempts and include evaluation of the synovial response to bupivacaine in clinical cases with joint disease.

OP17MICRORNA PROFILING USING SMALL RNA-SEQ IN PAEDIATRIC LOW GRADE GLIOMAS

PubMed Central

Jeyapalan, Jennie N.; Jones, Tania A.; Tatevossian, Ruth G.; Qaddoumi, Ibrahim; Ellison, David W.; Sheer, Denise

2014-01-01

INTRODUCTION: MicroRNAs regulate gene expression by targeting mRNAs for translational repression or degradation at the post-transcriptional level. In paediatric low-grade gliomas a few key genetic mutations have been identified, including BRAF fusions, FGFR1 duplications and MYB rearrangements. Our aim in the current study is to profile aberrant microRNA expression in paediatric low-grade gliomas and determine the role of epigenetic changes in the aetiology and behaviour of these tumours. METHOD: MicroRNA profiling of tumour samples (6 pilocytic, 2 diffuse, 2 pilomyxoid astrocytomas) and normal brain controls (4 adult normal brain samples and a primary glial progenitor cell-line) was performed using small RNA sequencing. Bioinformatic analysis included sequence alignment, analysis of the number of reads (CPM, counts per million) and differential expression. RESULTS: Sequence alignment identified 695 microRNAs, whose expression was compared in tumours v. normal brain. PCA and hierarchical clustering showed separate groups for tumours and normal brain. Computational analysis identified approximately 400 differentially expressed microRNAs in the tumours compared to matched location controls. Our findings will then be validated and integrated with extensive genetic and epigenetic information we have previously obtained for the full tumour cohort. CONCLUSION: We have identified microRNAs that are differentially expressed in paediatric low-grade gliomas. As microRNAs are known to target genes involved in the initiation and progression of cancer, they provide critical information on tumour pathogenesis and are an important class of biomarkers.

A Molecular Framework for Understanding DCIS

DTIC Science & Technology

2016-10-01

frozen patient biopsies, these have been annotated by our pathologist and prepared to be taken on for sequencing. The tissue includes DCIS, IDC...stroma adjacent to DCIS/IDC and normal tissue . We have initiated the RNA sequencing from these samples and also the DNA sequencing 15. SUBJECT TERMS DCIS...before they reach 55. Utilizing a unique bank of frozen mammary biopsies, containing samples with DCIS alone, and a combination of DCIS and IDC, we aim

A 57-year follow-up of occlusal changes, oral health, and attitudes toward teeth.

PubMed

Stenvik, Arild; Espeland, Lisen; Berg, Rolf E

2011-04-01

Very few studies have addressed long-term development and risks associated with untreated malocclusion. The purpose of this study was to examine changes in occlusion in a lifelong perspective and to compare oral health and attitudes toward teeth among persons with malocclusion with those having normal occlusion. In 1950 an epidemiologic survey of 2349 8-year-olds was conducted and included 4 intraoral photographs. Three selected samples with different malocclusions (deep bite, crossbite, or irregular teeth) and 1 sample with normal occlusion (a total of 183 subjects) were, 57 years later, invited for examination and an extensive interview about dental experiences and attitudes. Sixty-nine responded (38%) and constitute the subjects studied. Malocclusion remained the same or worsened except in subjects having deep bite in childhood, which in some improved and in others became worse. Crowding generally increased. Sixteen persons reported moderate or severe temporomandular joint (TMJ) problems, and of these 7 belonged to the group with crossbite in childhood. With few exceptions, the subjects in all samples had good oral hygiene, visited the dentist regularly, and had well-preserved dentitions. Mean number of missing teeth was significantly lower among those with normal occlusion compared with the malocclusion groups. Individuals with normal occlusion responded favorably to all questions related to attitudes and experiences about their teeth, while responses in the malocclusion groups varied. Persons with the particular malocclusions examined experienced more problems related to teeth later in life compared with those having normal occlusion in childhood. Copyright © 2011 American Association of Orthodontists. Published by Mosby, Inc. All rights reserved.

Ambient airborne solids concentrations including volcanic ash at Hanford, Washington sampling sites subsequent to the Mount St. Helens eruption

NASA Technical Reports Server (NTRS)

Sehmel, G. A.

1982-01-01

Airborne solids concentrations were measured on a near daily basis at two Hanford, Washington sites after the eruption of Mount St. Helens on May 18, 1980. These sites are about 211 km east of Mount St. Helens. Collected airborne solids included resuspended volcanic ash plus normal ambient solids. Average airborne solids concentrations were greater at the Hanford meteorological station sampling site which is 24 km northwest of the Horn Rapids dam sampling site. These increased concentrations reflect the sampling site proximity to greater ash fallout depths. Both sites are in low ash fallout areas although the Hanford meteorological station site is closer to the greater ash fallout areas. Airborne solids concentrations were decreased by rain, but airborne solids concentrations rapidly increased as surfaces dried. Airborne concentrations tended to become nearly the same at both sampling sites only for July 12 and 13.

Ex vivo characterization of normal and adenocarcinoma colon samples by Mueller matrix polarimetry.

PubMed

Ahmad, Iftikhar; Ahmad, Manzoor; Khan, Karim; Ashraf, Sumara; Ahmad, Shakil; Ikram, Masroor

2015-05-01

Mueller matrix polarimetry along with polar decomposition algorithm was employed for the characterization of ex vivo normal and adenocarcinoma human colon tissues by polarized light in the visible spectral range (425-725 nm). Six derived polarization metrics [total diattenuation (DT ), retardance (RT ), depolarization(ΔT ), linear diattenuation (DL), retardance (δ), and depolarization (ΔL)] were compared for normal and adenocarcinoma colon tissue samples. The results show that all six polarimetric properties for adenocarcinoma samples were significantly higher as compared to the normal samples for all wavelengths. The Wilcoxon rank sum test illustrated that total retardance is a good candidate for the discrimination of normal and adenocarcinoma colon samples. Support vector machine classification for normal and adenocarcinoma based on the four polarization properties spectra (ΔT , ΔL, RT ,and δ) yielded 100% accuracy, sensitivity, and specificity, while both DTa nd DL showed 66.6%, 33.3%, and 83.3% accuracy, sensitivity, and specificity, respectively. The combination of polarization analysis and given classification methods provides a framework to distinguish the normal and cancerous tissues.

Induction of chromosome aberrations in cultured human lymphocytes treated with sand dust storm fine particles (PM2.5).

PubMed

Wei, Aili; Meng, Ziqiang

2006-09-30

The clastogenic activity of airborne air fine particulate matter (PM2.5, particulates with an aerodynamic diameter < or =2.5 microm) has already been demonstrated. However little is known about the health risks associated with sand dust storm PM2.5 and its extract. In order to investigate the clastogenic activity of sand dust storm PM2.5 (include its organic and inorganic extract) on human lymphocytes, the normal PM2.5 and sand dust storm PM2.5 samples were collected in Wuwei city (Gansu Province) and Baotou city (Inner Mongolia), China. The chromosomal aberration (CA) test was employed and the cells were treated with 0, 33, 100, 300 microg ml(-1) sand dust storm or normal ambient air PM2.5 suspension (physiological saline as solvent control), or inorganic extract (0, 75, 150, 300 microg ml(-1), physiological saline as solvent control) or organic extract (0, 20, 40, 80 microg ml(-1), DMSO as solvent control) at the beginning of the cell culture. The results indicated that sand dust storm PM2.5 and its extract as well as normal samples can induce increase in CA frequency. With the increase of treatment concentrations the CA frequency increased and the mitotic index (MI) values declined in a dose-response manner. In the same concentrates, the CA frequency of normal ambient air PM2.5 and its extract were significant higher than those of sand dust storm PM2.5 (P<0.05 or 0.01) except the treatment of Wuwei sample at higher doses (100, 300 microg ml(-1)), the treatment of inorganic extract of PM2.5 at the highest dose (300 microg ml(-1)) and the treatment of organic extract of PM2.5 at the higher dose (40 and 80 microg ml(-1)) either in Baotou or in Wuwei (P>0.05). The toxicity of sand dust storm PM2.5 and its extract at high dose is very potent. CA frequency of normal PM2.5 (include its organic extract) from Baotou were higher than those of Wuwei especially in low and middle dose (P<0.05), but the treatment results of sand dust storm PM2.5 (include its all extract) was not significant different between the cities (P>0.05).

Actinobacillus actinomycetemcomitans in Human Periodontal Disease: a Cross-Sectional Microbiological Investigation

PubMed Central

Slots, Jørgen; Reynolds, Homer S.; Genco, Robert J.

1980-01-01

Actinobacillus actinomycetemcomitans is a facultative gram-negative bacterium which has been associated with severe oral and nonoral infections. This study examined its occurrence in the oral cavities of 10 normal juveniles, 11 normal adults, 10 juvenile periodontitis patients, and 12 adult periodontitis patients. Four deep periodontal pockets and two normal periodontal sites were sampled in the diseased patients, and six normal periodontal sites were sampled in the healthy individuals. In all subjects samples were obtained from the cheek, tongue, and saliva. Samples from a total of 172 normal periodontal sites, 83 deep periodontal pockets, 42 cheek mucosae, 42 tongue dorsa, and 42 salivas were examined. Isolation was performed by using a medium for selective isolation of A. actinomycetemcomitans (Trypticase soy agar [BBL Microbiology Systems] supplemented with 10% serum and 75 μg of bacitracin per ml). The carrier rates were 20% for normal juveniles, 36% for normal adults, 50% for adult periodontitis patients, and 90% for juvenile periodontitis patients. A. actinomycetemcomitans was on average recovered in about fivefold-higher numbers from infected deep periodontal pockets than from infected normal subgingival areas. Samples of periodontal pockets generally contained 100-fold-more cells of A. actinomycetemcomitans than did samples of the cheek, tongue, and saliva. A. actinomycetemcomitans is commonly isolated from patients with juvenile periodontitis, often isolated from patients with adult periodontitis, and occasionally isolated from normal juveniles and adults. Its primary oral ecological niche appears to be dental plaque and periodontal pockets. PMID:6968718

Tissue-aware RNA-Seq processing and normalization for heterogeneous and sparse data.

PubMed

Paulson, Joseph N; Chen, Cho-Yi; Lopes-Ramos, Camila M; Kuijjer, Marieke L; Platig, John; Sonawane, Abhijeet R; Fagny, Maud; Glass, Kimberly; Quackenbush, John

2017-10-03

Although ultrahigh-throughput RNA-Sequencing has become the dominant technology for genome-wide transcriptional profiling, the vast majority of RNA-Seq studies typically profile only tens of samples, and most analytical pipelines are optimized for these smaller studies. However, projects are generating ever-larger data sets comprising RNA-Seq data from hundreds or thousands of samples, often collected at multiple centers and from diverse tissues. These complex data sets present significant analytical challenges due to batch and tissue effects, but provide the opportunity to revisit the assumptions and methods that we use to preprocess, normalize, and filter RNA-Seq data - critical first steps for any subsequent analysis. We find that analysis of large RNA-Seq data sets requires both careful quality control and the need to account for sparsity due to the heterogeneity intrinsic in multi-group studies. We developed Yet Another RNA Normalization software pipeline (YARN), that includes quality control and preprocessing, gene filtering, and normalization steps designed to facilitate downstream analysis of large, heterogeneous RNA-Seq data sets and we demonstrate its use with data from the Genotype-Tissue Expression (GTEx) project. An R package instantiating YARN is available at http://bioconductor.org/packages/yarn .

Gene expression signature of benign prostatic hyperplasia revealed by cDNA microarray analysis.

PubMed

Luo, Jun; Dunn, Thomas; Ewing, Charles; Sauvageot, Jurga; Chen, Yidong; Trent, Jeffrey; Isaacs, William

2002-05-15

Despite the high prevalence of benign prostatic hyperplasia (BPH) in the aging male, little is known regarding the etiology of this disease. A better understanding of the molecular etiology of BPH would be facilitated by a comprehensive analysis of gene expression patterns that are characteristic of benign growth in the prostate gland. Since genes differentially expressed between BPH and normal prostate tissues are likely to reflect underlying pathogenic mechanisms involved in the development of BPH, we performed comparative gene expression analysis using cDNA microarray technology to identify candidate genes associated with BPH. Total RNA was extracted from a set of 9 BPH specimens from men with extensive hyperplasia and a set of 12 histologically normal prostate tissues excised from radical prostatectomy specimens. Each of these 21 RNA samples was labeled with Cy3 in a reverse transcription reaction and cohybridized with a Cy5 labeled common reference sample to a cDNA microarray containing 6,500 human genes. Normalized fluorescent intensity ratios from each hybridization experiment were extracted to represent the relative mRNA abundance for each gene in each sample. Weighted gene and random permutation analyses were performed to generate a subset of genes with statistically significant differences in expression between BPH and normal prostate tissues. Semi-quantitative PCR analysis was performed to validate differential expression. A subset of 76 genes involved in a wide range of cellular functions was identified to be differentially expressed between BPH and normal prostate tissues. Semi-quantitative PCR was performed on 10 genes and 8 were validated. Genes consistently upregulated in BPH when compared to normal prostate tissues included: a restricted set of growth factors and their binding proteins (e.g. IGF-1 and -2, TGF-beta3, BMP5, latent TGF-beta binding protein 1 and -2); hydrolases, proteases, and protease inhibitors (e.g. neuropathy target esterase, MMP2, alpha-2-macroglobulin); stress response enzymes (e.g. COX2, GSTM5); and extracellular matrix molecules (e.g. laminin alpha 4 and beta 1, chondroitin sulfate proteoglycan 2, lumican). Genes consistently expressing less mRNA in BPH than in normal prostate tissues were less commonly observed and included the transcription factor KLF4, thrombospondin 4, nitric oxide synthase 2A, transglutaminase 3, and gastrin releasing peptide. We identified a diverse set of genes that are potentially related to benign prostatic hyperplasia, including genes both previously implicated in BPH pathogenesis as well as others not previously linked to this disease. Further targeted validation and investigations of these genes at the DNA, mRNA, and protein levels are warranted to determine the clinical relevance and possible therapeutic utility of these genes. Copyright 2002 Wiley-Liss, Inc.

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

ERIC Educational Resources Information Center

Zimmerman, Donald W.

2011-01-01

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

Statistical analysis and machine learning algorithms for optical biopsy

NASA Astrophysics Data System (ADS)

Wu, Binlin; Liu, Cheng-hui; Boydston-White, Susie; Beckman, Hugh; Sriramoju, Vidyasagar; Sordillo, Laura; Zhang, Chunyuan; Zhang, Lin; Shi, Lingyan; Smith, Jason; Bailin, Jacob; Alfano, Robert R.

2018-02-01

Analyzing spectral or imaging data collected with various optical biopsy methods is often times difficult due to the complexity of the biological basis. Robust methods that can utilize the spectral or imaging data and detect the characteristic spectral or spatial signatures for different types of tissue is challenging but highly desired. In this study, we used various machine learning algorithms to analyze a spectral dataset acquired from human skin normal and cancerous tissue samples using resonance Raman spectroscopy with 532nm excitation. The algorithms including principal component analysis, nonnegative matrix factorization, and autoencoder artificial neural network are used to reduce dimension of the dataset and detect features. A support vector machine with a linear kernel is used to classify the normal tissue and cancerous tissue samples. The efficacies of the methods are compared.

Robust Bayesian Analysis of Heavy-tailed Stochastic Volatility Models using Scale Mixtures of Normal Distributions

PubMed Central

Abanto-Valle, C. A.; Bandyopadhyay, D.; Lachos, V. H.; Enriquez, I.

2009-01-01

A Bayesian analysis of stochastic volatility (SV) models using the class of symmetric scale mixtures of normal (SMN) distributions is considered. In the face of non-normality, this provides an appealing robust alternative to the routine use of the normal distribution. Specific distributions examined include the normal, student-t, slash and the variance gamma distributions. Using a Bayesian paradigm, an efficient Markov chain Monte Carlo (MCMC) algorithm is introduced for parameter estimation. Moreover, the mixing parameters obtained as a by-product of the scale mixture representation can be used to identify outliers. The methods developed are applied to analyze daily stock returns data on S&P500 index. Bayesian model selection criteria as well as out-of- sample forecasting results reveal that the SV models based on heavy-tailed SMN distributions provide significant improvement in model fit as well as prediction to the S&P500 index data over the usual normal model. PMID:20730043

Screening for genes and subnetworks associated with pancreatic cancer based on the gene expression profile.

PubMed

Long, Jin; Liu, Zhe; Wu, Xingda; Xu, Yuanhong; Ge, Chunlin

2016-05-01

The present study aimed to screen for potential genes and subnetworks associated with pancreatic cancer (PC) using the gene expression profile. The expression profile GSE 16515 was downloaded from the Gene Expression Omnibus database, which included 36 PC tissue samples and 16 normal samples. Limma package in R language was used to screen differentially expressed genes (DEGs), which were grouped as up‑ and downregulated genes. Then, PFSNet was applied to perform subnetwork analysis for all the DEGs. Moreover, Gene Ontology (GO) and REACTOME pathway enrichment analysis of up‑ and downregulated genes was performed, followed by protein‑protein interaction (PPI) network construction using Search Tool for the Retrieval of Interacting Genes Search Tool for the Retrieval of Interacting Genes. In total, 1,989 DEGs including 1,461 up‑ and 528 downregulated genes were screened out. Subnetworks including pancreatic cancer in PC tissue samples and intercellular adhesion in normal samples were identified, respectively. A total of 8 significant REACTOME pathways for upregulated DEGs, such as hemostasis and cell cycle, mitotic were identified. Moreover, 4 significant REACTOME pathways for downregulated DEGs, including regulation of β‑cell development and transmembrane transport of small molecules were screened out. Additionally, DEGs with high connectivity degrees, such as CCNA2 (cyclin A2) and PBK (PDZ binding kinase), of the module in the protein‑protein interaction network were mainly enriched with cell‑division cycle. CCNA2 and PBK of the module and their relative pathway cell‑division cycle, and two subnetworks (pancreatic cancer and intercellular adhesion subnetworks) may be pivotal for further understanding of the molecular mechanism of PC.

Children with minimal sensorineural hearing loss: prevalence, educational performance, and functional status.

PubMed

Bess, F H; Dodd-Murphy, J; Parker, R A

1998-10-01

This study was designed to determine the prevalence of minimal sensorineural hearing loss (MSHL) in school-age children and to assess the relationship of MSHL to educational performance and functional status. To determine prevalence, a single-staged sampling frame of all schools in the district was created for 3rd, 6th, and 9th grades. Schools were selected with probability proportional to size in each grade group. The final study sample was 1218 children. To assess the association of MSHL with educational performance, children identified with MSHL were assigned as cases into a subsequent case-control study. Scores of the Comprehensive Test of Basic Skills (4th Edition) (CTBS/4) then were compared between children with MSHL and children with normal hearing. School teachers completed the Screening Instrument for Targeting Education Risk (SIFTER) and the Revised Behavior Problem Checklist for a subsample of children with MSHL and their normally hearing counterparts. Finally, data on grade retention for a sample of children with MSHL were obtained from school records and compared with school district norm data. To assess the relationship between MSHL and functional status, test scores of all children with MSHL and all children with normal hearing in grades 6 and 9 were compared on the COOP Adolescent Chart Method (COOP), a screening tool for functional status. MSHL was exhibited by 5.4% of the study sample. The prevalence of all types of hearing impairment was 11.3%. Third grade children with MSHL exhibited significantly lower scores than normally hearing controls on a series of subtests of the CTBS/4; however, no differences were noted at the 6th and 9th grade levels. The SIFTER results revealed that children with MSHL scored poorer on the communication subtest than normal-hearing controls. Thirty-seven percent of the children with MSHL failed at least one grade. Finally, children with MSHL exhibited significantly greater dysfunction than children with normal hearing on several subtests of the COOP including behavior, energy, stress, social support, and self-esteem. The prevalence of hearing loss in the schools almost doubles when children with MSHL are included. This large, education-based study shows clinically important associations between MSHL and school behavior and performance. Children with MSHL experienced more difficulty than normally hearing children on a series of educational and functional test measures. Although additional research is necessary, results suggest the need for audiologists, speech-language pathologists, and educators to evaluate carefully our identification and management approaches with this population. Better efforts to manage these children could result in meaningful improvement in their educational progress and psychosocial well-being.

Downregulation of external death receptor genes FAS and DR5 in colorectal cancer samples positive for human papillomavirus infection.

PubMed

Karbasi, Ashraf; Borhani, Nasim; Daliri, Karim; Kazemi, Bahram; Manoochehri, Mehdi

2015-06-01

Human papillomaviruses (HPV) have frequently been detected in colorectal cancer tumor samples, and may play a role in the pathogenesis of colorectal cancer. This study was designed to investigate the presence of DNA and RNA for the high-risk HPV genotypes 16 and 18 in samples of colorectal cancer tumors and adjacent normal tissues. We also investigated the expression of proapoptotic genes in HPV-positive colorectal tumors compared to normal tissue samples. Samples of tumoral and adjacent normal tissues were fresh-frozen, and HPV DNA was identified by nested and semiquantitative PCR. Real time PCR was used to quantitatively compare the expression of HPV-18 E6 and nine proapoptotic genes in HPV-positive tumors and samples of adjacent normal tissue. HPV-16 DNA was found in 10.5% of the tumor samples, and HPV-18 DNA was found in 23.6% of the samples. Real time PCR results showed lower expression of the E6 gene in HPV-positive tumors than in adjacent normal tissue. The expression of two proapoptotic genes, FAS and DR5, was significantly lower in tumor samples than in adjacent normal tissues. HPV infection, especially HPV-18, may play a role in colorectal cancer tumorigenesis by downregulating death receptor genes and interfering with the extrinsic pathway of apoptosis. Copyright © 2015 Elsevier GmbH. All rights reserved.

Vitamin D Receptor Expression in Normal, Premalignant, and Malignant Human Lung Tissue

PubMed Central

Menezes, Ravi J.; Cheney, Richard T.; Husain, Aliya; Tretiakova, Maria; Loewen, Gregory; Johnson, Candace S.; Jayaprakash, Vijay; Moysich, Kirsten B.; Salgia, Ravi; Reid, Mary E.

2009-01-01

Background There is a strong interest in identifying chemopreventive agents that might help decrease the burden of lung cancer. The active metabolite of vitamin D, 1,25-dihydroxycholecalciferol (calcitriol), has been shown to have antiproliferative effects in several tumor types, mediated by the vitamin D receptor (VDR). This is the first comprehensive survey of VDR expression in a series of human lung tissues, including normal and premalignant central airway biopsies and lung tumors. Methods Immunohistochemical expression of nuclear and cytoplasmic VDR was examined in 180 premalignant or malignant bronchial biopsies from bronchoscopy of 78 high-risk individuals at the Roswell Park Cancer Institute and also in 63 tumor samples from 35 lung cancer patients from the University of Chicago Hospitals. Associations between clinicopathologic data and VDR expression were examined. Results VDR expression was present in many samples. In biopsies, VDR was commonly detected throughout the full epithelial layer. Most histologically normal (60%, 53 of 88) and metaplastic (61%, 39 of 64) samples had moderate to high nuclear intensity; dysplastic samples mostly had low nuclear intensity (10 of 18, 55%). In tumor samples, 62% (38 of 61) were lacking cytoplasmic VDR, with nuclear expression present in 79%(49 of 62). Analysis of all samples revealed a positive linear trend between proportion of samples with greater nuclear than cytoplasmic intensity and increasing histologic grade (P < 0.01). Conclusions VDR expression spanned the lung carcinogenesis spectrum. Nuclear expression was similar across various histologies, whereas cytoplasmic expression decreased with increasing histologic grade. These results indicate that there is potential for the use of calcitriol as a chemopreventive agent against the development of lung cancer. (Cancer Epidemiol Bio-markers Prev 2008;17(5):1104–10) PMID:18483332

Morphological Differences Between Seyfert Hosts and Normal Galaxies

NASA Astrophysics Data System (ADS)

Shlosman, Isaac

Using new sub-arcsecond resolution imaging we compare large-scale stellar bar fraction in CfA sample of Seyferts and a closely matched control sample of normal galaxies. We find a difference between the samples on the 2.5σ level. We further compare the axial ratios of bars in all available samples quoted in the literature and find a deficiency of small axial ratio bars in Seyferts compared to normal galaxies.

Measurement of soil moisture trends with airborne scatterometers. [Guymon, Oklahoma and Dalhart, Texas

NASA Technical Reports Server (NTRS)

Jones, C. L.; Mcfarland, M. J.; Rosethal, W. D.; Theis, S. W. (Principal Investigator)

1982-01-01

In an effort to investigate aircraft multisensor responses to soil moisture and vegetation in agricultural fields, an intensive ground sampling program was conducted in Guymon, Oklahoma and Dalhart, Texas in conjunction with aircraft data collected for visible/infrared and passive and active microwave systems. Field selections, sampling techniques, data processing, and the aircraft schedule are discussed for both sites. Field notes are included along with final (normalized and corrected) data sets.

Combining counts and incidence data: an efficient approach for estimating the log-normal species abundance distribution and diversity indices.

PubMed

Bellier, Edwige; Grøtan, Vidar; Engen, Steinar; Schartau, Ann Kristin; Diserud, Ola H; Finstad, Anders G

2012-10-01

Obtaining accurate estimates of diversity indices is difficult because the number of species encountered in a sample increases with sampling intensity. We introduce a novel method that requires that the presence of species in a sample to be assessed while the counts of the number of individuals per species are only required for just a small part of the sample. To account for species included as incidence data in the species abundance distribution, we modify the likelihood function of the classical Poisson log-normal distribution. Using simulated community assemblages, we contrast diversity estimates based on a community sample, a subsample randomly extracted from the community sample, and a mixture sample where incidence data are added to a subsample. We show that the mixture sampling approach provides more accurate estimates than the subsample and at little extra cost. Diversity indices estimated from a freshwater zooplankton community sampled using the mixture approach show the same pattern of results as the simulation study. Our method efficiently increases the accuracy of diversity estimates and comprehension of the left tail of the species abundance distribution. We show how to choose the scale of sample size needed for a compromise between information gained, accuracy of the estimates and cost expended when assessing biological diversity. The sample size estimates are obtained from key community characteristics, such as the expected number of species in the community, the expected number of individuals in a sample and the evenness of the community.

MR Morphology of Triangular Fibrocartilage Complex: Correlation with Quantitative MR and Biomechanical Properties

PubMed Central

Bae, Won C.; Ruangchaijatuporn, Thumanoon; Chang, Eric Y; Biswas, Reni; Du, Jiang; Statum, Sheronda

2016-01-01

Objective To evaluate pathology of the triangular fibrocartilage complex (TFCC) using high resolution morphologic magnetic resonance (MR) imaging, and compare with quantitative MR and biomechanical properties. Materials and Methods Five cadaveric wrists (22 to 70 yrs) were imaged at 3T using morphologic (proton density weighted spin echo, PD FS, and 3D spoiled gradient echo, 3D SPGR) and quantitative MR sequences to determine T2 and T1rho properties. In eight geographic regions, morphology of TFC disc and laminae were evaluated for pathology and quantitative MR values. Samples were disarticulated and biomechanical indentation testing was performed on the distal surface of the TFC disc. Results On morphologic PD SE images, TFC disc pathology included degeneration and tears, while that of the laminae included degeneration, degeneration with superimposed tear, mucinous transformation, and globular calcification. Punctate calcifications were highly visible on 3D SPGR images and found only in pathologic regions. Disc pathology occurred more frequently in proximal regions of the disc than distal regions. Quantitative MR values were lowest in normal samples, and generally higher in pathologic regions. Biomechanical testing demonstrated an inverse relationship, with indentation modulus being high in normal regions with low MR values. The laminae studied were mostly pathologic, and additional normal samples are needed to discern quantitative changes. Conclusion These results show technical feasibility of morphologic MR, quantitative MR, and biomechanical techniques to characterize pathology of the TFCC. Quantitative MRI may be a suitable surrogate marker of soft tissue mechanical properties, and a useful adjunct to conventional morphologic MR techniques. PMID:26691643

The impact of sample non-normality on ANOVA and alternative methods.

PubMed

Lantz, Björn

2013-05-01

In this journal, Zimmerman (2004, 2011) has discussed preliminary tests that researchers often use to choose an appropriate method for comparing locations when the assumption of normality is doubtful. The conceptual problem with this approach is that such a two-stage process makes both the power and the significance of the entire procedure uncertain, as type I and type II errors are possible at both stages. A type I error at the first stage, for example, will obviously increase the probability of a type II error at the second stage. Based on the idea of Schmider et al. (2010), which proposes that simulated sets of sample data be ranked with respect to their degree of normality, this paper investigates the relationship between population non-normality and sample non-normality with respect to the performance of the ANOVA, Brown-Forsythe test, Welch test, and Kruskal-Wallis test when used with different distributions, sample sizes, and effect sizes. The overall conclusion is that the Kruskal-Wallis test is considerably less sensitive to the degree of sample normality when populations are distinctly non-normal and should therefore be the primary tool used to compare locations when it is known that populations are not at least approximately normal. © 2012 The British Psychological Society.

Defining the Dormant Tumor Microenvironment for Breast Cancer Prevention and Treatment

DTIC Science & Technology

2011-09-01

USAMRMC a. REPORT U b . ABSTRACT U c. THIS PAGE U UU 36 19b. TELEPHONE NUMBER (include area code) 2 TABLE OF CONTENTS...Each group will include 12 rats. b ) Breed rats in the parous group. After parturition, normalize the number of pups to eight. Ten days after...solution ultrasonication assisted tryptic digestion (UATD) method. Parity arm completed. b ) Analyzed the digested mammary ECM samples from

Simulation techniques for estimating error in the classification of normal patterns

NASA Technical Reports Server (NTRS)

Whitsitt, S. J.; Landgrebe, D. A.

1974-01-01

Methods of efficiently generating and classifying samples with specified multivariate normal distributions were discussed. Conservative confidence tables for sample sizes are given for selective sampling. Simulation results are compared with classified training data. Techniques for comparing error and separability measure for two normal patterns are investigated and used to display the relationship between the error and the Chernoff bound.

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.

Systematic bias in genomic classification due to contaminating non-neoplastic tissue in breast tumor samples.

PubMed

Elloumi, Fathi; Hu, Zhiyuan; Li, Yan; Parker, Joel S; Gulley, Margaret L; Amos, Keith D; Troester, Melissa A

2011-06-30

Genomic tests are available to predict breast cancer recurrence and to guide clinical decision making. These predictors provide recurrence risk scores along with a measure of uncertainty, usually a confidence interval. The confidence interval conveys random error and not systematic bias. Standard tumor sampling methods make this problematic, as it is common to have a substantial proportion (typically 30-50%) of a tumor sample comprised of histologically benign tissue. This "normal" tissue could represent a source of non-random error or systematic bias in genomic classification. To assess the performance characteristics of genomic classification to systematic error from normal contamination, we collected 55 tumor samples and paired tumor-adjacent normal tissue. Using genomic signatures from the tumor and paired normal, we evaluated how increasing normal contamination altered recurrence risk scores for various genomic predictors. Simulations of normal tissue contamination caused misclassification of tumors in all predictors evaluated, but different breast cancer predictors showed different types of vulnerability to normal tissue bias. While two predictors had unpredictable direction of bias (either higher or lower risk of relapse resulted from normal contamination), one signature showed predictable direction of normal tissue effects. Due to this predictable direction of effect, this signature (the PAM50) was adjusted for normal tissue contamination and these corrections improved sensitivity and negative predictive value. For all three assays quality control standards and/or appropriate bias adjustment strategies can be used to improve assay reliability. Normal tissue sampled concurrently with tumor is an important source of bias in breast genomic predictors. All genomic predictors show some sensitivity to normal tissue contamination and ideal strategies for mitigating this bias vary depending upon the particular genes and computational methods used in the predictor.

[Differential expression genes of bone tissues surrounding implants in diabetic rats by gene chip].

PubMed

Wang, Xin-xin; Ma, Yue; Li, Qing; Jiang, Bao-qi; Lan, Jing

2012-10-01

To compare mRNA expression profiles of bone tissues surrounding implants between normal rats and rats with diabetes using microarray technology. Six Wistar rats were randomly selected and divided into normal model group and diabetic group. Diabetic model condition was established by injecting Streptozotocin into peritoneal space. Titanium implants were implanted into the epiphyseal end of the rats' tibia. Bone tissues surrounding implant were harvested and sampled after 3 months to perform comprehensive RNA gene expression profiling, including 17983 for genome-wide association study.GO analysis was used to compare different gene expression and real-time PCR was used to confirm the results on core samples. The results indicated that there were 1084 differential gene expression. In the diabetic model, there were 352 enhanced expression genes, 732 suppressed expression genes. GO analysis involved 1154 different functional type. Osteoblast related gene expressions in bone tissue samples of diabetic rats were decreased, and lipid metabolism pathway related gene expression was increased.

A DNA methylation map of human cancer at single base-pair resolution.

PubMed

Vidal, E; Sayols, S; Moran, S; Guillaumet-Adkins, A; Schroeder, M P; Royo, R; Orozco, M; Gut, M; Gut, I; Lopez-Bigas, N; Heyn, H; Esteller, M

2017-10-05

Although single base-pair resolution DNA methylation landscapes for embryonic and different somatic cell types provided important insights into epigenetic dynamics and cell-type specificity, such comprehensive profiling is incomplete across human cancer types. This prompted us to perform genome-wide DNA methylation profiling of 22 samples derived from normal tissues and associated neoplasms, including primary tumors and cancer cell lines. Unlike their invariant normal counterparts, cancer samples exhibited highly variable CpG methylation levels in a large proportion of the genome, involving progressive changes during tumor evolution. The whole-genome sequencing results from selected samples were replicated in a large cohort of 1112 primary tumors of various cancer types using genome-scale DNA methylation analysis. Specifically, we determined DNA hypermethylation of promoters and enhancers regulating tumor-suppressor genes, with potential cancer-driving effects. DNA hypermethylation events showed evidence of positive selection, mutual exclusivity and tissue specificity, suggesting their active participation in neoplastic transformation. Our data highlight the extensive changes in DNA methylation that occur in cancer onset, progression and dissemination.

Using partially labeled data for normal mixture identification with application to class definition

NASA Technical Reports Server (NTRS)

Shahshahani, Behzad M.; Landgrebe, David A.

1992-01-01

The problem of estimating the parameters of a normal mixture density when, in addition to the unlabeled samples, sets of partially labeled samples are available is addressed. The density of the multidimensional feature space is modeled with a normal mixture. It is assumed that the set of components of the mixture can be partitioned into several classes and that training samples are available from each class. Since for any training sample the class of origin is known but the exact component of origin within the corresponding class is unknown, the training samples as considered to be partially labeled. The EM iterative equations are derived for estimating the parameters of the normal mixture in the presence of partially labeled samples. These equations can be used to combine the supervised and nonsupervised learning processes.

Unravelling the Mysteries of Slip Histories, Validating Cosmogenic 36Cl Derived Slip Rates on Normal Faults

NASA Astrophysics Data System (ADS)

Goodall, H.; Gregory, L. C.; Wedmore, L.; Roberts, G.; Shanks, R. P.; McCaffrey, K. J. W.; Amey, R.; Hooper, A. J.

2017-12-01

The cosmogenic isotope chlorine-36 (36Cl) is increasingly used as a tool to investigate normal fault slip rates over the last 10-20 thousand years. These slip histories are being used to address complex questions, including investigating slip clustering and understanding local and large scale fault interaction. Measurements are time consuming and expensive, and as a result there has been little work done validating these 36Cl derived slip histories. This study aims to investigate if the results are repeatable and therefore reliable estimates of how normal faults have been moving in the past. Our approach is to test if slip histories derived from 36Cl are the same when measured at different points along the same fault. As normal fault planes are progressively exhumed from the surface they accumulate 36Cl. Modelling these 36Cl concentrations allows estimation of a slip history. In a previous study, samples were collected from four sites on the Magnola fault in the Italian Apennines. Remodelling of the 36Cl data using a Bayesian approach shows that the sites produced disparate slip histories, which we interpret as being due to variable site geomorphology. In this study, multiple sites have been sampled along the Campo Felice fault in the central Italian Apennines. Initial results show strong agreement between the sites we have processed so far and a previous study. This indicates that if sample sites are selected taking the geomorphology into account, then 36Cl derived slip histories will be highly similar when sampled at any point along the fault. Therefore our study suggests that 36Cl derived slip histories are a consistent record of fault activity in the past.

A closer look at the effect of preliminary goodness-of-fit testing for normality for the one-sample t-test.

PubMed

Rochon, Justine; Kieser, Meinhard

2011-11-01

Student's one-sample t-test is a commonly used method when inference about the population mean is made. As advocated in textbooks and articles, the assumption of normality is often checked by a preliminary goodness-of-fit (GOF) test. In a paper recently published by Schucany and Ng it was shown that, for the uniform distribution, screening of samples by a pretest for normality leads to a more conservative conditional Type I error rate than application of the one-sample t-test without preliminary GOF test. In contrast, for the exponential distribution, the conditional level is even more elevated than the Type I error rate of the t-test without pretest. We examine the reasons behind these characteristics. In a simulation study, samples drawn from the exponential, lognormal, uniform, Student's t-distribution with 2 degrees of freedom (t(2) ) and the standard normal distribution that had passed normality screening, as well as the ingredients of the test statistics calculated from these samples, are investigated. For non-normal distributions, we found that preliminary testing for normality may change the distribution of means and standard deviations of the selected samples as well as the correlation between them (if the underlying distribution is non-symmetric), thus leading to altered distributions of the resulting test statistics. It is shown that for skewed distributions the excess in Type I error rate may be even more pronounced when testing one-sided hypotheses. ©2010 The British Psychological Society.

Paleomagnetic results from Late Pennsylvanian marls and Early Permian red paleosols of the Dunkard group, Ohio and West Virginia, U.S.A.

NASA Astrophysics Data System (ADS)

Abrajevitch, A.; Oliva, B.; Peters, S.; Beehr, A.; van der Voo, R.

2006-12-01

Sediments of the Dunkard Gr. were deposited in the Appalachian foreland basin during the Pennsylvanian and Early Permian, an interval encompassing the long reverse polarity Kiaman chron. Lithofacies in the Dunkard Gr. in eastern Ohio and western West Virginia include lenticular and sheet-form cross-bedded micaceous sandstones, coal, mottled red and purple mudstones, gray laminated mudstones and argillaceous lime mudstones. They are indicative of deposition on a low-gradient, tropical wet-dry fluvial plain. Few lithofacies are laterally persistent over sufficiently long distances, so that correlation schemes are based largely on coal horizons, partly for historical economic reasons and partly because coal beds appear to be more laterally persistent than most other lithofacies. Magnetostratigraphy would therefore provide a powerful additional correlation tool in the Dunkard Gr, A short normal polarity interval has been reported in the Dunkard Gr. (Helsley, 1965), but to date such a change in magnetic field polarity has not been confirmed by later studies. To confirm the presence of the normal polarity subchron and to explore the possibility of using it as a correlation tool in the Dunkard Gr., we sampled 5 sections thought to straddle the Late Pennyslvanian-Early Permian boundary. Sampled lithofacies include red and mottled red-purple paleosols, grey mudstones containing siderite concretions, micaceous sandstones, and dark gray argillaceous limestones. Samples were demagnetized thermally and by AF. The remanent magnetic directions agree with those expected for the Early Permian. A change in polarity was detected in three of the studied sections. Magnetization is carried by several different magnetic minerals, mostly hematite in paleosols and iron sulfides in combination with magnetite in sandstones, marls and limestones. Although we have found good evidence for the normal polarity interval within Kiaman age rocks of the Dunkard Gr., additional magnetostratigraphic data are needed to validate the present lithology-based correlations and to determine the temporal extent of the normal polarity chron.

An explorative investigation of functional differences in plantar center of pressure of four foot types using sample entropy method.

PubMed

Mei, Zhanyong; Ivanov, Kamen; Zhao, Guoru; Li, Huihui; Wang, Lei

2017-04-01

In the study of biomechanics of different foot types, temporal or spatial parameters derived from plantar pressure are often used. However, there is no comparative study of complexity and regularity of the center of pressure (CoP) during the stance phase among pes valgus, pes cavus, hallux valgus and normal foot. We aim to analyze whether CoP sample entropy characteristics differ among these four foot types. In our experiment participated 40 subjects with normal feet, 40 with pes cavus, 19 with pes valgus and 36 with hallux valgus. A Footscan ® system was used to collect CoP data. We used sample entropy to quantify several parameters of the investigated four foot types. These are the displacement in medial-lateral (M/L) and anterior-posterior (A/P) directions, as well as the vertical ground reaction force of CoP during the stance phase. To fully examine the potential of the sample entropy method for quantification of CoP components, we provide results for two cases: calculating the sample entropy of normalized CoP components, as well as calculating it using the raw data of CoP components. We also explored what are the optimal values of parameters m (the matching length) and r (the tolerance range) when calculating the sample entropy of CoP data obtained during the stance phases. According to statistical results, some factors significantly influenced the sample entropy of CoP components. The sample entropies of non-normalized A/P values for the left foot, as well as for the right foot, were different between the normal foot and pes valgus, and between the normal foot and hallux valgus. The sample entropy of normalized M/L displacement of the right foot was different between the normal foot and pes cavus. The measured variable for A/P and M/L displacements could serve for the study of foot function.

Variable size computer-aided detection prompts and mammography film reader decisions

PubMed Central

Gilbert, Fiona J; Astley, Susan M; Boggis, Caroline RM; McGee, Magnus A; Griffiths, Pamela M; Duffy, Stephen W; Agbaje, Olorunsola F; Gillan, Maureen GC; Wilson, Mary; Jain, Anil K; Barr, Nicola; Beetles, Ursula M; Griffiths, Miriam A; Johnson, Jill; Roberts, Rita M; Deans, Heather E; Duncan, Karen A; Iyengar, Geeta

2008-01-01

Introduction The purpose of the present study was to investigate the effect of computer-aided detection (CAD) prompts on reader behaviour in a large sample of breast screening mammograms by analysing the relationship of the presence and size of prompts to the recall decision. Methods Local research ethics committee approval was obtained; informed consent was not required. Mammograms were obtained from women attending routine mammography at two breast screening centres in 1996. Films, previously double read, were re-read by a different reader using CAD. The study material included 315 cancer cases comprising all screen-detected cancer cases, all subsequent interval cancers and 861 normal cases randomly selected from 10,267 cases. Ground truth data were used to assess the efficacy of CAD prompting. Associations between prompt attributes and tumour features or reader recall decisions were assessed by chi-squared tests. Results There was a highly significant relationship between prompting and a decision to recall for cancer cases and for a random sample of normal cases (P < 0.001). Sixty-four per cent of all cases contained at least one CAD prompt. In cancer cases, larger prompts were more likely to be recalled (P = 0.02) for masses but there was no such association for calcifications (P = 0.9). In a random sample of 861 normal cases, larger prompts were more likely to be recalled (P = 0.02) for both mass and calcification prompts. Significant associations were observed with prompting and breast density (p = 0.009) for cancer cases but not for normal cases (P = 0.05). Conclusions For both normal cases and cancer cases, prompted mammograms were more likely to be recalled and the prompt size was also associated with a recall decision. PMID:18724867

Variable size computer-aided detection prompts and mammography film reader decisions.

PubMed

Gilbert, Fiona J; Astley, Susan M; Boggis, Caroline Rm; McGee, Magnus A; Griffiths, Pamela M; Duffy, Stephen W; Agbaje, Olorunsola F; Gillan, Maureen Gc; Wilson, Mary; Jain, Anil K; Barr, Nicola; Beetles, Ursula M; Griffiths, Miriam A; Johnson, Jill; Roberts, Rita M; Deans, Heather E; Duncan, Karen A; Iyengar, Geeta

2008-01-01

The purpose of the present study was to investigate the effect of computer-aided detection (CAD) prompts on reader behaviour in a large sample of breast screening mammograms by analysing the relationship of the presence and size of prompts to the recall decision. Local research ethics committee approval was obtained; informed consent was not required. Mammograms were obtained from women attending routine mammography at two breast screening centres in 1996. Films, previously double read, were re-read by a different reader using CAD. The study material included 315 cancer cases comprising all screen-detected cancer cases, all subsequent interval cancers and 861 normal cases randomly selected from 10,267 cases. Ground truth data were used to assess the efficacy of CAD prompting. Associations between prompt attributes and tumour features or reader recall decisions were assessed by chi-squared tests. There was a highly significant relationship between prompting and a decision to recall for cancer cases and for a random sample of normal cases (P < 0.001). Sixty-four per cent of all cases contained at least one CAD prompt. In cancer cases, larger prompts were more likely to be recalled (P = 0.02) for masses but there was no such association for calcifications (P = 0.9). In a random sample of 861 normal cases, larger prompts were more likely to be recalled (P = 0.02) for both mass and calcification prompts. Significant associations were observed with prompting and breast density (p = 0.009) for cancer cases but not for normal cases (P = 0.05). For both normal cases and cancer cases, prompted mammograms were more likely to be recalled and the prompt size was also associated with a recall decision.

Matuyama/Brunhes Polarity Transition in Owens Lake, CA, Sediment

NASA Astrophysics Data System (ADS)

Liddicoat, Joseph; Kravchinsky, Vadim

2014-05-01

The complexity of the Matuyama/Brunhes (M/B) polarity transition is becoming better understood from investigations of volcanic rocks (Coe et al., 2004), loess (Jin et al., 2012; Evans et al., 2011; Kravchinsky, 2013), and marine (Clement and Opdyke, 1982; Hartl and Tauxe, 1996; Macri et al., 2010) and lacustrine (Valet et al., 1988; Sagnotti et al., 2013) sediments. The transition appears to include a brief interval of normal polarity prior to the entry into the Brunhes Normal Chron (Coe et al., 2004; Jin et al., 2012; Evans et al., 2011), and the transition has Virtual Geomagnetic Poles rapidly moving from the Southern Hemisphere to the Northern Hemisphere (Coe et al., 2004; Jin et al., 2012; Evans et al., 2011; Sagnotti et al., 2013). The M/B polarity transition is recorded in exposed Pleistocene lake sediments near Bishop, CA, where the brief interval of normal polarity noted above is present and the change from full reverse to full normal polarity occurs rapidly. The brief interval of normal polarity is recorded at two sites separated laterally by about 150 m and is in single hand samples measured at vertical spacing of 2.0-2.5 cm using six samples per measured level and alternating field demagnetization at 20 mT (Liddicoat, 1993, Table 1 and Fig. 8). The siltstone is unweathered glacial flour from the Sierra Nevada that borders the western side of Owens Valley where the sediments were deposited in Owens Lake. In the siltstone, the majority of the samples have a percentage of about 60 percent where the grain diameter is less than 63 micrometres, and in those samples there is about a five percent fraction when the diameter is two micrometres or less. The Total Inorganic Carbon in most samples is about 0.25 percent (Bergeron, 2013), and magnetite is the dominant carrier of the magnetization (Liddicoat, 1993). The palaeomagnetic directions recording the terminus of the full M/B transition, which occurs before the field intensity is completely recovered, spans no more than 35 cm of siltstone at each of two localities about a km apart. We will present the results of a continuing palaeomagnetic investigation of the M/B transition at this locality.

Biostatistics Series Module 3: Comparing Groups: Numerical Variables.

PubMed

Hazra, Avijit; Gogtay, Nithya

2016-01-01

Numerical data that are normally distributed can be analyzed with parametric tests, that is, tests which are based on the parameters that define a normal distribution curve. If the distribution is uncertain, the data can be plotted as a normal probability plot and visually inspected, or tested for normality using one of a number of goodness of fit tests, such as the Kolmogorov-Smirnov test. The widely used Student's t-test has three variants. The one-sample t-test is used to assess if a sample mean (as an estimate of the population mean) differs significantly from a given population mean. The means of two independent samples may be compared for a statistically significant difference by the unpaired or independent samples t-test. If the data sets are related in some way, their means may be compared by the paired or dependent samples t-test. The t-test should not be used to compare the means of more than two groups. Although it is possible to compare groups in pairs, when there are more than two groups, this will increase the probability of a Type I error. The one-way analysis of variance (ANOVA) is employed to compare the means of three or more independent data sets that are normally distributed. Multiple measurements from the same set of subjects cannot be treated as separate, unrelated data sets. Comparison of means in such a situation requires repeated measures ANOVA. It is to be noted that while a multiple group comparison test such as ANOVA can point to a significant difference, it does not identify exactly between which two groups the difference lies. To do this, multiple group comparison needs to be followed up by an appropriate post hoc test. An example is the Tukey's honestly significant difference test following ANOVA. If the assumptions for parametric tests are not met, there are nonparametric alternatives for comparing data sets. These include Mann-Whitney U-test as the nonparametric counterpart of the unpaired Student's t-test, Wilcoxon signed-rank test as the counterpart of the paired Student's t-test, Kruskal-Wallis test as the nonparametric equivalent of ANOVA and the Friedman's test as the counterpart of repeated measures ANOVA.

Hyperspectral Imaging and K-Means Classification for Histologic Evaluation of Ductal Carcinoma In Situ.

PubMed

Khouj, Yasser; Dawson, Jeremy; Coad, James; Vona-Davis, Linda

2018-01-01

Hyperspectral imaging (HSI) is a non-invasive optical imaging modality that shows the potential to aid pathologists in breast cancer diagnoses cases. In this study, breast cancer tissues from different patients were imaged by a hyperspectral system to detect spectral differences between normal and breast cancer tissues. Tissue samples mounted on slides were identified from 10 different patients. Samples from each patient included both normal and ductal carcinoma tissue, both stained with hematoxylin and eosin stain and unstained. Slides were imaged using a snapshot HSI system, and the spectral reflectance differences were evaluated. Analysis of the spectral reflectance values indicated that wavelengths near 550 nm showed the best differentiation between tissue types. This information was used to train image processing algorithms using supervised and unsupervised data. The K-means method was applied to the hyperspectral data cubes, and successfully detected spectral tissue differences with sensitivity of 85.45%, and specificity of 94.64% with true negative rate of 95.8%, and false positive rate of 4.2%. These results were verified by ground-truth marking of the tissue samples by a pathologist. In the hyperspectral image analysis, the image processing algorithm, K-means, shows the greatest potential for building a semi-automated system that could identify and sort between normal and ductal carcinoma in situ tissues.

Geomagnetic paleosecular variation recorded in Plio-Pleistocene volcanic rocks from Possession Island (Crozet Archipelago, southern Indian Ocean)

NASA Astrophysics Data System (ADS)

Camps, Pierre; Henry, Bernard; PréVot, Michel; Faynot, Liliane

2001-02-01

Possession Island, in the Crozet Archipelago, consists of volcanic units erupted mainly between ˜5 and 0.5 Ma. A paleomagnetic sampling was carried out along several sections distributed near the northern, eastern, and southeastern coasts. A total of 45 independent flows were sampled (320 samples). For each flow a precisely defined characteristic remanence direction was usually isolated after a careful progressive cleaning in alternating fields. However, particularly complex remanence behavior is often observed. The magnetostratigraphy of the lava pile is quite simple, with reversed rocks in the lower part and normal units in the upper part of two sections. A third section is of normal polarity throughout its whole thickness, including three excursional directions. We did not find any intermediate directions between the normal and reverse magnetozones. Thus we have no evidence for the recording of the Matuyama-Brunhes transition expected from a previous study [Watkins et al., 1972]. The amplitude of paleosecular variation, estimated from between-flow dispersion from the field of an axial dipole, is 11.8° with 95% confidence limits between 9.3° and 14.0°. This value is consistent with the general anisotropic statistical model for paleosecular variation of Constable and Johnson [1999].

The Abnormal vs. Normal ECG Classification Based on Key Features and Statistical Learning

NASA Astrophysics Data System (ADS)

Dong, Jun; Tong, Jia-Fei; Liu, Xia

As cardiovascular diseases appear frequently in modern society, the medicine and health system should be adjusted to meet the new requirements. Chinese government has planned to establish basic community medical insurance system (BCMIS) before 2020, where remote medical service is one of core issues. Therefore, we have developed the "remote network hospital system" which includes data server and diagnosis terminal by the aid of wireless detector to sample ECG. To improve the efficiency of ECG processing, in this paper, abnormal vs. normal ECG classification approach based on key features and statistical learning is presented, and the results are analyzed. Large amount of normal ECG could be filtered by computer automatically and abnormal ECG is left to be diagnosed specially by physicians.

Two Extremely Red Galaxies

NASA Technical Reports Server (NTRS)

Joseph, Robert D.; Hora, Joseph; Stockton, Alan; Hu, Esther; Sanders, David

1997-01-01

This report concerns one of the major observational studies in the ISO Central Programme, the ISO Normal Galaxy Survey. This is a survey of an unbiased sample of spiral and lenticular galaxies selected from the Revised Shapley-Ames Catalog. It is therefore optically-selected, with a brightness limit of blue magnitude = 12, and otherwise randomly chosen. The original sample included 150 galaxies, but this was reduced to 74 when the allocated observing time was expended because the ISO overheads encountered in flight were much larger than predicted.

Investigation of Skin Cancers Using MicroRaman Spectroscopy

NASA Astrophysics Data System (ADS)

Short, M. A.; Chen, X. K.; Zeng, H.; Ajlan, A. A.; McLean, D. I.; Hui, H.

2004-03-01

We have measured the Raman spectra of skin cancers, including melanoma and basal cell carcinoma, using a confocal microRaman spectrograph. In an attempt to identify the origin of the observed Raman modes, we investigated the spectra obtained from different locations of the samples, compared the observed spectra with those measured from normal human skin and pig skin, and studied the polarization dependence of the spectra. In addition, we will discuss the effects of fluorescence in the measurement of Raman spectra of skin samples.

BloodSpot: a database of gene expression profiles and transcriptional programs for healthy and malignant haematopoiesis

PubMed Central

Bagger, Frederik Otzen; Sasivarevic, Damir; Sohi, Sina Hadi; Laursen, Linea Gøricke; Pundhir, Sachin; Sønderby, Casper Kaae; Winther, Ole; Rapin, Nicolas; Porse, Bo T.

2016-01-01

Research on human and murine haematopoiesis has resulted in a vast number of gene-expression data sets that can potentially answer questions regarding normal and aberrant blood formation. To researchers and clinicians with limited bioinformatics experience, these data have remained available, yet largely inaccessible. Current databases provide information about gene-expression but fail to answer key questions regarding co-regulation, genetic programs or effect on patient survival. To address these shortcomings, we present BloodSpot (www.bloodspot.eu), which includes and greatly extends our previously released database HemaExplorer, a database of gene expression profiles from FACS sorted healthy and malignant haematopoietic cells. A revised interactive interface simultaneously provides a plot of gene expression along with a Kaplan–Meier analysis and a hierarchical tree depicting the relationship between different cell types in the database. The database now includes 23 high-quality curated data sets relevant to normal and malignant blood formation and, in addition, we have assembled and built a unique integrated data set, BloodPool. Bloodpool contains more than 2000 samples assembled from six independent studies on acute myeloid leukemia. Furthermore, we have devised a robust sample integration procedure that allows for sensitive comparison of user-supplied patient samples in a well-defined haematopoietic cellular space. PMID:26507857

Methylation profiling identified novel differentially methylated markers including OPCML and FLRT2 in prostate cancer.

PubMed

Wu, Yu; Davison, Jerry; Qu, Xiaoyu; Morrissey, Colm; Storer, Barry; Brown, Lisha; Vessella, Robert; Nelson, Peter; Fang, Min

2016-04-02

To develop new methods to distinguish indolent from aggressive prostate cancers (PCa), we utilized comprehensive high-throughput array-based relative methylation (CHARM) assay to identify differentially methylated regions (DMRs) throughout the genome, including both CpG island (CGI) and non-CGI regions in PCa patients based on Gleason grade. Initially, 26 samples, including 8 each of low [Gleason score (GS) 6] and high (GS ≥7) grade PCa samples and 10 matched normal prostate tissues, were analyzed as a discovery cohort. We identified 3,567 DMRs between normal and cancer tissues, and 913 DMRs distinguishing low from high-grade cancers. Most of these DMRs were located at CGI shores. The top 5 candidate DMRs from the low vs. high Gleason comparison, including OPCML, ELAVL2, EXT1, IRX5, and FLRT2, were validated by pyrosequencing using the discovery cohort. OPCML and FLRT2 were further validated in an independent cohort consisting of 20 low-Gleason and 33 high-Gleason tissues. We then compared patients with biochemical recurrence (n=70) vs. those without (n=86) in a third cohort, and they showed no difference in methylation at these DMR loci. When GS 3+4 cases and GS 4+3 cases were compared, OPCML-DMR methylation showed a trend of lower methylation in the recurrence group (n=30) than in the no-recurrence (n=52) group. We conclude that whole-genome methylation profiling with CHARM revealed distinct patterns of differential DNA methylation between normal prostate and PCa tissues, as well as between different risk groups of PCa as defined by Gleason scores. A panel of selected DMRs may serve as novel surrogate biomarkers for Gleason score in PCa.

Profiling of adrenocorticotropic hormone and arginine vasopressin in human pituitary gland and tumor thin tissue sections using droplet-based liquid-microjunction surface-sampling-HPLC-ESI-MS-MS.

PubMed

Kertesz, Vilmos; Calligaris, David; Feldman, Daniel R; Changelian, Armen; Laws, Edward R; Santagata, Sandro; Agar, Nathalie Y R; Van Berkel, Gary J

2015-08-01

Described here are the results from the profiling of the proteins arginine vasopressin (AVP) and adrenocorticotropic hormone (ACTH) from normal human pituitary gland and pituitary adenoma tissue sections, using a fully automated droplet-based liquid-microjunction surface-sampling-HPLC-ESI-MS-MS system for spatially resolved sampling, HPLC separation, and mass spectrometric detection. Excellent correlation was found between the protein distribution data obtained with this method and data obtained with matrix-assisted laser desorption/ionization (MALDI) chemical imaging analyses of serial sections of the same tissue. The protein distributions correlated with the visible anatomic pattern of the pituitary gland. AVP was most abundant in the posterior pituitary gland region (neurohypophysis), and ATCH was dominant in the anterior pituitary gland region (adenohypophysis). The relative amounts of AVP and ACTH sampled from a series of ACTH-secreting and non-secreting pituitary adenomas correlated with histopathological evaluation. ACTH was readily detected at significantly higher levels in regions of ACTH-secreting adenomas and in normal anterior adenohypophysis compared with non-secreting adenoma and neurohypophysis. AVP was mostly detected in normal neurohypophysis, as expected. This work reveals that a fully automated droplet-based liquid-microjunction surface-sampling system coupled to HPLC-ESI-MS-MS can be readily used for spatially resolved sampling, separation, detection, and semi-quantitation of physiologically-relevant peptide and protein hormones, including AVP and ACTH, directly from human tissue. In addition, the relative simplicity, rapidity, and specificity of this method support the potential of this basic technology, with further advancement, for assisting surgical decision-making. Graphical Abstract Mass spectrometry based profiling of hormones in human pituitary gland and tumor thin tissue sections.

Exploring of the molecular mechanism of rhinitis via bioinformatics methods

PubMed Central

Song, Yufen; Yan, Zhaohui

2018-01-01

The aim of this study was to analyze gene expression profiles for exploring the function and regulatory network of differentially expressed genes (DEGs) in pathogenesis of rhinitis by a bioinformatics method. The gene expression profile of GSE43523 was downloaded from the Gene Expression Omnibus database. The dataset contained 7 seasonal allergic rhinitis samples and 5 non-allergic normal samples. DEGs between rhinitis samples and normal samples were identified via the limma package of R. The webGestal database was used to identify enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways of the DEGs. The differentially co-expressed pairs of the DEGs were identified via the DCGL package in R, and the differential co-expression network was constructed based on these pairs. A protein-protein interaction (PPI) network of the DEGs was constructed based on the Search Tool for the Retrieval of Interacting Genes database. A total of 263 DEGs were identified in rhinitis samples compared with normal samples, including 125 downregulated ones and 138 upregulated ones. The DEGs were enriched in 7 KEGG pathways. 308 differential co-expression gene pairs were obtained. A differential co-expression network was constructed, containing 212 nodes. In total, 148 PPI pairs of the DEGs were identified, and a PPI network was constructed based on these pairs. Bioinformatics methods could help us identify significant genes and pathways related to the pathogenesis of rhinitis. Steroid biosynthesis pathway and metabolic pathways might play important roles in the development of allergic rhinitis (AR). Genes such as CDC42 effector protein 5, solute carrier family 39 member A11 and PR/SET domain 10 might be also associated with the pathogenesis of AR, which provided references for the molecular mechanisms of AR. PMID:29257233

Establishment and characterization of a new and stable collagen-binding assay for the assessment of von Willebrand factor activity

PubMed Central

Ni, Y; Nesrallah, J; Agnew, M; Geske, F J; Favaloro, E J

2013-01-01

Introduction Laboratory diagnosis of von Willebrand disease (VWD) requires determination of both von Willebrand factor (VWF) protein levels and activity. Current VWF activity tests include the ristocetin cofactor assay and the collagen-binding assay (VWF:CB). The goal of this investigation is to characterize a new collagen-binding assay and to determine its effectiveness in identifying VWD. Methods Analytical studies were carried out to characterize the performance of a new VWF:CB ELISA. Additionally, samples from a normal population were tested as were well-characterized type 1 and type 2 VWD samples. Results Repeatability and within-laboratory precision studies resulted in coefficients of variation (CVs) of ≤11%. A linear range of 1–354% (0.01–3.54 IU/mL) was determined, along with a limit of detection and a lower limit of quantitation of 1.6% and 4.0% (0.016 and 0.04 IU/mL), respectively. Samples tested from apparently healthy individuals resulted in a normal range of 54–217% (0.54–2.17 IU/mL). Known VWD type 1 and type 2 samples were also analyzed by the ELISA, with 99% of samples having VWF:CB below the normal reference range and an estimated 96% sensitivity and 87% specificity using a VWF collagen-binding/antigen cutoff ratio of 0.50. Conclusion This new VWF:CB ELISA provides an accurate measure of collagen-binding activity that aids in the diagnosis and differentiation of type 1 from type 2 VWD. PMID:23107512

Fiber-probe optical spectroscopy discriminates normal brain from focal cortical dysplasia in pediatric subjects

NASA Astrophysics Data System (ADS)

Anand, Suresh; Cicchi, Riccardo; Giordano, Flavio; Conti, Valerio; Buccoliero, Anna Maria; Guerrini, Renzo; Pavone, Francesco S.

2017-02-01

Focal cortical dysplasia (FCD) is an abnormality in the cerebral cortex that is caused by malformations during cortical development. Currently, magnetic resonance imaging (MRI) and electro-corticography (ECoG) are used for detecting FCD. On the downside, MRI is very much insensitive to small malformations in the brain, while ECoG is an invasive and time consuming procedure. Recently, optical techniques were widely exploited as a minimally invasive and quantitative approaches for disease diagnosis. These techniques include fluorescence and Raman spectroscopy. The aim of this investigation is to study the diagnostic performances of optical spectroscopy incorporating fluorescence (at 378 nm and 445 nm excitation wavelengths) and Raman spectroscopy (at 785 nm excitation) for the discrimination of FCD from normal brain in pediatric subjects. The study included 10 normal and 17 FCD tissue sites from 3 normal and 7 FCD samples. The emission spectra of FCD at 378 nm excitation wavelength presented a blue-shifted peak with respect to normal tissue. Prominent spectral differences between normal and FCD tissue were observed at 1298 cm-1, 1302 cm-1, 1445 cm-1 and 1660 cm-1 using Raman spectroscopy. Tissue classification models were developed using a multivariate statistical method, principal component analysis. This study demonstrates that a combined spectroscopic approach can provide a better diagnostic capability for classifying normal and FCD tissues. Further, the implementation of the technology within a fiber probe could open the way for in vivo diagnostics and intra-operative surgical guidance.

Relation between Outcomes on a Continuous Performance Test and ADHD Symptoms over Time

ERIC Educational Resources Information Center

Vaughn, Aaron J.; Epstein, Jeffery N.; Rausch, Joseph; Altaye, Mekibib; Langberg, Joshua; Newcorn, Jeffrey H.; Hinshaw, Stephen P.; Hechtman, Lily; Arnold, L. Eugene; Swanson, James M.; Wigal, Timothy

2011-01-01

This study examined the relationship between the developmental trajectories of neuropsychological functioning and ADHD symptomatology in a longitudinal sample of children ages 9 to 14. Participants and measures were derived from the Multimodal Treatment Study for ADHD including 534MTA participants and 254 normal controls. Despite improvement over…

76 FR 12648 - Lowering Miners' Exposure to Respirable Coal Mine Dust, Including Continuous Personal Dust Monitors

Federal Register 2010, 2011, 2012, 2013, 2014

2011-03-08

... be appropriate to use on a short-term basis. 13. The proposed rule addresses (1) which occupations... for respirable coal mine dust, provide for full- shift sampling, redefine the term ``normal production... respect to their availability. If shorter or longer timeframes are recommended, please provide the...

Stability of personality traits in schizophrenia and schizoaffective disorder: a pilot project.

PubMed

Kentros, M; Smith, T E; Hull, J; McKee, M; Terkelsen, K; Capalbo, C

1997-09-01

This study was performed in an effort to begin characterization of personality traits in schizophrenia. Specific concerns included personality profiles relative to normal adults, personality profile stability over time, and trait-state issues. The authors administered the NEO Personality Inventory as well as symptom ratings at two time points to 21 patients. Patients were all stabilized outpatients attending an adult continuing day treatment program and diagnosed with either schizophrenia or schizoaffective disorder. Personality profiles were determined for all patients. Compared with a normal adult sample, this sample's scores on three out of five of the personality domains assessed were not distinguishable from normal adults. Test-retest correlations were highly significant over an average 28.2-week time interval. In general, the presence of positive symptoms did not appear related to NEO-PI stability, while negative symptoms did show a relationship to the stability of personality profiles. These data suggest that personality profiles can be looked at in schizophrenia, that these profiles do appear stable over time, and that negative symptoms have a strong influence on profile stability and appear to be "trait-like."

The identification of fungi collected from the ceca of commercial poultry.

PubMed

Byrd, J A; Caldwell, D Y; Nisbet, D J

2017-07-01

Under normal conditions, fungi are ignored unless a disease/syndrome clinical signs are reported. The scientific communities are largely unaware of the roles fungi play in normal production parameters. Numerous preharvest interventions have demonstrated that beneficial bacteria can play a role in improving productions parameters; however, most researchers have ignored the impact that fungi may have on production. The goal of the present study was to record fungi recovered from commercial broiler and layer houses during production. Over 3,000 cecal samples were isolated using conventional culture methodology and over 890 samples were further characterized using an automated repetitive sequence-based PCR (rep-PCR) methodology. Eighty-eight different fungal and yeast species were identified, including Aspergillus spp., Penicillium spp., and Sporidiobolus spp, and 18 unknown genera were separated using rep-PCR. The results from the present study will provide a normal fungi background genera under commercial conditions and will be a stepping stone for investigating the impact of fungi on the gastrointestinal tract and on the health of poultry. Published by Oxford University Press on behalf of Poultry Science Association 2017.

FREQUENCY DISTRIBUTIONS OF 90SR AND 137CS CONCENTRATIONS IN AN ECOSYSTEM OF THE 'RED FOREST' AREA IN THE CHERNOBYL EXCLUSION ZONE

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

Farfan, E.; Jannik, T.; Caldwell, E.

2011-10-01

In the most highly contaminated region of the Chernobyl Exclusion Zone: the 'Red Forest' site, the accumulation of the major dose-affecting radionuclides ({sup 90}Sr and {sup 137}Cs) within the components of an ecological system encompassing 3,000 m{sup 2} were characterized. The sampled components included soils (top 0-10 cm depth), Molina caerulea (blue moor grass), Camponotus vagus (carpenter ants) and Pelobates fuscus (spade-footed toad). In a comparison among the components of this ecosystem, the {sup 90}Sr and {sup 137}Cs concentrations measured in 40 separate grids exhibited significant differences, while the frequency distribution of the values were close to a logarithmically normalmore » leptokurtic distribution with a significant right-side skew. While it is important to identify localized areas of high contamination or 'hot spots,' including these values in the arithmetic mean may overestimate the exposure risk. In component sample sets that exhibited logarithmically normal distribution, the geometrical mean more accurately characterizes a site. Ideally, risk assessment is most confidently achieved when the arithmetic and geometrical means are most similar, meaning the distribution approaches normal. Through bioaccumulation, the highest concentrations of {sup 90}Sr and {sup 137}Cs were measured in the blue moor grass and spade-footed toad. These components also possessed distribution parameters that shifted toward a normal distribution.« less

Quantitative analysis of iris parameters in keratoconus patients using optical coherence tomography.

PubMed

Bonfadini, Gustavo; Arora, Karun; Vianna, Lucas M; Campos, Mauro; Friedman, David; Muñoz, Beatriz; Jun, Albert S

2015-01-01

To investigate the relationship between quantitative iris parameters and the presence of keratoconus. Cross-sectional observational study that included 15 affected eyes of 15 patients with keratoconus and 26 eyes of 26 normal age- and sex-matched controls. Iris parameters (area, thickness, and pupil diameter) of affected and unaffected eyes were measured under standardized light and dark conditions using anterior segment optical coherence tomography (AS-OCT). To identify optimal iris thickness cutoff points to maximize the sensitivity and specificity when discriminating keratoconus eyes from normal eyes, the analysis included the use of receiver operating characteristic (ROC) curves. Iris thickness and area were lower in keratoconus eyes than in normal eyes. The mean thickness at the pupillary margin under both light and dark conditions was found to be the best parameter for discriminating normal patients from keratoconus patients. Diagnostic performance was assessed by the area under the ROC curve (AROC), which had a value of 0.8256 with 80.0% sensitivity and 84.6% specificity, using a cutoff of 0.4125 mm. The sensitivity increased to 86.7% when a cutoff of 0.4700 mm was used. In our sample, iris thickness was lower in keratoconus eyes than in normal eyes. These results suggest that tomographic parameters may provide novel adjunct approaches for keratoconus screening.

DNA methylation profiling identifies global methylation differences and markers of adrenocortical tumors.

PubMed

Rechache, Nesrin S; Wang, Yonghong; Stevenson, Holly S; Killian, J Keith; Edelman, Daniel C; Merino, Maria; Zhang, Lisa; Nilubol, Naris; Stratakis, Constantine A; Meltzer, Paul S; Kebebew, Electron

2012-06-01

It is not known whether there are any DNA methylation alterations in adrenocortical tumors. The objective of the study was to determine the methylation profile of normal adrenal cortex and benign and malignant adrenocortical tumors. Genome-wide methylation status of CpG regions were determined in normal (n = 19), benign (n = 48), primary malignant (n = 8), and metastatic malignant (n = 12) adrenocortical tissue samples. An integrated analysis of genome-wide methylation and mRNA expression in benign vs. malignant adrenocortical tissue samples was also performed. Methylation profiling revealed the following: 1) that methylation patterns were distinctly different and could distinguish normal, benign, primary malignant, and metastatic tissue samples; 2) that malignant samples have global hypomethylation; and 3) that the methylation of CpG regions are different in benign adrenocortical tumors by functional status. Normal compared with benign samples had the least amount of methylation differences, whereas normal compared with primary and metastatic adrenocortical carcinoma samples had the greatest variability in methylation (adjusted P ≤ 0.01). Of 215 down-regulated genes (≥2-fold, adjusted P ≤ 0.05) in malignant primary adrenocortical tumor samples, 52 of these genes were also hypermethylated. Malignant adrenocortical tumors are globally hypomethylated as compared with normal and benign tumors. Methylation profile differences may accurately distinguish between primary benign and malignant adrenocortical tumors. Several differentially methylated sites are associated with genes known to be dysregulated in malignant adrenocortical tumors.

Predicting Sensitivity of Breast Tumors to Src-targeted Therapies Through Assessment of Cas/Src/BCAR3 Activity

DTIC Science & Technology

2017-10-01

expression is elevated in DCIS samples compared to normal mammary tissue, invasive ductal carcinoma (IDC) compared to normal mammary tissue, and DCIS... compared to IDC. (2) BCAR3 is significantly upregulated in triple negative breast cancer and normal tissue; (3) BCAR3 expression shows a modest...expression was seen to be elevated in DCIS samples compared to normal mammary tissue, invasive ductal carcinoma (IDC) compared to normal mammary tissue, and

Whole exome sequencing identifies driver mutations in asymptomatic computed tomography-detected lung cancers with normal karyotype.

PubMed

Belloni, Elena; Veronesi, Giulia; Rotta, Luca; Volorio, Sara; Sardella, Domenico; Bernard, Loris; Pece, Salvatore; Di Fiore, Pier Paolo; Fumagalli, Caterina; Barberis, Massimo; Spaggiari, Lorenzo; Pelicci, Pier Giuseppe; Riva, Laura

2015-04-01

The efficacy of curative surgery for lung cancer could be largely improved by non-invasive screening programs, which can detect the disease at early stages. We previously showed that 18% of screening-identified lung cancers demonstrate a normal karyotype and, following high-density genome scanning, can be subdivided into samples with 1) numerous; 2) none; and 3) few copy number alterations. Whole exome sequencing was applied to the two normal karyotype, screening-detected lung cancers, constituting group 2, as well as normal controls. We identified mutations in both tumors, including KEAP1 (commonly mutated in lung cancers) in one, and TP53, PMS1, and MSH3 (well-characterized DNA-repair genes) in the other. The two normal karyotype screening-detected lung tumors displayed a typical lung cancer mutational profile that only next generation sequencing could reveal, which offered an additional contribution to the over-diagnosis bias concept hypothesized within lung cancer screening programs. Copyright © 2015 Elsevier Inc. All rights reserved.

Normal villous architecture with increased intraepithelial lymphocytes: a duodenal manifestation of Crohn disease.

PubMed

Patterson, Emily R; Shmidt, Eugenia; Oxentenko, Amy S; Enders, Felicity T; Smyrk, Thomas C

2015-03-01

To assess a possible association between inflammatory bowel disease (IBD) and the histologic finding in duodenal biopsy specimens of increased intraepithelial lymphocytes (IELs) with normal villous architecture. We identified all patients with duodenal biopsy specimens obtained between 2000 and 2010 showing increased IELs and normal architecture. Among the 74 such patients who also had IBD, we characterized the clinical features of IBD and reviewed all available upper gastrointestinal biopsy specimens. Fifty-eight patients had Crohn disease, 13 had ulcerative colitis, and three had IBD, type unclassified. No duodenal sample with increased IELs had other histologic features of IBD. Among gastric biopsy specimens from 34 patients with Crohn disease, nearly half (16) had focal gastritis. We propose that Crohn disease be included in the differential diagnosis for increased IELs with normal villous architecture in duodenal biopsy specimens, particularly when gastric biopsy specimens show focal gastritis. Copyright© by the American Society for Clinical Pathology.

Personal exposure to volatile organic compounds. I. Direct measurements in breathing-zone air, drinking water, food, and exhaled breath

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

Wallace, L.A.; Pellizzari, E.; Hartwell, T.

A pilot study to test methods of estimating personal exposures to toxic substances and corresponding body burdens was carried out between July and December 1980. Individual exposures to about a dozen volatile organic compounds in air and drinking water were measured for volunteers in New Jersey and North Carolina. Breath samples were also collected from all subjects. About 230 personal air samples, 170 drinking water samples, 66 breath samples, and 4 food samples (16 composites) were analyzed for the target chemicals. Ten compounds were present in air and eight were transmitted mainly through that medium. Chloroform and bromodichloromethane were predominantlymore » transmitted through water and beverages. Food appeared to be a miner route of exposure, except possibly for trichloroethylene in margarine. Seven compounds were present in more than half of the breath samples. Diurnal and seasonal variations were noted in air and water concentrations of some compounds. Some, but not all, of the potentially occupationally exposed individuals had significantly higher workplace exposures to several chemicals. Distributions of air exposures were closer to log normal than normal for most chemicals. Several chemicals were highly correlated with each other in personal air samples, indicating possible common sources of exposures. Compounds detected included benzene, chlorinated aromatic hydrocarbons, chlorinated aliphatic hydrocarbons, halogens and vinyl chloride.« less

Predictive equations for total lung capacity and residual volume calculated from radiographs in a random sample of the Michigan population.

PubMed Central

Kilburn, K H; Warshaw, R H; Thornton, J C; Thornton, K; Miller, A

1992-01-01

BACKGROUND: Published predicted values for total lung capacity and residual volume are often based on a small number of subjects and derive from different populations from predicted spirometric values. Equations from the only two large studies gave smaller predicted values for total lung capacity than the smaller studies. A large number of subjects have been studied from a population which has already provided predicted values for spirometry and transfer factor for carbon monoxide. METHODS: Total lung capacity was measured from standard posteroanterior and lateral chest radiographs and forced vital capacity by spirometry in a population sample of 771 subjects. Prediction equations were developed for total lung capacity (TLC), residual volume (RV) and RV/TLC in two groups--normal and total. Subjects with signs or symptoms of cardiopulmonary disease were combined with the normal subjects and equations for all subjects were also modelled. RESULTS: Prediction equations for TLC and RV in non-smoking normal men and women were square root transformations which included height and weight but not age. They included a coefficient for duration of smoking in current smokers. The predictive equation for RV/TLC included weight, age, age and duration of smoking for current smokers and ex-smokers of both sexes. For the total population the equations took the same form but the height coefficients and constants were slightly different. CONCLUSION: These population based prediction equations for TLC, RV and RV/TLC provide reference standards in a population that has provided reference standards for spirometry and single breath transfer factor for carbon monoxide. PMID:1412094

Chemical mixtures in untreated water from public-supply wells in the U.S. — Occurrence, composition, and potential toxicity

USGS Publications Warehouse

Toccalino, Patricia L.; Norman, Julia E.; Scott, Jonathon C.

2012-01-01

Chemical mixtures are prevalent in groundwater used for public water supply, but little is known about their potential health effects. As part of a large-scale ambient groundwater study, we evaluated chemical mixtures across multiple chemical classes, and included more chemical contaminants than in previous studies of mixtures in public-supply wells. We (1) assessed the occurrence of chemical mixtures in untreated source-water samples from public-supply wells, (2) determined the composition of the most frequently occurring mixtures, and (3) characterized the potential toxicity of mixtures using a new screening approach. The U.S. Geological Survey collected one untreated water sample from each of 383 public wells distributed across 35 states, and analyzed the samples for as many as 91 chemical contaminants. Concentrations of mixture components were compared to individual human-health benchmarks; the potential toxicity of mixtures was characterized by addition of benchmark-normalized component concentrations. Most samples (84%) contained mixtures of two or more contaminants, each at concentrations greater than one-tenth of individual benchmarks. The chemical mixtures that most frequently occurred and had the greatest potential toxicity primarily were composed of trace elements (including arsenic, strontium, or uranium), radon, or nitrate. Herbicides, disinfection by-products, and solvents were the most common organic contaminants in mixtures. The sum of benchmark-normalized concentrations was greater than 1 for 58% of samples, suggesting that there could be potential for mixtures toxicity in more than half of the public-well samples. Our findings can be used to help set priorities for groundwater monitoring and suggest future research directions for drinking-water treatment studies and for toxicity assessments of chemical mixtures in water resources.

[Psychiatric disorders and cognitive deterioration in Friedreich ataxia].

PubMed

Ayuso Mateos, J L; Bayón, C; Santo-Domingo, J; Calvo, R; Anciones, B

1997-01-01

The present study was designed with the aim of examining the presence of psychiatric diagnosis and intellectual impairment in a sample of patients with Friedreich's ataxia. A consecutive sample of 21 patients presenting with Friedreich's Ataxia were evaluated by means of a neuropsychiatric interview. Only one patient was diagnosed as mentally retarded. Out of the 15 patients of the sample who were evaluated with be WAIS, all of them fell within a normal intellectual range. The idea that Friedreich's Ataxia produces cognitive impairment and serious psychiatric symptoms came from the earliest descriptions of the disease at the beginning of this century, which probably included many patients in their samples who had other diseases.

Seasonal variation of human sperm cells among 4,422 semen samples: A retrospective study in Turkey.

PubMed

Ozelci, Runa; Yılmaz, Saynur; Dilbaz, Berna; Akpınar, Funda; Akdag Cırık, Derya; Dilbaz, Serdar; Ocal, Aslı

2016-12-01

We aimed to assess the possible presence of a seasonal pattern in three parameters of semen analysis: sperm concentration, morphology, and motility as a function of the time of ejaculation and sperm production (spermatogenesis) in normal and oligozoospermic men. This retrospective study included a consecutive series of 4,422 semen samples that were collected from patients as a part of the basic evaluation of the infertile couples attending the Reproductive Endocrine Outpatient Clinic of a tertiary women's hospital in Ankara, Turkey, between January 1, 2012 and December 31, 2013. The samples were classified according to sperm concentration: ≥15 x10 6 /mL as normozoospermic samples and 4 -14.99 x10 6 /mL as oligozoospermic samples and seasonal analysis of the semen samples were carried out separately. When the data was analyzed according to the season of semen production, there was no seasonal effect on the sperm concentration. A gradual and consistent decrease in the rate of sperm with fast forward motility was observed from spring to fall with a recovery noticed during the winter. The percentage of sperms with normal morphology was found to be statistically significantly higher in the spring samples compared with the summer samples (p=0.001). Both normozoospermic and oligozoospermic semen samples appeared to have better sperm parameters in spring and winter. The circannual variation of semen parameters may be important in diagnosis and treatment desicions. WHO: World Health Organization; mRNA:messenger ribonucleic acid.

Method for measuring recovery of catalytic elements from fuel cells

DOEpatents

Shore, Lawrence [Edison, NJ; Matlin, Ramail [Berkeley, NJ

2011-03-08

A method is provided for measuring the concentration of a catalytic clement in a fuel cell powder. The method includes depositing on a porous substrate at least one layer of a powder mixture comprising the fuel cell powder and an internal standard material, ablating a sample of the powder mixture using a laser, and vaporizing the sample using an inductively coupled plasma. A normalized concentration of catalytic element in the sample is determined by quantifying the intensity of a first signal correlated to the amount of catalytic element in the sample, quantifying the intensity of a second signal correlated to the amount of internal standard material in the sample, and using a ratio of the first signal intensity to the second signal intensity to cancel out the effects of sample size.

Standard deviation and standard error of the mean.

PubMed

Lee, Dong Kyu; In, Junyong; Lee, Sangseok

2015-06-01

In most clinical and experimental studies, the standard deviation (SD) and the estimated standard error of the mean (SEM) are used to present the characteristics of sample data and to explain statistical analysis results. However, some authors occasionally muddle the distinctive usage between the SD and SEM in medical literature. Because the process of calculating the SD and SEM includes different statistical inferences, each of them has its own meaning. SD is the dispersion of data in a normal distribution. In other words, SD indicates how accurately the mean represents sample data. However the meaning of SEM includes statistical inference based on the sampling distribution. SEM is the SD of the theoretical distribution of the sample means (the sampling distribution). While either SD or SEM can be applied to describe data and statistical results, one should be aware of reasonable methods with which to use SD and SEM. We aim to elucidate the distinctions between SD and SEM and to provide proper usage guidelines for both, which summarize data and describe statistical results.

Standard deviation and standard error of the mean

PubMed Central

In, Junyong; Lee, Sangseok

2015-01-01

In most clinical and experimental studies, the standard deviation (SD) and the estimated standard error of the mean (SEM) are used to present the characteristics of sample data and to explain statistical analysis results. However, some authors occasionally muddle the distinctive usage between the SD and SEM in medical literature. Because the process of calculating the SD and SEM includes different statistical inferences, each of them has its own meaning. SD is the dispersion of data in a normal distribution. In other words, SD indicates how accurately the mean represents sample data. However the meaning of SEM includes statistical inference based on the sampling distribution. SEM is the SD of the theoretical distribution of the sample means (the sampling distribution). While either SD or SEM can be applied to describe data and statistical results, one should be aware of reasonable methods with which to use SD and SEM. We aim to elucidate the distinctions between SD and SEM and to provide proper usage guidelines for both, which summarize data and describe statistical results. PMID:26045923

The Generation R Study: Biobank update 2015.

PubMed

Kruithof, Claudia J; Kooijman, Marjolein N; van Duijn, Cornelia M; Franco, Oscar H; de Jongste, Johan C; Klaver, Caroline C W; Mackenbach, Johan P; Moll, Henriëtte A; Raat, Hein; Rings, Edmond H H M; Rivadeneira, Fernando; Steegers, Eric A P; Tiemeier, Henning; Uitterlinden, Andre G; Verhulst, Frank C; Wolvius, Eppo B; Hofman, Albert; Jaddoe, Vincent W V

2014-12-01

The Generation R Study is a population-based prospective cohort study from fetal life until adulthood. The study is designed to identify early environmental and genetic causes and causal pathways leading to normal and abnormal growth, development and health from fetal life, childhood and young adulthood. In total, 9,778 mothers were enrolled in the study. Data collection in children and their parents include questionnaires, interviews, detailed physical and ultrasound examinations, behavioural observations, Magnetic Resonance Imaging and biological samples. Efforts have been conducted for collecting biological samples including blood, hair, faeces, nasal swabs, saliva and urine samples and generating genomics data on DNA, RNA and microbiome. In this paper, we give an update of the collection, processing and storage of these biological samples and available measures. Together with detailed phenotype measurements, these biological samples provide a unique resource for epidemiological studies focused on environmental exposures, genetic and genomic determinants and their interactions in relation to growth, health and development from fetal life onwards.

Flux pinning mechanism in codoped-MgB2 with Al2O3 and SiC

NASA Astrophysics Data System (ADS)

Kiafiroozkoohi, Narjess Sadat; Ghorbani, Shaban Reza; Arabi, Hadi

2018-05-01

MgB2 superconductor samples, co-doped with 0.02 wt of Al2O3 and 0.02 wt SiC, have been examined by M-H loop measurements and calculation of the critical current density based on the Bean model. Normalized volume pinning force, f = F/Fmax, as a function of the reduced magnetic field, h = H/Hmax has been obtained at each temperature. Hughochi flux pinning model, which was included the normal point pinning, the normal surface pinning, and the pinning based on spatial variation in the Ginzburg-Landau parameter, was used to study the flux pinning mechanisms. It was found that the Δκ effect and the normal point pinning mechanisms play the main role in the flux pinning at the magnetic field lower than Hmax and the contribution of the Δκ mechanism increases with the increasing temperature, while the contribution of normal point pinning mechanism decreases. At magnetic field larger than Hmax, the only mechanism that acts as the flux pinning was the normal surface pinning mechanism.

Brain shape in human microcephalics and Homo floresiensis.

PubMed

Falk, Dean; Hildebolt, Charles; Smith, Kirk; Morwood, M J; Sutikna, Thomas; Jatmiko; Saptomo, E Wayhu; Imhof, Herwig; Seidler, Horst; Prior, Fred

2007-02-13

Because the cranial capacity of LB1 (Homo floresiensis) is only 417 cm(3), some workers propose that it represents a microcephalic Homo sapiens rather than a new species. This hypothesis is difficult to assess, however, without a clear understanding of how brain shape of microcephalics compares with that of normal humans. We compare three-dimensional computed tomographic reconstructions of the internal braincases (virtual endocasts that reproduce details of external brain morphology, including cranial capacities and shape) from a sample of 9 microcephalic humans and 10 normal humans. Discriminant and canonical analyses are used to identify two variables that classify normal and microcephalic humans with 100% success. The classification functions classify the virtual endocast from LB1 with normal humans rather than microcephalics. On the other hand, our classification functions classify a pathological H. sapiens specimen that, like LB1, represents an approximately 3-foot-tall adult female and an adult Basuto microcephalic woman that is alleged to have an endocast similar to LB1's with the microcephalic humans. Although microcephaly is genetically and clinically variable, virtual endocasts from our highly heterogeneous sample share similarities in protruding and proportionately large cerebella and relatively narrow, flattened orbital surfaces compared with normal humans. These findings have relevance for hypotheses regarding the genetic substrates of hominin brain evolution and may have medical diagnostic value. Despite LB1's having brain shape features that sort it with normal humans rather than microcephalics, other shape features and its small brain size are consistent with its assignment to a separate species.

Comparison of analytical methods of brain [18F]FDG-PET after severe traumatic brain injury.

PubMed

Madsen, Karine; Hesby, Sara; Poulsen, Ingrid; Fuglsang, Stefan; Graff, Jesper; Larsen, Karen B; Kammersgaard, Lars P; Law, Ian; Siebner, Hartwig R

2017-11-01

Loss of consciousness has been shown to reduce cerebral metabolic rates of glucose (CMRglc) measured by brain [ 18 F]FDG-PET. Measurements of regional metabolic patterns by normalization to global cerebral metabolism or cerebellum may underestimate widespread reductions. The aim of this study was to compare quantification methods of whole brain glucose metabolism, including whole brain [18F]FDG uptake normalized to uptake in cerebellum, normalized to injected activity, normalized to plasma tracer concentration, and two methods for estimating CMRglc. Six patients suffering from severe traumatic brain injury (TBI) and ten healthy controls (HC) underwent a 10min static [ 18 F]FDG-PET scan and venous blood sampling. Except from normalizing to cerebellum, all quantification methods found significant lower level of whole brain glucose metabolism of 25-33% in TBI patients compared to HC. In accordance these measurements correlated to level of consciousness. Our study demonstrates that the analysis method of the [ 18 F]FDG PET data has a substantial impact on the estimated whole brain cerebral glucose metabolism in patients with severe TBI. Importantly, the SUVR method which is often used in a clinical setting was not able to distinguish patients with severe TBI from HC at the whole-brain level. We recommend supplementing a static [ 18 F]FDG scan with a single venous blood sample in future studies of patients with severe TBI or reduced level of consciousness. This can be used for simple semi-quantitative uptake values by normalizing brain activity uptake to plasma tracer concentration, or quantitative estimates of CMRglc. Copyright © 2017 Elsevier B.V. All rights reserved.

Tools for T-RFLP data analysis using Excel.

PubMed

Fredriksson, Nils Johan; Hermansson, Malte; Wilén, Britt-Marie

2014-11-08

Terminal restriction fragment length polymorphism (T-RFLP) analysis is a DNA-fingerprinting method that can be used for comparisons of the microbial community composition in a large number of samples. There is no consensus on how T-RFLP data should be treated and analyzed before comparisons between samples are made, and several different approaches have been proposed in the literature. The analysis of T-RFLP data can be cumbersome and time-consuming, and for large datasets manual data analysis is not feasible. The currently available tools for automated T-RFLP analysis, although valuable, offer little flexibility, and few, if any, options regarding what methods to use. To enable comparisons and combinations of different data treatment methods an analysis template and an extensive collection of macros for T-RFLP data analysis using Microsoft Excel were developed. The Tools for T-RFLP data analysis template provides procedures for the analysis of large T-RFLP datasets including application of a noise baseline threshold and setting of the analysis range, normalization and alignment of replicate profiles, generation of consensus profiles, normalization and alignment of consensus profiles and final analysis of the samples including calculation of association coefficients and diversity index. The procedures are designed so that in all analysis steps, from the initial preparation of the data to the final comparison of the samples, there are various different options available. The parameters regarding analysis range, noise baseline, T-RF alignment and generation of consensus profiles are all given by the user and several different methods are available for normalization of the T-RF profiles. In each step, the user can also choose to base the calculations on either peak height data or peak area data. The Tools for T-RFLP data analysis template enables an objective and flexible analysis of large T-RFLP datasets in a widely used spreadsheet application.

Gene Expression Profiling Reveals a Massive, Aneuploidy-Dependent Transcriptional Deregulation and Distinct Differences between Lymph Node–Negative and Lymph Node–Positive Colon Carcinomas

PubMed Central

Grade, Marian; Hörmann, Patrick; Becker, Sandra; Hummon, Amanda B.; Wangsa, Danny; Varma, Sudhir; Simon, Richard; Liersch, Torsten; Becker, Heinz; Difilippantonio, Michael J.; Ghadimi, B. Michael; Ried, Thomas

2016-01-01

To characterize patterns of global transcriptional deregulation in primary colon carcinomas, we did gene expression profiling of 73 tumors [Unio Internationale Contra Cancrum stage II (n = 33) and stage III (n = 40)] using oligonucleotide microarrays. For 30 of the tumors, expression profiles were compared with those from matched normal mucosa samples. We identified a set of 1,950 genes with highly significant deregulation between tumors and mucosa samples (P < 1e–7). A significant proportion of these genes mapped to chromosome 20 (P = 0.01). Seventeen genes had a >5-fold average expression difference between normal colon mucosa and carcinomas, including up-regulation of MYC and of HMGA1, a putative oncogene. Furthermore, we identified 68 genes that were significantly differentially expressed between lymph node–negative and lymph node–positive tumors (P < 0.001), the functional annotation of which revealed a preponderance of genes that play a role in cellular immune response and surveillance. The microarray-derived gene expression levels of 20 deregulated genes were validated using quantitative real-time reverse transcription-PCR in >40 tumor and normal mucosa samples with good concordance between the techniques. Finally, we established a relationship between specific genomic imbalances, which were mapped for 32 of the analyzed colon tumors by comparative genomic hybridization, and alterations of global transcriptional activity. Previously, we had conducted a similar analysis of primary rectal carcinomas. The systematic comparison of colon and rectal carcinomas revealed a significant overlap of genomic imbalances and transcriptional deregulation, including activation of the Wnt/β-catenin signaling cascade, suggesting similar pathogenic pathways. PMID:17210682

Gene expression profiling reveals a massive, aneuploidy-dependent transcriptional deregulation and distinct differences between lymph node-negative and lymph node-positive colon carcinomas.

PubMed

Grade, Marian; Hörmann, Patrick; Becker, Sandra; Hummon, Amanda B; Wangsa, Danny; Varma, Sudhir; Simon, Richard; Liersch, Torsten; Becker, Heinz; Difilippantonio, Michael J; Ghadimi, B Michael; Ried, Thomas

2007-01-01

To characterize patterns of global transcriptional deregulation in primary colon carcinomas, we did gene expression profiling of 73 tumors [Unio Internationale Contra Cancrum stage II (n = 33) and stage III (n = 40)] using oligonucleotide microarrays. For 30 of the tumors, expression profiles were compared with those from matched normal mucosa samples. We identified a set of 1,950 genes with highly significant deregulation between tumors and mucosa samples (P < 1e-7). A significant proportion of these genes mapped to chromosome 20 (P = 0.01). Seventeen genes had a >5-fold average expression difference between normal colon mucosa and carcinomas, including up-regulation of MYC and of HMGA1, a putative oncogene. Furthermore, we identified 68 genes that were significantly differentially expressed between lymph node-negative and lymph node-positive tumors (P < 0.001), the functional annotation of which revealed a preponderance of genes that play a role in cellular immune response and surveillance. The microarray-derived gene expression levels of 20 deregulated genes were validated using quantitative real-time reverse transcription-PCR in >40 tumor and normal mucosa samples with good concordance between the techniques. Finally, we established a relationship between specific genomic imbalances, which were mapped for 32 of the analyzed colon tumors by comparative genomic hybridization, and alterations of global transcriptional activity. Previously, we had conducted a similar analysis of primary rectal carcinomas. The systematic comparison of colon and rectal carcinomas revealed a significant overlap of genomic imbalances and transcriptional deregulation, including activation of the Wnt/beta-catenin signaling cascade, suggesting similar pathogenic pathways.

The global star formation law of galaxies revisited in the radio continuum

NASA Astrophysics Data System (ADS)

Liu, LiJie; Gao, Yu

2012-02-01

We study the global star formation law, the relation between the gas and star formation rate (SFR) in a sample of 130 local galaxies with infrared (IR) luminosities spanning over three orders of magnitude (109-1012 L⊙), which includes 91 normal spiral galaxies and 39 (ultra)luminous IR galaxies [(U)LIRGs]. We derive their total (atomic and molecular) gas and dense molecular gas masses using newly available HI, CO and HCN data from the literature. The SFR of galaxies is determined from total IR (8-1000 μm) and 1.4 GHz radio continuum (RC) luminosities. The galaxy disk sizes are defined by the de-convolved elliptical Gaussian FWHM of the RC maps. We derive the galaxy disk-averaged SFRs and various gas surface densities, and investigate their relationships. We find that the galaxy disk-averaged surface density of dense molecular gas mass has the tightest correlation with that of SFR (scatter ˜0.26 dex), and is linear in log-log space (power-law slope of N=1.03±0.02) across the full galaxy sample. The correlation between the total gas and SFR surface densities for the full sample has a somewhat larger scatter (˜0.48 dex), and is best fit by a power-law with slope 1.45±0.02. However, the slope changes from ˜1 when only normal spirals are considered, to ˜1.5 when more and more (U)LIRGs are included in the fitting. When different CO-to-H2 conversion factors are used to infer molecular gas masses for normal galaxies and (U)LIRGs, the bi-modal relations claimed recently in CO observations of high-redshift galaxies appear to also exist in local populations of star-forming galaxies.

Association between serum total testosterone and Body Mass Index in middle aged healthy men

PubMed Central

Shamim, Muhammad Omar; Ali Khan, Farooq Munfaet; Arshad, Rabia

2015-01-01

Objective: To determine correlation of serum total testosterone with body mass index (BMI) and waist hip ratio (WHR) in healthy adult males. Methods: A cross sectional study was conducted on 200 nonsmoker healthy males (aged 30-50 years) university employees. They were selected by convenience sampling technique after a detailed medical history and clinical examination including BMI and Waist Hip Ratio (WHR) calculation. Blood sampling was carried out to measure serum total testosterone (TT) using facilities of Chemiluminescence assay (CLIA) technique in Dow Chemical Laboratory. Independent sample T test was used for mean comparisons of BMI and WHR in between low and normal testosterone groups. (Subjects having < 9.7 nmol/L of total testosterone in blood were placed in low testosterone group and subjects having ≥ 9.7 nmol/L of total testosterone in blood were placed in normal testosterone group). Correlation of testosterone with BMI and WHR was analyzed by Pearson Correlation. Results: Mean (± SD) age of the subjects included in this study was 38.7 (± 6.563) years mean (± SD) total testosterone was 15.92 (±6.322)nmol/L. The mean (± SD) BMI, and WHR were 24.95 (±3.828) kg/m2 and 0.946 (±0.0474) respectively. Statistically significant differences were observed in the mean values of BMI and WHR for the two groups of testosterone. Significant inverse correlation of serum total testosterone with BMI(r = -0.311, p = 0.000) was recorded in this study. However testosterone was not significantly correlated with waist/hip ratio.(r = -0.126, p = 0.076) Conclusion: Middle age men working at DUHS who have low level of serum total testosterone are more obese than individuals with normal total testosterone level. PMID:26101490

Diagnostic Performance and Utility of Quantitative EEG Analyses in Delirium: Confirmatory Results From a Large Retrospective Case-Control Study.

PubMed

Fleischmann, Robert; Tränkner, Steffi; Bathe-Peters, Rouven; Rönnefarth, Maria; Schmidt, Sein; Schreiber, Stephan J; Brandt, Stephan A

2018-03-01

The lack of objective disease markers is a major cause of misdiagnosis and nonstandardized approaches in delirium. Recent studies conducted in well-selected patients and confined study environments suggest that quantitative electroencephalography (qEEG) can provide such markers. We hypothesize that qEEG helps remedy diagnostic uncertainty not only in well-defined study cohorts but also in a heterogeneous hospital population. In this retrospective case-control study, EEG power spectra of delirious patients and age-/gender-matched controls (n = 31 and n = 345, respectively) were fitted in a linear model to test their performance as binary classifiers. We subsequently evaluated the diagnostic performance of the best classifiers in control samples with normal EEGs (n = 534) and real-world samples including pathologic findings (n = 4294). Test reliability was estimated through split-half analyses. We found that the combination of spectral power at F3-P4 at 2 Hz (area under the curve [AUC] = .994) and C3-O1 at 19 Hz (AUC = .993) provided a sensitivity of 100% and a specificity of 99% to identify delirious patients among normal controls. These classifiers also yielded a false positive rate as low as 5% and increased the pretest probability of being delirious by 57% in an unselected real-world sample. Split-half reliabilities were .98 and .99, respectively. This retrospective study yielded preliminary evidence that qEEG provides excellent diagnostic performance to identify delirious patients even outside confined study environments. It furthermore revealed reduced beta power as a novel specific finding in delirium and that a normal EEG excludes delirium. Prospective studies including parameters of pretest probability and delirium severity are required to elaborate on these promising findings.

Microstructural Evaluation of Inductively Sintered Aluminum Matrix Nanocomposites Reinforced with Silicon Carbide and/or Graphene Nanoplatelets for Tribological Applications

NASA Astrophysics Data System (ADS)

Islam, Mohammad; Khalid, Yasir; Ahmad, Iftikhar; Almajid, Abdulhakim A.; Achour, Amine; Dunn, Theresa J.; Akram, Aftab; Anwar, Saqib

2018-04-01

Silicon carbide (SiC) nanoparticles (NP) and/or graphene nanoplatelets (GNP) were incorporated into the aluminum matrix through colloidal dispersion and mixing of the powders, followed by consolidation using a high-frequency induction heat sintering process. All the nanocomposite samples exhibited high densification (> 96 pct) with a maximum increase in Vickers microhardness by 92 pct relative to that of pure aluminum. The tribological properties of the samples were determined at the normal frictional forces of 10 and 50 N. At relatively low load of 10 N, the adhesive wear was found to be the predominant wear mechanism, whereas in the case of a 50 N normal load, there was significant contribution from abrasive wear possibly by hard SiC NP. From wear tests, the values for the coefficient of friction (COF) and the normalized wear rate were determined. The improvement in hardness and wear resistance may be attributed to multiple factors, including high relative density, uniform SiC and GNP dispersion in the aluminum matrix, grain refinement through GNP pinning, as well as inhibition of dislocation movement by SiC NP. The nanocomposite sample containing 10 SiC and 0.5 GNP (by wt pct) yielded the maximum wear resistance at 10 N normal load. Microstructural characterization of the nanocomposite surfaces and wear debris was performed using scanning electron microscope (SEM) and transmission electron microscope (TEM). The synergistic effect of the GNP and SiC nanostructures accounts for superior wear resistance in the aluminum matrix nanocomposites.

Microstructural Evaluation of Inductively Sintered Aluminum Matrix Nanocomposites Reinforced with Silicon Carbide and/or Graphene Nanoplatelets for Tribological Applications

NASA Astrophysics Data System (ADS)

Islam, Mohammad; Khalid, Yasir; Ahmad, Iftikhar; Almajid, Abdulhakim A.; Achour, Amine; Dunn, Theresa J.; Akram, Aftab; Anwar, Saqib

2018-07-01

Silicon carbide (SiC) nanoparticles (NP) and/or graphene nanoplatelets (GNP) were incorporated into the aluminum matrix through colloidal dispersion and mixing of the powders, followed by consolidation using a high-frequency induction heat sintering process. All the nanocomposite samples exhibited high densification (> 96 pct) with a maximum increase in Vickers microhardness by 92 pct relative to that of pure aluminum. The tribological properties of the samples were determined at the normal frictional forces of 10 and 50 N. At relatively low load of 10 N, the adhesive wear was found to be the predominant wear mechanism, whereas in the case of a 50 N normal load, there was significant contribution from abrasive wear possibly by hard SiC NP. From wear tests, the values for the coefficient of friction (COF) and the normalized wear rate were determined. The improvement in hardness and wear resistance may be attributed to multiple factors, including high relative density, uniform SiC and GNP dispersion in the aluminum matrix, grain refinement through GNP pinning, as well as inhibition of dislocation movement by SiC NP. The nanocomposite sample containing 10 SiC and 0.5 GNP (by wt pct) yielded the maximum wear resistance at 10 N normal load. Microstructural characterization of the nanocomposite surfaces and wear debris was performed using scanning electron microscope (SEM) and transmission electron microscope (TEM). The synergistic effect of the GNP and SiC nanostructures accounts for superior wear resistance in the aluminum matrix nanocomposites.

Short Polarity Albian Events in the Cretaceous Normal Superchron - Magnetostratigraphy of the Morelos and Tlayua Formations (Mexico)

NASA Astrophysics Data System (ADS)

Benammi, M.; Urrutia-Fucugauchi, J.

2007-12-01

Interest in the long period of normal polarity in the Cretaceous has continued to increase since the early study of Helsley and Steiner (1969), who suspected that it corresponded to vast stretches of relatively low amplitude behaviour in the sea-floor magnetic anomaly profiles known informally as the "Cretaceous quiet zone". Since these first studies, paleomagnetists have continued to explore what is now known as the Cretaceous Normal Superchron, an interval of prolonged normal polarity from 118 to 84 Ma. Paleomagnetic data from sediment cores from the DSDP Holes 369, 386, and 364, were interpreted as brief reverse intervals (Keating and Helsley, 1978, 1979). Relatively fewer studies have been reported for land-based sections of pelagic and platform limestones; reports include studies in northern and central Italy (Vandenberg et al., 1978; Tarduno et al., 1992; Tarduno, 1990; Cronin et al., 2001) and Mexico (Urrutia-Fucugauchi, 1988; Benammi et al., 2006). We present here new magnetostratigraphic data for limestone sequences in central and southern Mexico from the Cretaceous Morelos and Tlayua Formations, which record short intervals of reversed polarity during the K normal superchron. The Morelos Formation has been revisited in Guerrero, southern Mexico, where the sequence of platform limestones with almost horizontal thick beds is well-exposed. The magnetostratigraphy shows dominant normal polarity for the sampled sections, with the occurrence of three short reverse polarity intervals corresponding to the Albian, which have been re-sampled and studied in additional detail for magnetic mineralogy and remanent acquisition. The Tlayua Formation is sampled in Tepeji de Rodriguez area, which is known for its rich and well-preserved fossil contents. Age control has mainly been provided from studies on ammonites, belemnites and benthic foraminifera (Cantu, 1987; Seibertz and Buitron, 1987; Kashiyama et al., 2003). Nine polarity intervals are documented in the Tlayua Middle Member, which correlate with middle part of chron C34n (C34n.1n-C34n.2n, 100-105 Ma). Results give further evidence for occurrence of short polarity events within the K normal superchron, and provide additional documentation on the polarity events.

Qualification of serological infectious disease assays for the screening of samples from deceased tissue donors.

PubMed

Kitchen, A D; Newham, J A

2011-05-01

Whilst some of the assays used for serological screening of post-mortem blood samples from deceased tissue donors in some countries have been specifically validated by the manufacturer for this purpose, a significant number of those currently in use globally have not. Although specificity has previously been considered a problem in the screening of such samples, we believe that ensuring sensitivity is more important. The aim of this study was to validate a broader range of assays for the screening of post-mortem blood samples from deceased tissue donors. Six microplate immunoassays currently in use within National Health Service Blood and Transplant (NHSBT) for the screening of blood, tissue and stem cell donations were included. Representative samples from confirmed positive donors were titrated in screen negative post-mortem samples in parallel with normal pooled negative serum to determine if there was any inhibition with the post-mortem samples. There were no significant differences seen (P < 0.005) between the dilution curves obtained for the positive samples diluted in post-mortem samples and normal pooled sera. Although small numbers of samples were studied, it can be surmised that the post-mortem blood samples from deceased tissue donors, collected according to United Kingdom guidelines, are a suitable substrate for the assays evaluated. No diminution of reactivity was seen when dilution with sera from deceased donors was compared to dilution using pooled serum from live donors. In the absence of genuine low titre positive post-mortem samples, the use of samples spiked with various levels of target material provides a means of qualifying serological screening assays used by NHSBT for the screening of post-mortem blood samples from deceased tissue donors.

The evaluation of an analytical protocol for the determination of substances in waste for hazard classification

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

Hennebert, Pierre, E-mail: pierre.hennebert@ineris.fr; Papin, Arnaud; Padox, Jean-Marie

Highlights: • Knowledge of wastes in substances will be necessary to assess HP1–HP15 hazard properties. • A new analytical protocol is proposed for this and tested by two service laboratories on 32 samples. • Sixty-three percentage of the samples have a satisfactory analytical balance between 90% and 110%. • Eighty-four percentage of the samples were classified identically (Seveso Directive) for their hazardousness by the two laboratories. • The method, in progress, is being normalized in France and is be proposed to CEN. - Abstract: The classification of waste as hazardous could soon be assessed in Europe using largely the hazardmore » properties of its constituents, according to the the Classification, Labelling and Packaging (CLP) regulation. Comprehensive knowledge of the component constituents of a given waste will therefore be necessary. An analytical protocol for determining waste composition is proposed, which includes using inductively coupled plasma (ICP) screening methods to identify major elements and gas chromatography/mass spectrometry (GC–MS) screening techniques to measure organic compounds. The method includes a gross or indicator measure of ‘pools’ of higher molecular weight organic substances that are taken to be less bioactive and less hazardous, and of unresolved ‘mass’ during the chromatography of volatile and semi-volatile compounds. The concentration of some elements and specific compounds that are linked to specific hazard properties and are subject to specific regulation (examples include: heavy metals, chromium(VI), cyanides, organo-halogens, and PCBs) are determined by classical quantitative analysis. To check the consistency of the analysis, the sum of the concentrations (including unresolved ‘pools’) should give a mass balance between 90% and 110%. Thirty-two laboratory samples comprising different industrial wastes (liquids and solids) were tested by two routine service laboratories, to give circa 7000 parameter results. Despite discrepancies in some parameters, a satisfactory sum of estimated or measured concentrations (analytical balance) of 90% was reached for 20 samples (63% of the overall total) during this first test exercise, with identified reasons for most of the unsatisfactory results. Regular use of this protocol (which is now included in the French legislation) has enabled service laboratories to reach a 90% mass balance for nearly all the solid samples tested, and most of liquid samples (difficulties were caused in some samples from polymers in solution and vegetable oil). The protocol is submitted to French and European normalization bodies (AFNOR and CEN) and further improvements are awaited.« less

Surface-enhanced Raman spectroscopy for differentiation between benign and malignant thyroid tissues

NASA Astrophysics Data System (ADS)

Li, Zuanfang; Li, Chao; Lin, Duo; Huang, Zufang; Pan, Jianji; Chen, Guannan; Lin, Juqiang; Liu, Nenrong; Yu, Yun; Feng, Shangyuan; Chen, Rong

2014-04-01

The aim of this study was to evaluate the potential of applying silver nano-particle based surface-enhanced Raman scattering (SERS) to discriminate different types of human thyroid tissues. SERS measurements were performed on three groups of tissue samples including thyroid cancers (n = 32), nodular goiters (n = 20) and normal thyroid tissues (n = 25). Tentative assignments of the measured tissue SERS spectra suggest interesting cancer specific biomolecular differences. The principal component analysis (PCA) and linear discriminate analysis (LDA) together with the leave-one-out, cross-validated technique yielded diagnostic sensitivities of 92%, 75% and 87.5%; and specificities of 82.6%, 89.4% and 84.4%, respectively, for differentiation among normal, nodular and malignant thyroid tissue samples. This work demonstrates that tissue SERS spectroscopy associated with multivariate analysis diagnostic algorithms has great potential for detection of thyroid cancer at the molecular level.

Experiment on aggregation of red cells under microgravity on STS 51-C

NASA Astrophysics Data System (ADS)

Dintenfass, L.; Osman, P.; Maguire, B.; Jedrzejczyk, H.

Kinetics and morphology of aggregation of red cells were studied using automatic slit-capillary photo-viscometers, one situated on the middeck of the space shuttle `Discovery', and the other in the ground laboratory at KSC. Experiments were run simultaneously, blood samples being adjusted to haematocrit of 0.30 using native plasma, at temp. of 25°C, and anticoagulated by EDTA. Donors included patients with myocardial infarction, insulin-dependent diabetes, hyperlipidaemia and hypertension. Macro and microphotographs were obtained during flow and statis. There was a striking difference in the morphology of aggregates formed in space and on the ground. Aggregates formed under zero gravity showed rouleaux formation, while the same blood samples showed severe clumping on the ground, in all patients blood. Normal blood showed rouleaux on the ground, but a random swarm-like pattern in space. The shape of the red cells remained normal under zero gravity.

Lack of correlation between serum soluble Fas/APO-1 levels and autoimmune disease.

PubMed

Goel, N; Ulrich, D T; St Clair, E W; Fleming, J A; Lynch, D H; Seldin, M F

1995-12-01

To determine whether elevated soluble Fas/APO-1 (sFas/APO-1) levels are associated with either autoimmune disease or evidence of flares in autoimmune disease. Thirty-seven serum samples were retrospectively obtained from normal controls and patients with laboratory evidence of autoimmune disease activity. These samples were assayed for sFas/APO-1 levels by an enzyme-linked immunosorbent assay, and hospital medical records were retrospectively reviewed for clinical and laboratory characteristics of the patients. Soluble Fas/APO-1 levels did not correlate with clinical diagnoses or laboratory abnormalities. The mean and range of sFas/APO-1 levels were similar in systemic lupus erythematosus patients (including those with active disease), patients with other autoimmune diseases, and normal controls. These data strongly suggest that measurement of sFas/APO-1 levels is unlikely to hold clinical value or play a role in the pathogenesis of autoimmune disease.

21 CFR 320.31 - Applicability of requirements regarding an “Investigational New Drug Application.”

Code of Federal Regulations, 2010 CFR

2010-04-01

... patients where either the maximum single or total daily dose exceeds that specified in the labeling of the... application. (2) A multiple-dose study in normal subjects or patients where either the single or total daily... conducting the study, including any contract research organization, shall retain reserve samples of any test...

Osteosarcoma

Cancer.gov

The TARGET Osteosarcoma (OS) project elucidates comprehensive molecular characterization to determine the genetic changes that drive the initiation and progression of high-risk or hard-to-treat childhood cancers.The OS project has produced comprehensive genomic profiles of nearly 100 clinically annotated patient cases within the discovery dataset. Each fully-characterized TARGET OS case includes data from nucleic acid samples extracted from tumor and normal tissue.

The Alzheimer’s Disease Centers’ Uniform Data Set (UDS): The Neuropsychological Test Battery

PubMed Central

Weintraub, Sandra; Salmon, David; Mercaldo, Nathaniel; Ferris, Steven; Graff-Radford, Neill R.; Chui, Helena; Cummings, Jeffrey; DeCarli, Charles; Foster, Norman L.; Galasko, Douglas; Peskind, Elaine; Dietrich, Woodrow; Beekly, Duane L.; Kukull, Walter A.; Morris, John C.

2009-01-01

The neuropsychological test battery from the Uniform Data Set (UDS) of the Alzheimer’s Disease Centers (ADC) program of the National Institute on Aging (NIA) consists of brief measures of attention, processing speed, executive function, episodic memory and language. This paper describes development of the battery and preliminary data from the initial UDS evaluation of 3,268 clinically cognitively normal men and women collected over the first 24 months of utilization. The subjects represent a sample of community-dwelling, individuals who volunteer for studies of cognitive aging. Subjects were considered “clinically cognitively normal” based on clinical assessment, including the Clinical Dementia Rating scale and the Functional Assessment Questionnaire. The results demonstrate performance on tests sensitive to cognitive aging and to the early stages of Alzheimer disease (AD) in a relatively well-educated sample. Regression models investigating the impact of age, education, and gender on test scores indicate that these variables will need to be incorporated in subsequent normative studies. Future plans include: 1) determining the psychometric properties of the battery; 2) establishing normative data, including norms for different ethnic minority groups; and 3) conducting longitudinal studies on cognitively normal subjects, individuals with mild cognitive impairment, and individuals with AD and other forms of dementia. PMID:19474567

MetaSRA: normalized human sample-specific metadata for the Sequence Read Archive.

PubMed

Bernstein, Matthew N; Doan, AnHai; Dewey, Colin N

2017-09-15

The NCBI's Sequence Read Archive (SRA) promises great biological insight if one could analyze the data in the aggregate; however, the data remain largely underutilized, in part, due to the poor structure of the metadata associated with each sample. The rules governing submissions to the SRA do not dictate a standardized set of terms that should be used to describe the biological samples from which the sequencing data are derived. As a result, the metadata include many synonyms, spelling variants and references to outside sources of information. Furthermore, manual annotation of the data remains intractable due to the large number of samples in the archive. For these reasons, it has been difficult to perform large-scale analyses that study the relationships between biomolecular processes and phenotype across diverse diseases, tissues and cell types present in the SRA. We present MetaSRA, a database of normalized SRA human sample-specific metadata following a schema inspired by the metadata organization of the ENCODE project. This schema involves mapping samples to terms in biomedical ontologies, labeling each sample with a sample-type category, and extracting real-valued properties. We automated these tasks via a novel computational pipeline. The MetaSRA is available at metasra.biostat.wisc.edu via both a searchable web interface and bulk downloads. Software implementing our computational pipeline is available at http://github.com/deweylab/metasra-pipeline. cdewey@biostat.wisc.edu. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

Microminiature gas chromatograph

DOEpatents

Yu, Conrad M.

1996-01-01

A microminiature gas chromatograph (.mu.GC) comprising a least one silicon wafer, a gas injector, a column, and a detector. The gas injector has a normally closed valve for introducing a mobile phase including a sample gas in a carrier gas. The valve is fully disposed in the silicon wafer(s). The column is a microcapillary in silicon crystal with a stationary phase and is mechanically connected to receive the mobile phase from the gas injector for the molecular separation of compounds in the sample gas. The detector is mechanically connected to the column for the analysis of the separated compounds of sample gas with electronic means, e.g., ion cell, field emitter and PIN diode.

Sample size determination for logistic regression on a logit-normal distribution.

PubMed

Kim, Seongho; Heath, Elisabeth; Heilbrun, Lance

2017-06-01

Although the sample size for simple logistic regression can be readily determined using currently available methods, the sample size calculation for multiple logistic regression requires some additional information, such as the coefficient of determination ([Formula: see text]) of a covariate of interest with other covariates, which is often unavailable in practice. The response variable of logistic regression follows a logit-normal distribution which can be generated from a logistic transformation of a normal distribution. Using this property of logistic regression, we propose new methods of determining the sample size for simple and multiple logistic regressions using a normal transformation of outcome measures. Simulation studies and a motivating example show several advantages of the proposed methods over the existing methods: (i) no need for [Formula: see text] for multiple logistic regression, (ii) available interim or group-sequential designs, and (iii) much smaller required sample size.

The classification of secondary colorectal liver cancer in human biopsy samples using angular dispersive x-ray diffraction and multivariate analysis

NASA Astrophysics Data System (ADS)

Theodorakou, Chrysoula; Farquharson, Michael J.

2009-08-01

The motivation behind this study is to assess whether angular dispersive x-ray diffraction (ADXRD) data, processed using multivariate analysis techniques, can be used for classifying secondary colorectal liver cancer tissue and normal surrounding liver tissue in human liver biopsy samples. The ADXRD profiles from a total of 60 samples of normal liver tissue and colorectal liver metastases were measured using a synchrotron radiation source. The data were analysed for 56 samples using nonlinear peak-fitting software. Four peaks were fitted to all of the ADXRD profiles, and the amplitude, area, amplitude and area ratios for three of the four peaks were calculated and used for the statistical and multivariate analysis. The statistical analysis showed that there are significant differences between all the peak-fitting parameters and ratios between the normal and the diseased tissue groups. The technique of soft independent modelling of class analogy (SIMCA) was used to classify normal liver tissue and colorectal liver metastases resulting in 67% of the normal tissue samples and 60% of the secondary colorectal liver tissue samples being classified correctly. This study has shown that the ADXRD data of normal and secondary colorectal liver cancer are statistically different and x-ray diffraction data analysed using multivariate analysis have the potential to be used as a method of tissue classification.

Bromelain has paradoxical effects on blood coagulability: a study using thromboelastography.

PubMed

Kaur, Harmanpreet; Corscadden, Kathryn; Lott, Carlene; Elbatarny, Hisham S; Othman, Maha

2016-10-01

Bromelain is a crude extract from pineapple that is known for a wide array of pharmacological effects including protein digestion, fibrinolytic and anti-immune inflammatory effects and has been popularly used as a phytotherapeutic drug. However, its clinical values and applications remain understudied. The aim of this study was to investigate the effect of bromelain on the coagulability of blood using thromboelastography (TEG). We identified 0.4 U/ml as the minimum concentration of bromelain that results in modification of a normal TEG tracing. We studied the effects of this dose on whole blood samples obtained from normal and hypercoagulable individuals using TEG and evaluated their plasma using conventional tests including prothrombin time (PT) and activated partial thromboplastin time (APTT). We extended this analysis to investigate the effect of bromelain on platelet aggregation in normal blood and on the coagulability of mice blood in vivo in response to a clinically relevant dose injected intraperitoenally. The addition of bromelain ex vivo reduced coagulability of both normal and hypercoagulable blood significantly and resulted in 47 and 22% prolongation of PT and 20 and 10% prolongation of APTT in normal and hypercoagulable samples, respectively and inhibited adenosine di-phosphate (ADP)-induced platelet aggregation by 19%. In vivo, there was a considerable variation in TEG parameters in blood obtained from mice and unexpectedly a paradoxical effect toward hypercoagulability was shown in response to 1.5 mg/kg bromelain injected intraperitoneally into seven different animals. However, these results were not statistically significant when compared with the saline-injected animals. Although the in-vitro findings in this small study indicate a potential anticoagulant effect for bromelain, this needs to be interpreted with caution as neither an oral nor intravenous routes were evaluated. The paradoxical in-vivo data following intraperitoneal administration show the complexity of the effects of bromelain beyond platelets and indicate possible effects on other cells or proteins that require further investigations.

Artist Material BRDF Database for Computer Graphics Rendering

NASA Astrophysics Data System (ADS)

Ashbaugh, Justin C.

The primary goal of this thesis was to create a physical library of artist material samples. This collection provides necessary data for the development of a gonio-imaging system for use in museums to more accurately document their collections. A sample set was produced consisting of 25 panels and containing nearly 600 unique samples. Selected materials are representative of those commonly used by artists both past and present. These take into account the variability in visual appearance resulting from the materials and application techniques used. Five attributes of variability were identified including medium, color, substrate, application technique and overcoat. Combinations of these attributes were selected based on those commonly observed in museum collections and suggested by surveying experts in the field. For each sample material, image data is collected and used to measure an average bi-directional reflectance distribution function (BRDF). The results are available as a public-domain image and optical database of artist materials at art-si.org. Additionally, the database includes specifications for each sample along with other information useful for computer graphics rendering such as the rectified sample images and normal maps.

Characterization of bacterial community structure in a drinking water distribution system during an occurrence of red water.

PubMed

Li, Dong; Li, Zheng; Yu, Jianwei; Cao, Nan; Liu, Ruyin; Yang, Min

2010-11-01

The role of bacteria in the occasional emergence of red water, which has been documented worldwide, has yet to be determined. To better understand the mechanisms that drive occurrences of red water, the bacterial community composition and the relative abundance of several functional bacterial groups in a water distribution system of Beijing during a large-scale red water event were determined using several molecular methods. Individual clone libraries of the 16S rRNA gene were constructed for three red water samples and one sample of normal water. Beta-, Alpha-, and Gammaproteobacteria comprised the major bacterial communities in both red water and normal water samples, in agreement with previous reports. A high percentage of red water clones (25.2 to 57.1%) were affiliated with or closely related to a diverse array of iron-oxidizing bacteria, including the neutrophilic microaerobic genera Gallionella and Sideroxydans, the acidophilic species Acidothiobacillus ferrooxidans, and the anaerobic denitrifying Thermomonas bacteria. The genus Gallionella comprised 18.7 to 28.6% of all clones in the three red water libraries. Quantitative real-time PCR analysis showed that the 16S rRNA gene copy concentration of Gallionella spp. was between (4.1 ± 0.9) × 10⁷ (mean ± standard deviation) and (1.6 ± 0.3) × 10⁸ per liter in red water, accounting for 13.1% ± 2.9% to 17.2% ± 3.6% of the total Bacteria spp. in these samples. By comparison, the percentages of Gallionella spp. in the normal water samples were 0.1% or lower (below the limit of detection), suggesting an important role of Gallionella spp. in the formation of red water.

Bayesian Nonparametric Ordination for the Analysis of Microbial Communities.

PubMed

Ren, Boyu; Bacallado, Sergio; Favaro, Stefano; Holmes, Susan; Trippa, Lorenzo

2017-01-01

Human microbiome studies use sequencing technologies to measure the abundance of bacterial species or Operational Taxonomic Units (OTUs) in samples of biological material. Typically the data are organized in contingency tables with OTU counts across heterogeneous biological samples. In the microbial ecology community, ordination methods are frequently used to investigate latent factors or clusters that capture and describe variations of OTU counts across biological samples. It remains important to evaluate how uncertainty in estimates of each biological sample's microbial distribution propagates to ordination analyses, including visualization of clusters and projections of biological samples on low dimensional spaces. We propose a Bayesian analysis for dependent distributions to endow frequently used ordinations with estimates of uncertainty. A Bayesian nonparametric prior for dependent normalized random measures is constructed, which is marginally equivalent to the normalized generalized Gamma process, a well-known prior for nonparametric analyses. In our prior, the dependence and similarity between microbial distributions is represented by latent factors that concentrate in a low dimensional space. We use a shrinkage prior to tune the dimensionality of the latent factors. The resulting posterior samples of model parameters can be used to evaluate uncertainty in analyses routinely applied in microbiome studies. Specifically, by combining them with multivariate data analysis techniques we can visualize credible regions in ecological ordination plots. The characteristics of the proposed model are illustrated through a simulation study and applications in two microbiome datasets.

DNA Methylation Patterns in Normal Tissue Correlate more Strongly with Breast Cancer Status than Copy-Number Variants.

PubMed

Gao, Yang; Widschwendter, Martin; Teschendorff, Andrew E

2018-05-04

Normal tissue at risk of neoplastic transformation is characterized by somatic mutations, copy-number variation and DNA methylation changes. It is unclear however, which type of alteration may be more informative of cancer risk. We analyzed genome-wide DNA methylation and copy-number calls from the same DNA assay in a cohort of healthy breast samples and age-matched normal samples collected adjacent to breast cancer. Using statistical methods to adjust for cell type heterogeneity, we show that DNA methylation changes can discriminate normal-adjacent from normal samples better than somatic copy-number variants. We validate this important finding in an independent dataset. These results suggest that DNA methylation alterations in the normal cell of origin may offer better cancer risk prediction and early detection markers than copy-number changes. Copyright © 2018. Published by Elsevier B.V.

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

Liu, Xing; Xu, Yanli; Meng, Qian

Colorectal cancer (CRC) is one of the most common types of malignant tumor worldwide. Currently, although many researchers have been devoting themselves in CRC studies, the process of locating biomarkers for CRC early diagnosis and prognostic is still very slow. Using a centrifugal proteomic reactor-based proteomic analysis of minute amount of colonic biopsies by enteroscopy sampling, 2620 protein groups were quantified between cancer mucosa and adjacent normal colorectal mucosa. Of which, 403 protein groups were differentially expressed with statistic significance between cancer and normal tissues, including 195 up-regulated and 208 down-regulated proteins in cancer tissues. Three proteins (SOD3, PRELP andmore » NGAL) were selected for further Western blot validation. And the resulting Western blot experimental results were consistent with the quantitative proteomic data. SOD3 and PRELP are down-regulated in CRC mucosa comparing to adjacent normal tissue, while NGAL is up-regulated in CRC mucosa. In conclusion, the centrifugal proteomic reactor-based label-free quantitative proteomic approach provides a highly sensitive and powerful tool for analyzing minute protein sample from tiny colorectal biopsies, which may facilitate CRC biomarkers discovery for diagnoses and prognoses. -- Highlights: •Minute amount of colonic biopsies by endoscopy is suitable for proteomic analysis. •Centrifugal proteomic reactor can be used for processing tiny clinic biopsy sample. •SOD3 and PRELP are down-regulated in CRC, while NGAL is up-regulated in CRC.« less

Measurement of the sound absorption coefficient for an advanced undergraduate physics laboratory

NASA Astrophysics Data System (ADS)

Macho-Stadler, E.; Elejalde-García, M. J.

2017-09-01

We present a simple experiment that allows advanced undergraduates to learn the basics of the acoustic properties of materials. The impedance tube-standing wave method is applied to study the normal absorption coefficient of acoustics insulators. The setup includes a tube, a speaker, a microphone, a digital function generator and an oscilloscope, material available in an undergraduate laboratory. Results of the change of the absorption coefficient with the frequency, the sample thickness and the sample density are analysed and compared with those obtained with a commercial system.

In Vitro Tissue Differentiation using Dynamics of Tissue Mechanical Properties

NASA Astrophysics Data System (ADS)

Lin, Wei-Chiang; Phillips, Paul J.

2002-03-01

Dynamics of tissue mechanical properties of various human tissue types were studied at macroscopic as well as microscopic level in vitro. This study was conducted to enable the development of a feedback system based on dynamics of tissue mechanical properties for intraoperative guidance for tumor treatment (e.g., RF ablation of liver tumor) and noninvasive tumor localization. Human liver tissues, including normal, cancerous, and cirrhotic tissues, were obtained from patients receiving liver transplant or tumor resection at Vanderbilt University Medical Center with the approval of the Vanderbilt Institutional Review Board. Tissue samples, once resected from the patients, were snap-frozen using liquid nitrogen and stored at -70 oC. Measurements of the mechanical properties of these tissue samples were conducted at the University of Tennessee at Knoxville. Dynamics of tissue mechanical properties were measured from both native and thermally coagulated tissue samples at macroscopic and microscopic level. Preliminary results suggest the dynamics of mechanical properties of normal liver tissues are very different from those of cancerous liver tissues. The correlation between the dynamics of mechanical properties at macroscopic level and those at microscopic level is currently under investigation.

Central Appalachian basin natural gas database: distribution, composition, and origin of natural gases

USGS Publications Warehouse

Román Colón, Yomayra A.; Ruppert, Leslie F.

2015-01-01

The U.S. Geological Survey (USGS) has compiled a database consisting of three worksheets of central Appalachian basin natural gas analyses and isotopic compositions from published and unpublished sources of 1,282 gas samples from Kentucky, Maryland, New York, Ohio, Pennsylvania, Tennessee, Virginia, and West Virginia. The database includes field and reservoir names, well and State identification number, selected geologic reservoir properties, and the composition of natural gases (methane; ethane; propane; butane, iso-butane [i-butane]; normal butane [n-butane]; iso-pentane [i-pentane]; normal pentane [n-pentane]; cyclohexane, and hexanes). In the first worksheet, location and American Petroleum Institute (API) numbers from public or published sources are provided for 1,231 of the 1,282 gas samples. A second worksheet of 186 gas samples was compiled from published sources and augmented with public location information and contains carbon, hydrogen, and nitrogen isotopic measurements of natural gas. The third worksheet is a key for all abbreviations in the database. The database can be used to better constrain the stratigraphic distribution, composition, and origin of natural gas in the central Appalachian basin.

A DNA methylation map of human cancer at single base-pair resolution

PubMed Central

Vidal, E; Sayols, S; Moran, S; Guillaumet-Adkins, A; Schroeder, M P; Royo, R; Orozco, M; Gut, M; Gut, I; Lopez-Bigas, N; Heyn, H; Esteller, M

2017-01-01

Although single base-pair resolution DNA methylation landscapes for embryonic and different somatic cell types provided important insights into epigenetic dynamics and cell-type specificity, such comprehensive profiling is incomplete across human cancer types. This prompted us to perform genome-wide DNA methylation profiling of 22 samples derived from normal tissues and associated neoplasms, including primary tumors and cancer cell lines. Unlike their invariant normal counterparts, cancer samples exhibited highly variable CpG methylation levels in a large proportion of the genome, involving progressive changes during tumor evolution. The whole-genome sequencing results from selected samples were replicated in a large cohort of 1112 primary tumors of various cancer types using genome-scale DNA methylation analysis. Specifically, we determined DNA hypermethylation of promoters and enhancers regulating tumor-suppressor genes, with potential cancer-driving effects. DNA hypermethylation events showed evidence of positive selection, mutual exclusivity and tissue specificity, suggesting their active participation in neoplastic transformation. Our data highlight the extensive changes in DNA methylation that occur in cancer onset, progression and dissemination. PMID:28581523

Quantitative Profiling of Colorectal Cancer-Associated Bacteria Reveals Associations between Fusobacterium spp., Enterotoxigenic Bacteroides fragilis (ETBF) and Clinicopathological Features of Colorectal Cancer

PubMed Central

Viljoen, Katie S.; Dakshinamurthy, Amirtha; Goldberg, Paul; Blackburn, Jonathan M.

2015-01-01

Various studies have presented clinical or in vitro evidence linking bacteria to colorectal cancer, but these bacteria have not previously been concurrently quantified by qPCR in a single cohort. We quantify these bacteria (Fusobacterium spp., Streptococcus gallolyticus, Enterococcus faecalis, Enterotoxigenic Bacteroides fragilis (ETBF), Enteropathogenic Escherichia coli (EPEC), and afaC- or pks-positive E. coli) in paired tumour and normal tissue samples from 55 colorectal cancer patients. We further investigate the relationship between a) the presence and b) the level of colonisation of each bacterial species with site and stage of disease, age, gender, ethnicity and MSI-status. With the exception of S. gallolyticus, we detected all bacteria profiled here in both tumour and normal samples at varying frequencies. ETBF (FDR = 0.001 and 0.002 for normal and tumour samples) and afaC-positive E. coli (FDR = 0.03, normal samples) were significantly enriched in the colon compared to the rectum. ETBF (FDR = 0.04 and 0.002 for normal and tumour samples, respectively) and Fusobacterium spp. (FDR = 0.03 tumour samples) levels were significantly higher in late stage (III/IV) colorectal cancers. Fusobacterium was by far the most common bacteria detected, occurring in 82% and 81% of paired tumour and normal samples. Fusobacterium was also the only bacterium that was significantly higher in tumour compared to normal samples (p = 6e-5). We also identified significant associations between high-level colonisation by Fusobacterium and MSI-H (FDR = 0.05), age (FDR = 0.03) or pks-positive E. coli (FDR = 0.01). Furthermore, we exclusively identified atypical EPEC in our cohort, which has not been previously reported in association with colorectal cancer. By quantifying colorectal cancer-associated bacteria across a single cohort, we uncovered inter- and intra-individual patterns of colonization not previously recognized, as well as important associations with clinicopathological features, especially in the case of Fusobacterium and ETBF. PMID:25751261

BloodSpot: a database of gene expression profiles and transcriptional programs for healthy and malignant haematopoiesis.

PubMed

Bagger, Frederik Otzen; Sasivarevic, Damir; Sohi, Sina Hadi; Laursen, Linea Gøricke; Pundhir, Sachin; Sønderby, Casper Kaae; Winther, Ole; Rapin, Nicolas; Porse, Bo T

2016-01-04

Research on human and murine haematopoiesis has resulted in a vast number of gene-expression data sets that can potentially answer questions regarding normal and aberrant blood formation. To researchers and clinicians with limited bioinformatics experience, these data have remained available, yet largely inaccessible. Current databases provide information about gene-expression but fail to answer key questions regarding co-regulation, genetic programs or effect on patient survival. To address these shortcomings, we present BloodSpot (www.bloodspot.eu), which includes and greatly extends our previously released database HemaExplorer, a database of gene expression profiles from FACS sorted healthy and malignant haematopoietic cells. A revised interactive interface simultaneously provides a plot of gene expression along with a Kaplan-Meier analysis and a hierarchical tree depicting the relationship between different cell types in the database. The database now includes 23 high-quality curated data sets relevant to normal and malignant blood formation and, in addition, we have assembled and built a unique integrated data set, BloodPool. Bloodpool contains more than 2000 samples assembled from six independent studies on acute myeloid leukemia. Furthermore, we have devised a robust sample integration procedure that allows for sensitive comparison of user-supplied patient samples in a well-defined haematopoietic cellular space. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

[Study of near infrared spectral preprocessing and wavelength selection methods for endometrial cancer tissue].

PubMed

Zhao, Li-Ting; Xiang, Yu-Hong; Dai, Yin-Mei; Zhang, Zhuo-Yong

2010-04-01

Near infrared spectroscopy was applied to measure the tissue slice of endometrial tissues for collecting the spectra. A total of 154 spectra were obtained from 154 samples. The number of normal, hyperplasia, and malignant samples was 36, 60, and 58, respectively. Original near infrared spectra are composed of many variables, for example, interference information including instrument errors and physical effects such as particle size and light scatter. In order to reduce these influences, original spectra data should be performed with different spectral preprocessing methods to compress variables and extract useful information. So the methods of spectral preprocessing and wavelength selection have played an important role in near infrared spectroscopy technique. In the present paper the raw spectra were processed using various preprocessing methods including first derivative, multiplication scatter correction, Savitzky-Golay first derivative algorithm, standard normal variate, smoothing, and moving-window median. Standard deviation was used to select the optimal spectral region of 4 000-6 000 cm(-1). Then principal component analysis was used for classification. Principal component analysis results showed that three types of samples could be discriminated completely and the accuracy almost achieved 100%. This study demonstrated that near infrared spectroscopy technology and chemometrics method could be a fast, efficient, and novel means to diagnose cancer. The proposed methods would be a promising and significant diagnosis technique of early stage cancer.

DGEM--a microarray gene expression database for primary human disease tissues.

PubMed

Xia, Yuni; Campen, Andrew; Rigsby, Dan; Guo, Ying; Feng, Xingdong; Su, Eric W; Palakal, Mathew; Li, Shuyu

2007-01-01

Gene expression patterns can reflect gene regulations in human tissues under normal or pathologic conditions. Gene expression profiling data from studies of primary human disease samples are particularly valuable since these studies often span many years in order to collect patient clinical information and achieve a large sample size. Disease-to-Gene Expression Mapper (DGEM) provides a beneficial community resource to access and analyze these data; it currently includes Affymetrix oligonucleotide array datasets for more than 40 human diseases and 1400 samples. The data are normalized to the same scale and stored in a relational database. A statistical-analysis pipeline was implemented to identify genes abnormally expressed in disease tissues or genes whose expressions are associated with clinical parameters such as cancer patient survival. Data-mining results can be queried through a web-based interface at http://dgem.dhcp.iupui.edu/. The query tool enables dynamic generation of graphs and tables that are further linked to major gene and pathway resources that connect the data to relevant biology, including Entrez Gene and Kyoto Encyclopedia of Genes and Genomes (KEGG). In summary, DGEM provides scientists and physicians a valuable tool to study disease mechanisms, to discover potential disease biomarkers for diagnosis and prognosis, and to identify novel gene targets for drug discovery. The source code is freely available for non-profit use, on request to the authors.

The Effect on Non-Normal Distributions on the Integrated Moving Average Model of Time-Series Analysis.

ERIC Educational Resources Information Center

Doerann-George, Judith

The Integrated Moving Average (IMA) model of time series, and the analysis of intervention effects based on it, assume random shocks which are normally distributed. To determine the robustness of the analysis to violations of this assumption, empirical sampling methods were employed. Samples were generated from three populations; normal,…

Integrative transcriptome analysis identifies deregulated microRNA-transcription factor networks in lung adenocarcinoma

PubMed Central

Cinegaglia, Naiara C.; Andrade, Sonia Cristina S.; Tokar, Tomas; Pinheiro, Maísa; Severino, Fábio E.; Oliveira, Rogério A.; Hasimoto, Erica N.; Cataneo, Daniele C.; Cataneo, Antônio J.M.; Defaveri, Júlio; Souza, Cristiano P.; Marques, Márcia M.C.; Carvalho, Robson F.; Coutinho, Luiz L.; Gross, Jefferson L.; Rogatto, Silvia R.; Lam, Wan L.; Jurisica, Igor; Reis, Patricia P.

2016-01-01

Herein, we aimed at identifying global transcriptome microRNA (miRNA) changes and miRNA target genes in lung adenocarcinoma. Samples were selected as training (N = 24) and independent validation (N = 34) sets. Tissues were microdissected to obtain >90% tumor or normal lung cells, subjected to miRNA transcriptome sequencing and TaqMan quantitative PCR validation. We further integrated our data with published miRNA and mRNA expression datasets across 1,491 lung adenocarcinoma and 455 normal lung samples. We identified known and novel, significantly over- and under-expressed (p ≤ 0.01 and FDR≤0.1) miRNAs in lung adenocarcinoma compared to normal lung tissue: let-7a, miR-10a, miR-15b, miR-23b, miR-26a, miR-26b, miR-29a, miR-30e, miR-99a, miR-146b, miR-181b, miR-181c, miR-421, miR-181a, miR-574 and miR-1247. Validated miRNAs included let-7a-2, let-7a-3, miR-15b, miR-21, miR-155 and miR-200b; higher levels of miR-21 expression were associated with lower patient survival (p = 0.042). We identified a regulatory network including miR-15b and miR-155, and transcription factors with prognostic value in lung cancer. Our findings may contribute to the development of treatment strategies in lung adenocarcinoma. PMID:27081085

Comprehensive analysis of a microRNA expression profile in pediatric medulloblastoma.

PubMed

Dai, Junqiang; Li, Qiao; Bing, Zhitong; Zhang, Yinian; Niu, Liang; Yin, Hang; Yuan, Guoqiang; Pan, Yawen

2017-06-01

Medulloblastoma is the most common malignant brain tumor of the central nervous system among children. Medulloblastoma is an embryonal tumor, of which little is known about the pathogenesis. Several efforts have been made to understand the molecular aspects of its tumorigenic pathways; however, these are poorly understood. microRNA (miRNA), a type of non‑coding short RNA, has been proven to be associated with a number of physiological processes and pathological processes of serious diseases, including brain tumors. Differentially expressed miRNAs serve an important role in numerous types of malignancy. The present study aims to define a differentially expressed set of miRNAs in medulloblastoma tumor tissue, compared with normal samples, to improve the understanding of the tumorigenesis. It was identified that 22 miRNAs were upregulated and 26 miRNAs were downregulated in the tumor tissue compared with the normal group. However, when the medulloblastoma tissue was compared with normal cerebellum tissue, 9 miRNAs were identified to be up or downregulated in the tumor samples. The differentially expressed miRNAs in the tumor tissue were identified in order to clarify the networks and pathways of tumorigenesis using Ingenuity Pathway Analysis. Subsequently, key regulatory genes associated with the development of medulloblastoma were identified, including tumor protein p53, insulin like growth factor 1 receptor, argonaute 2, mitogen‑activated protein kinases 1 and 3, sirtuin 1 and Y box binding protein 1.

Microbiological identification and analysis of swine tonsils collected from carcasses at slaughter

PubMed Central

O’Sullivan, Terri; Friendship, Robert; Blackwell, Tim; Pearl, David; McEwen, Beverly; Carman, Susy; Slavić, Đurđa; Dewey, Catherine

2011-01-01

The primary objective of this 7-month study was to determine the prevalence of porcine pathogens of the tonsil of the soft palate of swine at slaughter. Additional objectives were to determine if sampling the carcasses of normal or abnormal hogs provided different microbiological profiles and if the slaughter plant provides a feasible sampling frame and environment for detecting and monitoring important pathogens in tonsils that have health implications for both swine and humans. A total of 395 samples were collected from 264 farms. Of these, 180 tonsils were collected from normal carcasses and 215 tonsils were collected from carcasses that were diverted to the hold rail. Laboratory testing included bacteriological culture and identification as well as real time-polymerase chain reaction (PCR) testing for porcine reproductive and respiratory syndrome virus (PPRSV) and immunohistochemistry (IHC) for porcine circovirus-2 (PCV-2). The most commonly isolated bacteria included: Streptococcus suis (53.7%), Arcanobacterium pyogenes (29.9%), Pasteurella multocida (27.3%), and Streptococcus porcinus (19.5%). Virus screening revealed evidence of PRRSV and PCV-2 in 22.0% and 11.9% of the samples, respectively. Salmonella Typhimurium and Yersinia enterocolitica were isolated in 0.5% and 1.8% of the samples, respectively. Tonsils collected from the hold rail were more likely to be positive for Staphylococcus hyicus [odds ratio (OR) = 7.51, confidence interval (CI) = 2.89 to 19.54], Streptococcus porcinus (OR = 9.93, CI = 4.27 to 23.10), and Streptococcus suis (OR = 2.16, CI = 1.45 to 3.24). Tonsils collected from abnormal carcasses were less likely to be positive for Staphylococcus aureus (OR = 0.05, CI = 0.005 to 0.482). PMID:21731180

Sample processing, protocol, and statistical analysis of the time-of-flight secondary ion mass spectrometry (ToF-SIMS) of protein, cell, and tissue samples.

PubMed

Barreto, Goncalo; Soininen, Antti; Sillat, Tarvo; Konttinen, Yrjö T; Kaivosoja, Emilia

2014-01-01

Time-of-flight secondary ion mass spectrometry (ToF-SIMS) is increasingly being used in analysis of biological samples. For example, it has been applied to distinguish healthy and osteoarthritic human cartilage. This chapter discusses ToF-SIMS principle and instrumentation including the three modes of analysis in ToF-SIMS. ToF-SIMS sets certain requirements for the samples to be analyzed; for example, the samples have to be vacuum compatible. Accordingly, sample processing steps for different biological samples, i.e., proteins, cells, frozen and paraffin-embedded tissues and extracellular matrix for the ToF-SIMS are presented. Multivariate analysis of the ToF-SIMS data and the necessary data preprocessing steps (peak selection, data normalization, mean-centering, and scaling and transformation) are discussed in this chapter.

Differentiating oral lesions in different carcinogenesis stages with optical coherence tomography

NASA Astrophysics Data System (ADS)

Tsai, Meng-Tsan; Lee, Cheng-Kuang; Lee, Hsiang-Chieh; Chen, Hsin-Ming; Chiang, Chun-Pin; Wang, Yih-Ming; Yang, Chih-Chung

2009-07-01

A swept-source optical coherence tomography (SS-OCT) system is used to clinically scan oral lesions in different oral carcinogenesis stages, including normal oral mucosa control, mild dysplasia (MiD), moderate dysplasia (MoD), early-stage squamous cell carcinoma (ES-SCC), and well-developed SCC (WD-SCC), for diagnosis purpose. On the basis of the analyses of the SS-OCT images, the stages of dysplasia (MiD and MoD), and SCC (ES-SCC and WD-SCC) can be differentiated from normal control by evaluating the depth-dependent standard deviation (SD) values of lateral variations. In the dysplasia stage, the boundary between the epithelium (EP) and lamina propria (LP) layers can still be identified and the EP layer becomes significantly thicker than that of normal control. Also, in a certain range of the EP layer above the EP/LP boundary, the SD value becomes larger than a certain percentage of the maximum level, which is observed around the EP/LP boundary. On the other hand, in the ES-SCC and WD-SCC stages, the EP/LP boundary disappears. Because of the higher density of connective tissue papillae in the ES-SCC stage, the SD values of the slowly varying lateral scan profiles in the ES-SCC samples are significantly larger than those in the WD-SCC sample. Also, ES-SCC can be differentiated from WD-SCC by comparing the exponential decay constants of averaged A-mode scan profiles. Because of the higher tissue absorption in the WD-SCC lesion, the decay constants in the WD-SCC samples are significantly higher than those in the ES-SCC samples.

[Characteristics of lip-mouth region in smiling position from 80 adults with acceptable faces and individual normal occlusions].

PubMed

Zhang, J; Chen, Y; Zhou, X

1997-07-01

The Characteristics of Lip-mouth region including the soft and hard tissues in smiling position with frontal fixed position photographic computered analysis was studied. The examples were 80 adults (40 males and 40 females) with acceptable faces and individual normal occlusions. The age was between 17-25 years of age. The method adopting maximum smiling position to study the lip-mouth region is scientific, and the maximum smile line could be divided into three categories: low smile line-a-counted for 16.25% of the total samples; average smile line--68.75%; high smile line--15%.

Nontraditional families and childhood progress through school.

PubMed

Rosenfeld, Michael J

2010-08-01

luse U.S. census data to perform the first large-sample, nationally representative tests of outcomes for children raised by same-sex couples. The results show that children of same-sex couples are as likely to make normal progress through school as the children of most other family structures. Heterosexual married couples are the family type whose children have the lowest rates of grade retention, but the advantage of heterosexual married couples is mostly due to their higher socioeconomic status. Children ofallfamily types (including children ofsame-sex couples) are far more likely to make normal progress through school than are children living in group quarters (such as orphanages and shelters).

Expression of microphthalmia transcription factor, S100 protein, and HMB-45 in malignant melanoma and pigmented nevi.

PubMed

Xia, Jianxin; Wang, Yanlong; Li, Fuqiu; Wang, Jinfeng; Mu, Yan; Mei, Xianglin; Li, Xue; Zhu, Wenjing; Jin, Xianhua; Yu, Kai

2016-09-01

Malignant melanoma (MM) is a type of malignant tumor, which originates from neural crest melanocytes. MM progresses rapidly and results in a high mortality rate. The present study aims to investigate the expression of microphthalmia transcription factor (MITF), the S100 protein, and HMB-45 in MM and pigmented nevi. A total of 32 MM samples (including three skin metastasis, three lymph node metastasis and two spindle cell MM samples), two Spitz nevus samples, four pigmented nevus samples and two blue nevus samples were collected. The expression levels of S100 protein, HMB-45, and MITF were observed via immunostaining. The S100 protein exhibited high positive rates in MM and pigment disorders (96.7 and 100%, respectively), but with low specificity. The S100 protein was also expressed in fibroblasts, myoepithelial cells, histocytes and Langerhans cells in normal skin samples. HMB-45 had high specificity. Its positive expression was only confined to MM cells and junctional nevus cells. Furthermore, HMB-45 was not expressed in melanocytes in the normal tissue samples around the tumor or in the benign intradermal nevus cells. MITF exhibited high specificity and high sensitivity. It was expressed in the nuclei of melanocytes, MM cells and nevus cells. It was observed to be strongly expressed in metastatic MM and spindle cell MMs. Thus, MITF may present as a specific immunomarker for the diagnosis and differential diagnosis of MM.

Equilibrium sampling of environmental pollutants in fish: comparison with lipid-normalized concentrations and homogenization effects on chemical activity.

PubMed

Jahnke, Annika; Mayer, Philipp; Adolfsson-Erici, Margaretha; McLachlan, Michael S

2011-07-01

Equilibrium sampling of organic pollutants into the silicone polydimethylsiloxane (PDMS) has recently been applied in biological tissues including fish. Pollutant concentrations in PDMS can then be multiplied with lipid/PDMS distribution coefficients (D(Lipid,PDMS) ) to obtain concentrations in fish lipids. In the present study, PDMS thin films were used for equilibrium sampling of polychlorinated biphenyls (PCBs) in intact tissue of two eels and one salmon. A classical exhaustive extraction technique to determine lipid-normalized PCB concentrations, which assigns the body burden of the chemical to the lipid fraction of the fish, was additionally applied. Lipid-based PCB concentrations obtained by equilibrium sampling were 85 to 106% (Norwegian Atlantic salmon), 108 to 128% (Baltic Sea eel), and 51 to 83% (Finnish lake eel) of those determined using total extraction. This supports the validity of the equilibrium sampling technique, while at the same time confirming that the fugacity capacity of these lipid-rich tissues for PCBs was dominated by the lipid fraction. Equilibrium sampling was also applied to homogenates of the same fish tissues. The PCB concentrations in the PDMS were 1.2 to 2.0 times higher in the homogenates (statistically significant in 18 of 21 cases, p < 0.05), indicating that homogenization increased the chemical activity of the PCBs and decreased the fugacity capacity of the tissue. This observation has implications for equilibrium sampling and partition coefficients determined using tissue homogenates. Copyright © 2011 SETAC.

Telomere length in normal and neoplastic canine tissues.

PubMed

Cadile, Casey D; Kitchell, Barbara E; Newman, Rebecca G; Biller, Barbara J; Hetler, Elizabeth R

2007-12-01

To determine the mean telomere restriction fragment (TRF) length in normal and neoplastic canine tissues. 57 solid-tissue tumor specimens collected from client-owned dogs, 40 samples of normal tissue collected from 12 clinically normal dogs, and blood samples collected from 4 healthy blood donor dogs. Tumor specimens were collected from client-owned dogs during diagnostic or therapeutic procedures at the University of Illinois Veterinary Medical Teaching Hospital, whereas 40 normal tissue samples were collected from 12 control dogs. Telomere restriction fragment length was determined by use of an assay kit. A histologic diagnosis was provided for each tumor by personnel at the Veterinary Diagnostic Laboratory at the University of Illinois. Mean of the mean TRF length for 44 normal samples was 19.0 kilobases (kb; range, 15.4 to 21.4 kb), and the mean of the mean TRF length for 57 malignant tumors was 19.0 kb (range, 12.9 to 23.5 kb). Although the mean of the mean TRF length for tumors and normal tissues was identical, tumor samples had more variability in TRF length. Telomerase, which represents the main mechanism by which cancer cells achieve immortality, is an attractive therapeutic target. The ability to measure telomere length is crucial to monitoring the efficacy of telomerase inhibition. In contrast to many other mammalian species, the length of canine telomeres and the rate of telomeric DNA loss are similar to those reported in humans, making dogs a compelling choice for use in the study of human anti-telomerase strategies.

Canine epidermal lipid sampling by skin scrub revealed variations between different body sites and normal and atopic dogs

PubMed Central

2014-01-01

Background Previously, we evaluated a minimally invasive epidermal lipid sampling method called skin scrub, which achieved reproducible and comparable results to skin scraping. The present study aimed at investigating regional variations in canine epidermal lipid composition using the skin scrub technique and its suitability for collecting skin lipids in dogs suffering from certain skin diseases. Eight different body sites (5 highly and 3 lowly predisposed for atopic lesions) were sampled by skin scrub in 8 control dogs with normal skin. Additionally, lesional and non-lesional skin was sampled from 12 atopic dogs and 4 dogs with other skin diseases by skin scrub. Lipid fractions were separated by high performance thin layer chromatography and analysed densitometrically. Results No significant differences in total lipid content were found among the body sites tested in the control dogs. However, the pinna, lip and caudal back contained significantly lower concentrations of ceramides, whereas the palmar metacarpus and the axillary region contained significantly higher amounts of ceramides and cholesterol than most other body sites. The amount of total lipids and ceramides including all ceramide classes were significantly lower in both lesional and non-lesional skin of atopic dogs compared to normal skin, with the reduction being more pronounced in lesional skin. The sampling by skin scrub was relatively painless and caused only slight erythema at the sampled areas but no oedema. Histological examinations of skin biopsies at 2 skin scrubbed areas revealed a potential lipid extraction from the transition zone between stratum corneum and granulosum. Conclusions The present study revealed regional variations in the epidermal lipid and ceramide composition in dogs without skin abnormalities but no connection between lipid composition and predilection sites for canine atopic dermatitis lesions. The skin scrub technique proved to be a practicable sampling method for canine epidermal lipids, revealed satisfying results regarding alterations of skin lipid composition in canine atopic dermatitis and might be suitable for epidermal lipid investigations of further canine skin diseases. Although the ceramide composition should be unaffected by the deeper lipid sampling of skin scrub compared to other sampling methods, further studies are required to determine methodological differences. PMID:25012966

Sensitivity and specificity of univariate MRI analysis of experimentally degraded cartilage

PubMed Central

Lin, Ping-Chang; Reiter, David A.; Spencer, Richard G.

2010-01-01

MRI is increasingly used to evaluate cartilage in tissue constructs, explants, and animal and patient studies. However, while mean values of MR parameters, including T1, T2, magnetization transfer rate km, apparent diffusion coefficient ADC, and the dGEMRIC-derived fixed charge density, correlate with tissue status, the ability to classify tissue according to these parameters has not been explored. Therefore, the sensitivity and specificity with which each of these parameters was able to distinguish between normal and trypsin- degraded, and between normal and collagenase-degraded, cartilage explants were determined. Initial analysis was performed using a training set to determine simple group means to which parameters obtained from a validation set were compared. T1 and ADC showed the greatest ability to discriminate between normal and degraded cartilage. Further analysis with k-means clustering, which eliminates the need for a priori identification of sample status, generally performed comparably. Use of fuzzy c-means (FCM) clustering to define centroids likewise did not result in improvement in discrimination. Finally, a FCM clustering approach in which validation samples were assigned in a probabilistic fashion to control and degraded groups was implemented, reflecting the range of tissue characteristics seen with cartilage degradation. PMID:19705467

Commonly dysregulated genes in murine APL cells

PubMed Central

Yuan, Wenlin; Payton, Jacqueline E.; Holt, Matthew S.; Link, Daniel C.; Watson, Mark A.; DiPersio, John F.; Ley, Timothy J.

2007-01-01

To identify genes that are commonly dysregulated in a murine model of acute promyelocytic leukemia (APL), we first defined gene expression patterns during normal murine myeloid development; serial gene expression profiling studies were performed with primary murine hematopoietic progenitors that were induced to undergo myeloid maturation in vitro with G-CSF. Many genes were reproducibly expressed in restricted developmental “windows,” suggesting a structured hierarchy of expression that is relevant for the induction of developmental fates and/or differentiated cell functions. We compared the normal myeloid developmental transcriptome with that of APL cells derived from mice expressing PML-RARα under control of the murine cathepsin G locus. While many promyelocyte-specific genes were highly expressed in all APL samples, 116 genes were reproducibly dysregulated in many independent APL samples, including Fos, Jun, Egr1, Tnf, and Vcam1. However, this set of commonly dysregulated genes was expressed normally in preleukemic, early myeloid cells from the same mouse model, suggesting that dysregulation occurs as a “downstream” event during disease progression. These studies suggest that the genetic events that lead to APL progression may converge on common pathways that are important for leukemia pathogenesis. PMID:17008535

Comparison of CyTOF assays across sites: Results of a six-center pilot study.

PubMed

Leipold, Michael D; Obermoser, Gerlinde; Fenwick, Craig; Kleinstuber, Katja; Rashidi, Narges; McNevin, John P; Nau, Allison N; Wagar, Lisa E; Rozot, Virginie; Davis, Mark M; DeRosa, Stephen; Pantaleo, Giuseppe; Scriba, Thomas J; Walker, Bruce D; Olsen, Lars R; Maecker, Holden T

2018-02-01

For more than five years, high-dimensional mass cytometry has been employed to study immunology. However, these studies have typically been performed in one laboratory on one or few instruments. We present the results of a six-center study using healthy control human peripheral blood mononuclear cells (PBMCs) and commercially available reagents to test the intra-site and inter-site variation of mass cytometers and operators. We used prestained controls generated by the primary center as a reference to compare against samples stained at each individual center. Data were analyzed at the primary center, including investigating the effects of two normalization methods. All six sites performed similarly, with CVs for both Frequency of Parent and median signal intensity (MSI) values<30%. Increased background was seen when using the premixed antibody cocktail aliquots at each site, suggesting that cocktails are best made fresh. Both normalization methods tested performed adequately for normalizing MSI values between centers. Clustering algorithms revealed slight differences between the prestained and the sites-stained samples, due mostly to the increased background of a few antibodies. Therefore, we believe that multicenter mass cytometry assays are feasible. Copyright © 2017 The Author(s). Published by Elsevier B.V. All rights reserved.

Physical and mechanical properties of self-compacting concrete containing superplasticizer and metakaolin

NASA Astrophysics Data System (ADS)

Shahidan, Shahiron; Tayeh, Bassam A.; Jamaludin, A. A.; Bahari, N. A. A. S.; Mohd, S. S.; Zuki Ali, N.; Khalid, F. S.

2017-11-01

The development of concrete technology shows a variety of admixtures in concrete to produce special concrete. This includes the production of self-compacting concrete which is able to fill up all spaces, take formwork shapes and pass through congested reinforcement bars without vibrating or needing any external energy. In this study, the main objective is to compare the physical and mechanical properties of self-compacting concrete containing metakaolin with normal concrete. Four types of samples were produced to study the effect of metakaolin towards the physical and mechanical properties of self-compacting concrete where 0%, 5%, 10% and 15% of metakaolin were used as cement replacement. The physical properties were investigated using slump test for normal concrete and slump flow test for self-compacting concrete. The mechanical properties were tested for compressive strength and tensile strength. The findings of this study show that the inclusion of metakaolin as cement replacement can increase both compressive and tensile strength compared to normal concrete. The highest compressive strength was found in self-compacting concrete with 15% metakaolin replacement at 53.3 MPa while self-compacting concrete with 10% metakaolin replacement showed the highest tensile strength at 3.6 MPa. On top of that, the finishing or concrete surface of both cube and cylinder samples made of self-compacting concrete produced a smooth surface with the appearance of less honeycombs compared to normal concrete.

Role of Insulin-like growth factors in initiation of follicle growth in normal and polycystic human ovaries.

PubMed

Stubbs, Sharron A; Webber, Lisa J; Stark, Jaroslav; Rice, Suman; Margara, Raul; Lavery, Stuart; Trew, Geoffrey H; Hardy, Kate; Franks, Stephen

2013-08-01

Polycystic ovary syndrome (PCOS), the commonest cause of anovulatory infertility, is characterized by disordered follicle development including increased activation and accelerated growth of preantral follicles. Data from experimental animals and preliminary results from studies of human ovarian tissue suggest that IGFs affect preantral follicle development. Our objectives were to investigate the expression of the type-1 IGF receptor (IGFR-1) in the human ovary and to determine whether IGFs are involved in stimulating the transition of follicles from primordial to primary stage in normal and polycystic ovaries. We used archived ovarian tissue for protein expression studies and small cortical biopsies for follicle isolation and for tissue culture. This was a laboratory-based study, using clinical tissue samples. A total of 54 women, 33 with normal ovaries and 21 with polycystic ovaries, were classified by reference to menstrual cycle history and ultrasonography. We evaluated expression of IGFR-1 mRNA in isolated preantral follicles and of IGFR-1 protein in archived ovarian tissue samples from normal and polycystic ovaries and effects of exogenous IGF-1 on preantral follicle development and survival in cultured fragments of normal and polycystic ovaries. IGFR-1 mRNA and protein was expressed in preantral follicles at all stages of development and enhanced expression was noted in PCOS follicles during early preantral development. IGF-1 stimulated initiation of follicle growth in normal tissue but had little effect on preantral follicle growth in polycystic ovaries in which, characteristically, there was a higher proportion of follicles that had entered the growing phase even before culture. IGFs are plausible candidates in regulation of initiation of human follicle growth, and accelerated preantral follicle growth in PCOS may be due to increased activity of endogenous IGFs.

Lipid regulatory genes polymorphism in children with and without obesity and cardiometabolic risk factors: The CASPIAN-III study

PubMed Central

Hovsepian, Silva; Javanmard, Shaghayegh Haghjooy; Mansourian, Marjan; Hashemipour, Mahin; Tajadini, Mohamadhasan; Kelishadi, Roya

2018-01-01

Background: Genetically, predisposed children are considered as at-risk individuals for cardiovascular disease. In this study, we aimed to compare the frequency of four-lipid regulatory polymorphism in obese and normal-weight children with and without cardiometabolic risk factors. Materials and Methods: In this nested case–control study, 600 samples of four groups of participants consisted of those with normal weight with and without cardiometabolic risk factors and obese with and without cardiometabolic risk factors. Allelic and genotypic frequencies of GCKR (rs780094), GCKR (rs1260333), MLXIPL (rs3812316), and FADS (rs174547) polymorphisms were compared in the four studied groups. Results: Data of 528 samples were complete and included in this study. The mean (standard deviation) age of participants was 15.01 (2.21) years. Frequency of tt allele (minor allele) of GCKR (rs1260333) polymorphism was significantly lower in normal weight metabolically healthy participants than metabolically unhealthy normal weight (MUHNW) and obese children with and without cardiometabolic risk factor (P = 0.01). Frequency of ga allele of GCKR (rs780094) polymorphism was significantly higher in normal weight children with cardiometabolic risk factor than in their obese counterparts with cardiometabolic risk factor (P = 0.04). Frequency of cg and gg alleles (minor type) of MLXIPL (rs3812316) polymorphism in normal weight metabolically healthy participants was significantly higher than MUHNW (P = 0.04) and metabolically healthy obese children (P = 0.04). Conclusion: The findings of our study indicated that the minor allele of GCKR (rs1260333) single nucleotide polymorphisms (SNPs) could have pathogenic effect for obesity and cardiometabolic risk factors. Ga allele of GCKR (rs780094) SNPs had a protective effect on obesity. Minor alleles of MLXIPL (rs3812316) could have a protective effect for obesity and cardiometabolic risk factors. PMID:29531563

Myeloperoxidase in the plasma and placenta of normal pregnant women and women with pregnancies complicated by preeclampsia and intrauterine growth restriction.

PubMed

Hung, T-H; Chen, S-F; Lo, L-M; Li, M-J; Yeh, Y-L; Hsieh, T-T

2012-04-01

Myeloperoxidase (MPO) is a heme protein produced and released by activated neutrophils and monocytes, and increased MPO is considered important in the pathophysiology of cardiovascular diseases (CVD). Accumulating evidence suggests that preeclampsia (PE), idiopathic intrauterine growth restriction (IUGR), and CVD share many similar metabolic disturbances, including an enhanced systemic inflammatory response and endothelial dysfunction. We hypothesized that MPO plays an important role in the development of PE and IUGR. Plasma samples were collected mid-gestation and at delivery from women with normal pregnancies (n = 40) and those who subsequently developed PE (n = 20), IUGR (n = 11) or both (PE + IUGR, n = 8). Placental samples were obtained immediately after delivery from 22 women with normal pregnancies, 19 women with PE, 14 women with IUGR, and 14 women with PE + IUGR. The MPO concentrations were measured using ELISA. Women with PE + IUGR had significantly higher plasma MPO before delivery than normal pregnant women. There was no difference in plasma levels at mid-gestation or the placental concentrations between women with normal pregnancies and those who developed PE, IUGR, or PE + IUGR. Using explants prepared from the placentas of 8 women with normal pregnancies and 8 women with PE, we found no difference in the levels of MPO in the tissue homogenates and culture media between these two groups of women. Together, these results indicate that increased maternal circulating MPO in women with PE + IUGR is likely a result of enhanced systemic inflammation caused by the established disease rather than a primary pathophysiological factor. Copyright © 2012 Elsevier Ltd. All rights reserved.

Comparison of Performance on Two Nonverbal Intelligence Tests by Adolescents with and without Language Impairment

ERIC Educational Resources Information Center

Miller, Carol A.; Gilbert, Erin

2008-01-01

Definitions of specific language impairment (SLI), for both research and clinical purposes, often state that nonverbal IQ scores must be within normal limits. This use of nonverbal IQ has been criticized on several grounds, including lack of equivalence between tests. In the current study, a sample of 204 adolescents with and without language…

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 diagnostic plot proposed in this paper can be used to assess how adequate ChIP/Input normalization constants are, and thus it allows the user to choose the most adequate estimate for the analysis.

Wastewater effluent, combined sewer overflows, and other sources of organic compounds to Lake Champlain

USGS Publications Warehouse

Phillips, P.; Chalmers, A.

2009-01-01

Some sources of organic wastewater compounds (OWCs) to streams, lakes, and estuaries, including wastewater-treatment-plant effluent, have been well documented, but other sources, particularly wet-weather discharges from combined-sewer-overflow (CSO) and urban runoff, may also be major sources of OWCs. Samples of wastewater-treatment-plant (WWTP) effluent, CSO effluent, urban streams, large rivers, a reference (undeveloped) stream, and Lake Champlain were collected from March to August 2006. The highest concentrations of many OWCs associated with wastewater were in WWTP-effluent samples, but high concentrations of some OWCs in samples of CSO effluent and storm runoff from urban streams subject to leaky sewer pipes or CSOs were also detected. Total concentrations and numbers of compounds detected differed substantially among sampling sites. The highest total OWC concentrations (10-100 ??g/l) were in samples of WWTP and CSO effluent. Total OWC concentrations in samples from urban streams ranged from 0.1 to 10 ??g/l, and urban stream-stormflow samples had higher concentrations than baseflow samples because of contributions of OWCs from CSOs and leaking sewer pipes. The relations between OWC concentrations in WWTP-effluent and those in CSO effluent and urban streams varied with the degree to which the compound is removed through normal wastewater treatment. Concentrations of compounds that are highly removed during normal wastewater treatment [including caffeine, Tris(2-butoxyethyl)phosphate, and cholesterol] were generally similar to or higher in CSO effluent than in WWTP effluent (and ranged from around 1 to over 10 ??g/l) because CSO effluent is untreated, and were higher in urban-stream stormflow samples than in baseflow samples as a result of CSO discharge and leakage from near-surface sources during storms. Concentrations of compounds that are poorly removed during treatment, by contrast, are higher in WWTP effluent than in CSO, due to dilution. Results indicate that CSO effluent and urban stormwaters can be a significant major source of OWCs entering large water bodies such as Burlington Bay. ?? 2008 American Water Resources Association.

Negotiating weight and body image in the UAE: strategies among young Emirati women.

PubMed

Trainer, Sarah

2012-01-01

The goal of this study was to evaluate weight, nutritional status, and attitudes toward weight and health among a cohort of young women drawn from local populations in the United Arab Emirates. This sample was composed of 103 female Emiratis, aged 18-30. Eighty of the women were students at Zayed University (ZU) in Dubai and 23 were students at UAE University (UAEU) in Al Ain. Research was divided into two phases. Methods included the collection of weight and height measurements (to analyze BMIs) and body fat percentages; 24-h food and activity recalls; semistructured, structured, and unstructured interviews; and participant observation. The distribution of BMIs in this sample was skewed toward underweight and normal weight in the ZU sample and split evenly between underweight-to-normal and overweight-to-obese in the UAEU sample, a finding that stands in contrast to the high rates of overweight and obesity reported in other age cohorts in local populations. This lower distribution of BMIs was correlated with widely expressed concern over body image, whereas reported interest in nutrition was much lower. Dietary patterns reflected attempts to manage weight. There was a marked trend toward nutritionally poor diets and sedentary living. Obesity and overweight among young women in the Emirati population do not appear to be as significant a problem as they are in older populations. However, several other health-related causes for concern emerged in this study, including extreme dieting strategies, insufficient micronutrient and protein intake, and widespread inactivity. Copyright © 2012 Wiley Periodicals, Inc.

Evaluation of cell count and classification capabilities in body fluids using a fully automated Sysmex XN equipped with high-sensitive Analysis (hsA) mode and DI-60 hematology analyzer system.

PubMed

Takemura, Hiroyuki; Ai, Tomohiko; Kimura, Konobu; Nagasaka, Kaori; Takahashi, Toshihiro; Tsuchiya, Koji; Yang, Haeun; Konishi, Aya; Uchihashi, Kinya; Horii, Takashi; Tabe, Yoko; Ohsaka, Akimichi

2018-01-01

The XN series automated hematology analyzer has been equipped with a body fluid (BF) mode to count and differentiate leukocytes in BF samples including cerebrospinal fluid (CSF). However, its diagnostic accuracy is not reliable for CSF samples with low cell concentration at the border between normal and pathologic level. To overcome this limitation, a new flow cytometry-based technology, termed "high sensitive analysis (hsA) mode," has been developed. In addition, the XN series analyzer has been equipped with the automated digital cell imaging analyzer DI-60 to classify cell morphology including normal leukocytes differential and abnormal malignant cells detection. Using various BF samples, we evaluated the performance of the XN-hsA mode and DI-60 compared to manual microscopic examination. The reproducibility of the XN-hsA mode showed good results in samples with low cell densities (coefficient of variation; % CV: 7.8% for 6 cells/μL). The linearity of the XN-hsA mode was established up to 938 cells/μL. The cell number obtained using the XN-hsA mode correlated highly with the corresponding microscopic examination. Good correlation was also observed between the DI-60 analyses and manual microscopic classification for all leukocyte types, except monocytes. In conclusion, the combined use of cell counting with the XN-hsA mode and automated morphological analyses using the DI-60 mode is potentially useful for the automated analysis of BF cells.

Structural Equation Analysis of the Wechsler Adult Intelligence Scale-Revised in a Normal Elderly Sample.

ERIC Educational Resources Information Center

Burton, D. Bradley; And Others

1994-01-01

A maximum-likelihood confirmatory factor analysis was performed by applying LISREL VII to the Wechsler Adult Intelligence Scale-Revised results of a normal elderly sample of 225 adults. Results indicate that a three-factor model fits best across all sample combinations. A mild gender effect is discussed. (SLD)

Vitamin D deficiency and insufficiency among patients with prostate cancer

PubMed Central

Trump, Donald L.; Chadha, Manpreet K.; Sunga, Annette Y.; Fakih, Marwan G.; Ashraf, Umeer; Silliman, Carrie G.; Hollis, Bruce W.; Nesline, Mary K.; Tian, Lili; Tan, Wei; Johnson, Candace S.

2009-01-01

Objective To assess the frequency of vitamin D deficiency among men with prostate cancer, as considerable epidemiological, in vitro, in vivo and clinical data support an association between vitamin D deficiency and prostate cancer outcome. Patients, subjects and methods The study included 120 ambulatory men with recurrent prostate cancer and 50 with clinically localized prostate cancer who were evaluated and serum samples assayed for 25-OH vitamin D levels. Then 100 controls (both sexes), matched for age and season of serum sample, were chosen from a prospective serum banking protocol. The relationship between age, body mass index, disease stage, Eastern Cooperative Oncology Group performance status, season and previous therapy on vitamin D status were evaluated using univariate and multivariate analyses. Results The mean 25-OH vitamin D level was 25.9 ng/mL in those with recurrent disease, 27.5 ng/mL in men with clinically localized prostate cancer and 24.5 ng/mL in controls. The frequency of vitamin D deficiency (< 20 ng/mL) and insufficiency (20–31 ng/mL) was 40% and 32% in men with recurrent prostate; 28% had vitamin D levels that were normal (32–100 ng/mL). Among men with localized prostate cancer, 18% were deficient, 50% were insufficient and 32% were normal. Among controls, 31% were deficient, 40% were insufficient and 29% were normal. Metastatic disease (P = 0.005) and season of blood sampling (winter/spring; P = 0.01) were associated with vitamin D deficiency in patients with prostate cancer, while age, race, performance status and body mass index were not. Conclusions Vitamin D deficiency and insufficiency were common among men with prostate cancer and apparently normal controls in the western New York region. PMID:19426195

Vitamin D deficiency and insufficiency among patients with prostate cancer.

PubMed

Trump, Donald L; Chadha, Manpreet K; Sunga, Annette Y; Fakih, Marwan G; Ashraf, Umeer; Silliman, Carrie G; Hollis, Bruce W; Nesline, Mary K; Tian, Lili; Tan, Wei; Johnson, Candace S

2009-10-01

To assess the frequency of vitamin D deficiency among men with prostate cancer, as considerable epidemiological, in vitro, in vivo and clinical data support an association between vitamin D deficiency and prostate cancer outcome. The study included 120 ambulatory men with recurrent prostate cancer and 50 with clinically localized prostate cancer who were evaluated and serum samples assayed for 25-OH vitamin D levels. Then 100 controls (both sexes), matched for age and season of serum sample, were chosen from a prospective serum banking protocol. The relationship between age, body mass index, disease stage, Eastern Cooperative Oncology Group performance status, season and previous therapy on vitamin D status were evaluated using univariate and multivariate analyses. The mean 25-OH vitamin D level was 25.9 ng/mL in those with recurrent disease, 27.5 ng/mL in men with clinically localized prostate cancer and 24.5 ng/mL in controls. The frequency of vitamin D deficiency (<20 ng/mL) and insufficiency (20-31 ng/mL) was 40% and 32% in men with recurrent prostate; 28% had vitamin D levels that were normal (32-100 ng/mL). Among men with localized prostate cancer, 18% were deficient, 50% were insufficient and 32% were normal. Among controls, 31% were deficient, 40% were insufficient and 29% were normal. Metastatic disease (P = 0.005) and season of blood sampling (winter/spring; P = 0.01) were associated with vitamin D deficiency in patients with prostate cancer, while age, race, performance status and body mass index were not. Vitamin D deficiency and insufficiency were common among men with prostate cancer and apparently normal controls in the western New York region.

Urine melanin test

MedlinePlus

Thormahlen's test; Melanin - urine ... A clean-catch urine sample is needed. ... this substance that it shows up in the urine. ... Normally, melanin is not present in urine. Normal value ranges may ... measurements or test different samples. Talk to your health ...

Cardiometabolic risks profile of normal weight obese and multi-ethnic women in a developing country.

PubMed

Moy, Foong Ming; Loh, Debbie Ann

2015-07-01

To determine the prevalence of normal weight obesity among multi-ethnic women in Peninsular Malaysia and examine its associations with cardiometabolic risks and lifestyle behaviours. This was a cross-sectional study involving women recruited via multi-stage sampling from six states in Malaysia. Anthropometric and body composition analysis were performed. Normal weight obese (NWO) was defined as normal body mass index for Asians and the highest tertile of % body fat (BF). Biochemical measurements included fasting lipid and blood glucose levels. Metabolic syndrome was diagnosed based on the Harmonization criteria. Participants completed self-reported questionnaires that included physical activity, smoking, alcohol consumption, fruit and vegetable intake and sleep duration. Body mass index, %BF, cardiometabolic risk factors, lifestyle behaviours. A total of 6854 women were recruited and the prevalence of NWO was 19.8% (95% CI: 17.3-22.5). NWO was more prevalent among the Indians and older women. NWO women had higher odds for abdominal obesity (OR: 2.64, 95% CI: 1.73-4.04), hypertriglyceridemia (2.51, 1.47-4.29) and hypertension (1.63, 1.15-2.31) compared to women with lower % body fat after adjusted for age and ethnicity. The prevalence of metabolic syndrome among NWO women was 5.4% (95% CI: 3.0-9.8). None of the lifestyle behaviours were significantly associated with NWO. Women with NWO had cardiometabolic abnormalities including abdominal obesity, dyslipidaemia and increased blood pressure. Health promotion efforts should include NWO women who may be oblivious of their deleterious health risks. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Minimally-invasive Sampling of Interleukin-1α and Interleukin-1 Receptor Antagonist from the Skin: A Systematic Review of In vivo Studies in Humans.

PubMed

Falcone, Denise; Spee, Pieter; van de Kerkhof, Peter C M; van Erp, Piet E J

2017-10-02

Interleukin-1α (IL-1α) and its receptor antagonist IL-1RA play a pivotal role in skin homeostasis and disease. Although the use of biopsies to sample these cytokines from human skin is widely employed in dermatological practice, knowledge about less invasive, in vivo sampling methods is scarce. The aim of this study was to provide an overview of such methods by systematically reviewing studies in Medline, EMBASE, Web of Science and Cochrane Library using combinations of the terms "IL-1α", IL-1RA", "skin", "human", including all possible synonyms. Quality was assessed using the STrengthening the Reporting of OBservational studies in Epidemiology (STROBE) checklist. The search, performed on 14 October 2016, revealed 10 different sampling methods, with varying degrees of invasiveness and wide application spectrum, including assessment of both normal and diseased skin, from several body sites. The possibility to sample quantifiable amounts of cytokines from human skin with no or minimal discomfort holds promise for linking clinical outcomes to molecular profiles of skin inflammation.

Study of gastric cancer samples using terahertz techniques

NASA Astrophysics Data System (ADS)

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

2014-08-01

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

Microminiature gas chromatograph

DOEpatents

Yu, C.M.

1996-12-10

A microminiature gas chromatograph ({mu}GC) comprising a least one silicon wafer, a gas injector, a column, and a detector. The gas injector has a normally closed valve for introducing a mobile phase including a sample gas in a carrier gas. The valve is fully disposed in the silicon wafer(s). The column is a microcapillary in silicon crystal with a stationary phase and is mechanically connected to receive the mobile phase from the gas injector for the molecular separation of compounds in the sample gas. The detector is mechanically connected to the column for the analysis of the separated compounds of sample gas with electronic means, e.g., ion cell, field emitter and PIN diode. 7 figs.

A bias in the "mass-normalized" DTT response - An effect of non-linear concentration-response curves for copper and manganese

NASA Astrophysics Data System (ADS)

Charrier, Jessica G.; McFall, Alexander S.; Vu, Kennedy K.-T.; Baroi, James; Olea, Catalina; Hasson, Alam; Anastasio, Cort

2016-11-01

The dithiothreitol (DTT) assay is widely used to measure the oxidative potential of particulate matter. Results are typically presented in mass-normalized units (e.g., pmols DTT lost per minute per microgram PM) to allow for comparison among samples. Use of this unit assumes that the mass-normalized DTT response is constant and independent of the mass concentration of PM added to the DTT assay. However, based on previous work that identified non-linear DTT responses for copper and manganese, this basic assumption (that the mass-normalized DTT response is independent of the concentration of PM added to the assay) should not be true for samples where Cu and Mn contribute significantly to the DTT signal. To test this we measured the DTT response at multiple PM concentrations for eight ambient particulate samples collected at two locations in California. The results confirm that for samples with significant contributions from Cu and Mn, the mass-normalized DTT response can strongly depend on the concentration of PM added to the assay, varying by up to an order of magnitude for PM concentrations between 2 and 34 μg mL-1. This mass dependence confounds useful interpretation of DTT assay data in samples with significant contributions from Cu and Mn, requiring additional quality control steps to check for this bias. To minimize this problem, we discuss two methods to correct the mass-normalized DTT result and we apply those methods to our samples. We find that it is possible to correct the mass-normalized DTT result, although the correction methods have some drawbacks and add uncertainty to DTT analyses. More broadly, other DTT-active species might also have non-linear concentration-responses in the assay and cause a bias. In addition, the same problem of Cu- and Mn-mediated bias in mass-normalized DTT results might affect other measures of acellular redox activity in PM and needs to be addressed.

The influence of normal and high ultimate muscle pH on the microbiology and colour stability of previously frozen black wildebeest (Connochaetes gnou) meat.

PubMed

Shange, Nompumelelo; Makasi, Thandeka N; Gouws, Pieter A; Hoffman, Louwrens C

2018-01-01

Changes in pH, colour and microbiological counts were investigated in previously frozen Biceps femoris (BF) muscles from black wildebeest. Samples were stored under vacuum at refrigerated conditions (4.2±0.8°C) for 12days. Seven BF muscles had a high pH (DFD) (pH≥6) and five had a normal pH (pH<6). Overtime the pH of DFD did not significantly change whilst that of normal pH meat decreased. Browning under anaerobic storage conditions was seen, more for normal meat than DFD meat. Initial total viable counts, lactic acid bacteria and coliform counts from samples with normal pH, were significantly higher than counts from the DFD samples. However, overtime DFD meat showed a faster increase for all microorganisms tested compared to normal pH meat. Overall, this study revealed that DFD meat can have a shorter shelf-life than normal pH meat stored at 4.2±0.8°C. Copyright © 2017 Elsevier Ltd. All rights reserved.

High resolution DNA melting analysis: an application for prenatal control of alpha-thalassemia.

PubMed

Sirichotiyakul, Supatra; Wanapirak, Chanane; Saetung, Rattika; Sanguansermsri, Torpong

2010-04-01

To report the use of real-time gap-PCR using SYTO9 with high-resolution melting analysis (HRMA) in prenatal diagnosis of alpha-thalassemia 1. Real-time gap-PCR using SYTO9 with HRMA was performed in 33 DNA samples from chorionic villi sampling (8 normal, 16 heterozygous, and 9 homozygous) to determine the alpha-thalassemia 1 gene [normal and Southeast Asia (-SEA) allele]. The dissociation curve analysis in normal and - SEA allele gave a peak of T(m) at 91.80 +/- 0.14 degrees C and 88.67 +/- 0.08 degrees C, respectively. Normal genotype and homozygous alpha-thalassemia 1 showed a single peak of T(m) that corresponded to their alleles. The heterozygotes gave both peaks with higher normal peak and smaller - SEA peak. Thirty one samples showed consistent results with the conventional gap-PCR. Two samples with ambiguous results were confirmed to be maternal DNA contamination on real-time quantitative PCR and microsatellite assay. HRMA from both samples showed similar pattern to that of heterozygotes. However, they showed much smaller normal peak compared with the - SEA peak, which is in contrast to those of heterozygotes and can readily be distinguished. HRMA with SYTO9 is feasible for prenatal diagnosis of alpha-thalassemia. It had potential advantage of prompt detection maternal DNA contamination. Copyright (c) 2010 John Wiley & Sons, Ltd.

The normal mycoflora of commodities from Thailand. 1. Nuts and oilseeds.

PubMed

Pitt, J I; Hocking, A D; Bhudhasamai, K; Miscamble, B F; Wheeler, K A; Tanboon-Ek, P

1993-12-01

A comprehensive study was carried out of the fungi occurring in commodities normally traded in Thailand. Samples of major commodities were obtained from farmers' stocks and middlemen in major producing areas throughout the country. Retail samples were obtained from outlets in and around Bankok. Samples were divided into two portions, one being examined in Bangkok, and the second in Sydney. After surface disinfection, fungi were enumerated by direct plating on dichloran rose bengal chloramphenicol agar, dichloran 18% glycerol agar, Aspergillus flavus and parasiticus agar and dichloran chloramphenicol peptone agar. Figures for percentage infection were calculated, and fungi were isolated and identified to species level. In all 602 samples were examined, and at North Ryde about 18,000 fungal isolates identified. Data obtained from 329 samples are reported here, comprising maize (154), peanuts (109), cashews (45) and copra (21). Major fungi in maize included Fusarium moniliforme (present in 97% of samples), Aspergillus flavus (85%), Penicillium citrinum (67%), Aspergillus niger (64%), Lasiodiplodia theobromae (58%) and Fusarium semitectum (45%). In peanuts, the major fungi were Aspergillus flavus (95% of samples), Aspergillus niger (86%), Rhizopus oryzae (60%), Eurotium rubrum (51%), Macromina phaseolina (49%), Penicillium citrinum (46%) and Eurotium chevalieri (46%). Invasion in cashews was lower, major fungi being Aspergillus flavus (60%), Nigrospora oryzae (58%), Aspergillus niger (53%), Chaetomium globosum (47%) and Eurotium chevalieri (40%). Aspergillus flavus (86% of samples) was again dominant in copra, with Rhizopus oryzae (52%), Aspergillus niger (43%), Eurotium chevalieri (43%) the only other species exceeding 40% infection. Aspergillus parasiticus was rarely seen, and Aspergillus nomius was reported from foods for the first time.

Internal Kinematics of AGN Hosts

NASA Astrophysics Data System (ADS)

Masegosa, Josefa; Márquez, Isabel; Durret, Florence; DEGAS Consortium

In order to understand the fueling mechanism to power AGNs, a large effort has been done by the DEGAS (Dynamics and nuclear Engine of GAlaxies of Spiral type) consortium to collect the necessary observational material. We defined an AGN sample which is not contaminated by interacting galaxies and a control sample made of normal spirals with the same properties than the AGN sample, i.e. luminosity and redshift distribution, morphology and percentage of bars. In total we have analyzed a sample of 17 active galaxies and 16 normal spirals. All the galaxies are isolated with the following criteria: not having a companion within 0.4 Mpc and cz < 500 km/s. We want to stress this aspect of our sample, since claimed differences between active and normal galaxies (Knapen et al. 2000) disappear when the samples are decontaminated of interacting systems.

Compression stiffening of brain and its effect on mechanosensing by glioma cells

NASA Astrophysics Data System (ADS)

Pogoda, Katarzyna; Chin, LiKang; Georges, Penelope C.; Byfield, FitzRoy J.; Bucki, Robert; Kim, Richard; Weaver, Michael; Wells, Rebecca G.; Marcinkiewicz, Cezary; Janmey, Paul A.

2014-07-01

Many cell types, including neurons, astrocytes and other cells of the central nervous system, respond to changes in the extracellular matrix or substrate viscoelasticity, and increased tissue stiffness is a hallmark of several disease states, including fibrosis and some types of cancers. Whether the malignant tissue in brain, an organ that lacks the protein-based filamentous extracellular matrix of other organs, exhibits the same macroscopic stiffening characteristic of breast, colon, pancreatic and other tumors is not known. In this study we show that glioma cells, like normal astrocytes, respond strongly in vitro to substrate stiffness in the range of 100 to 2000 Pa, but that macroscopic (mm to cm) tissue samples isolated from human glioma tumors have elastic moduli in the order of 200 Pa that are indistinguishable from those of normal brain. However, both normal brain and glioma tissues increase their shear elastic moduli under modest uniaxial compression, and glioma tissue stiffens more strongly under compression than normal brain. These findings suggest that local tissue stiffness has the potential to alter glial cell function, and that stiffness changes in brain tumors might arise not from increased deposition or crosslinking of the collagen-rich extracellular matrix, but from pressure gradients that form within the tumors in vivo.

A Single-Dose, Open-Label Study of the Pharmacokinetics, Safety, and Tolerability of Lisdexamfetamine Dimesylate in Individuals With Normal and Impaired Renal Function

PubMed Central

Ermer, James; Corcoran, Mary; Lasseter, Kenneth; Marbury, Thomas; Yan, Brian

2016-01-01

Background: Lisdexamfetamine (LDX) and d-amphetamine pharmacokinetics were assessed in individuals with normal and impaired renal function after a single LDX dose; LDX and d-amphetamine dialyzability was also examined. Methods: Adults (N = 40; 8/group) were enrolled in 1 of 5 renal function groups [normal function, mild impairment, moderate impairment, severe impairment/end-stage renal disease (ESRD) not requiring hemodialysis, and ESRD requiring hemodialysis] as estimated by glomerular filtration rate (GFR). Participants with normal and mild to severe renal impairment received 30 mg LDX; blood samples were collected predose and serially for 96 hours. Participants with ESRD requiring hemodialysis received 30 mg LDX predialysis and postdialysis separated by a washout period of 7–14 days. Predialysis blood samples were collected predose, serially for 72 hours, and from the dialyzer during hemodialysis; postdialysis blood samples were collected predose and serially for 48 hours. Pharmacokinetic end points included maximum plasma concentration (Cmax) and area under the plasma concentration versus time curve from time 0 to infinity (AUC0–∞) or to last assessment (AUClast). Results: Mean LDX Cmax, AUClast, and AUC0–∞ in participants with mild to severe renal impairment did not differ from those with normal renal function; participants with ESRD had higher mean Cmax and AUClast than those with normal renal function. d-amphetamine exposure (AUClast and AUC0–∞) increased and Cmax decreased as renal impairment increased. Almost no LDX and little d-amphetamine were recovered in the dialyzate. Conclusions: There seems to be prolonged d-amphetamine exposure after 30 mg LDX as renal impairment increases. In individuals with severe renal impairment (GFR: 15 ≤ 30 mL·min−1·1.73 m−2), the maximum LDX dose is 50 mg/d; in patients with ESRD (GFR: <15 mL·min−1·1.73 m−2), the maximum LDX dose is 30 mg/d. Neither LDX nor d-amphetamine is dialyzable. PMID:26926668

Low Stretch PMMA Burning in Microgravity: Status of the Ground-Based Program and New ISS Glovebox Experiment SALSA

NASA Technical Reports Server (NTRS)

Olson, S. L.; T'ien, J. S.; Armstrong, J. B.

2001-01-01

The objective of this ground-based program is to study low stretch diffusion flames burning PMMA as the solid fuel to determine the relationship between buoyant low stretch burning in normal gravity and forced flow low stretch burning in microgravity. The low stretch is generated in normal gravity by using the buoyant convection induced by burning the bottom of a large radius of curvature sample. Low stretch is also generated using the Combustion Tunnel drop tower rig (2.2 and 5.2 second facilities), which provides a forced convective low velocity flow past smaller radius of curvature samples. Lastly, an ISS glovebox investigation is being developed to study low stretch burning of PMMA spheres to obtain long duration testing needed to accurately assess the flammability and burning characteristics of the material in microgravity. A comparison of microgravity experiment results with normal gravity test results allows us to establish a direct link between a material's burning characteristics in normal gravity (easily measured) with its burning characteristics in extraterrestrial environments, including microgravity forced convective environments. Theoretical predictions and recent experimental results indicate that it should be possible to understand a material's burning characteristics in the low stretch environment of spacecraft (non-buoyant air movement induced by fans and crew disturbances) by understanding its burning characteristics in an equivalent Earth-based low stretch environment (induced by normal gravity buoyancy). Similarly, Earth-based stretch environments can be made equivalent to those in Lunar- and Martian-surface stretch environments (which would induce partial-gravity buoyancy).

Effects of normalization on quantitative traits in association test

PubMed Central

2009-01-01

Background Quantitative trait loci analysis assumes that the trait is normally distributed. In reality, this is often not observed and one strategy is to transform the trait. However, it is not clear how much normality is required and which transformation works best in association studies. Results We performed simulations on four types of common quantitative traits to evaluate the effects of normalization using the logarithm, Box-Cox, and rank-based transformations. The impact of sample size and genetic effects on normalization is also investigated. Our results show that rank-based transformation gives generally the best and consistent performance in identifying the causal polymorphism and ranking it highly in association tests, with a slight increase in false positive rate. Conclusion For small sample size or genetic effects, the improvement in sensitivity for rank transformation outweighs the slight increase in false positive rate. However, for large sample size and genetic effects, normalization may not be necessary since the increase in sensitivity is relatively modest. PMID:20003414

Instrumental texture characteristics of broiler pectoralis major with the wooden breast condition.

PubMed

Chatterjee, D; Zhuang, H; Bowker, B C; Rincon, A M; Sanchez-Brambila, G

2016-10-01

The objective was to characterize texture properties of raw and cooked broiler fillets (Pectoralis major) with the wooden breast condition (WBC) using the instrumental texture techniques of Meullenet-Owens Razor Shear (MORS) and Texture Profile Analysis (TPA). Deboned (3 h postmortem) broiler fillets were collected from a commercial plant and categorized as normal, moderate, or severe WBC based on the incidence and severity of diffuse hardened areas throughout fillets and the degree of palpable hardness. The fillets were then either stored at 4°C overnight or in a -20°C freezer. The MORS and TPA of the raw samples were determined at 24 h postmortem for fresh samples and after thawing overnight for frozen samples. The same measurements were also taken after the samples were cooked to 78°C. Regardless of freshness (fresh vs. frozen-thawed), cooking (raw vs. cooked), and degree of WBC, both MORS force and energy of the WBC samples were higher than that of the normal samples (P < 0.05). For TPA adhesiveness and resilience, there were no differences between normal and WBC samples (P > 0.05). However, average TPA hardness and chewiness measurements of the fillets with WBC were higher than the normal fillets (P < 0.05). Regardless of texture measurement, there were no interactions between freshness and the wooden condition or no differences between moderate and severe WBC fillets (P > 0.05). These results demonstrate that there are significant differences in instrumental texture properties between normal fillets and those exhibiting the WBC. The WBC fillets required more force to cut through, harder, and chewier than normal breast muscles. These results suggest that cooked WBC meat would likely be tougher than cooked normal meat. Published by Oxford University Press on behalf of Poultry Science Association 2016. This work is written by (a) US Government employee(s) and is in the public domain in the US.

Monitoring and identification of spatiotemporal landscape changes in multiple remote sensing images by using a stratified conditional Latin hypercube sampling approach and geostatistical simulation.

PubMed

Lin, Yu-Pin; Chu, Hone-Jay; Huang, Yu-Long; Tang, Chia-Hsi; Rouhani, Shahrokh

2011-06-01

This study develops a stratified conditional Latin hypercube sampling (scLHS) approach for multiple, remotely sensed, normalized difference vegetation index (NDVI) images. The objective is to sample, monitor, and delineate spatiotemporal landscape changes, including spatial heterogeneity and variability, in a given area. The scLHS approach, which is based on the variance quadtree technique (VQT) and the conditional Latin hypercube sampling (cLHS) method, selects samples in order to delineate landscape changes from multiple NDVI images. The images are then mapped for calibration and validation by using sequential Gaussian simulation (SGS) with the scLHS selected samples. Spatial statistical results indicate that in terms of their statistical distribution, spatial distribution, and spatial variation, the statistics and variograms of the scLHS samples resemble those of multiple NDVI images more closely than those of cLHS and VQT samples. Moreover, the accuracy of simulated NDVI images based on SGS with scLHS samples is significantly better than that of simulated NDVI images based on SGS with cLHS samples and VQT samples, respectively. However, the proposed approach efficiently monitors the spatial characteristics of landscape changes, including the statistics, spatial variability, and heterogeneity of NDVI images. In addition, SGS with the scLHS samples effectively reproduces spatial patterns and landscape changes in multiple NDVI images.

Comparing cancer vs normal gene expression profiles identifies new disease entities and common transcriptional programs in AML patients.

PubMed

Rapin, Nicolas; Bagger, Frederik Otzen; Jendholm, Johan; Mora-Jensen, Helena; Krogh, Anders; Kohlmann, Alexander; Thiede, Christian; Borregaard, Niels; Bullinger, Lars; Winther, Ole; Theilgaard-Mönch, Kim; Porse, Bo T

2014-02-06

Gene expression profiling has been used extensively to characterize cancer, identify novel subtypes, and improve patient stratification. However, it has largely failed to identify transcriptional programs that differ between cancer and corresponding normal cells and has not been efficient in identifying expression changes fundamental to disease etiology. Here we present a method that facilitates the comparison of any cancer sample to its nearest normal cellular counterpart, using acute myeloid leukemia (AML) as a model. We first generated a gene expression-based landscape of the normal hematopoietic hierarchy, using expression profiles from normal stem/progenitor cells, and next mapped the AML patient samples to this landscape. This allowed us to identify the closest normal counterpart of individual AML samples and determine gene expression changes between cancer and normal. We find the cancer vs normal method (CvN method) to be superior to conventional methods in stratifying AML patients with aberrant karyotype and in identifying common aberrant transcriptional programs with potential importance for AML etiology. Moreover, the CvN method uncovered a novel poor-outcome subtype of normal-karyotype AML, which allowed for the generation of a highly prognostic survival signature. Collectively, our CvN method holds great potential as a tool for the analysis of gene expression profiles of cancer patients.

Strength of Wet and Dry Montmorillonite

NASA Astrophysics Data System (ADS)

Morrow, C. A.; Lockner, D. A.; Moore, D. E.

2015-12-01

Montmorillonite, an expandable smectite clay, is a common mineral in fault zones to a depth of around 3 km. Its low strength relative to other common fault gouge minerals is important in many models of fault rheology. However, the coefficient of friction is not well constrained in the literature due to the difficulty of establishing fully drained or fully dried states in the laboratory. For instance, in some reported studies, samples were either partially saturated or possibly over pressured, leading to wide variability in reported shear strength. In this study, the coefficient of friction, μ, of both saturated and oven-dried (at 150°C) Na-montmorillonite was measured at normal stresses up to 680 MPa at room temperature and shortening rates from 1.0 to 0.01 μm/s. Care was taken to shear saturated samples slowly enough to avoid pore fluid overpressure in the clay layers. Coefficients of friction are reported after 8 mm of axial displacement in a triaxial apparatus on saw-cut samples containing a layer of montmorillonite gouge, with either granite or sandstone driving blocks. For saturated samples, μ increased from around 0.1 at low pressure to 0.25 at the highest test pressures. In contrast, values for oven-dried samples decreased asymptotically from approximately 0.78 at 10 MPa normal stress to around 0.45 at 400-680 MPa. While wet and dry strengths approached each other with increasing effective normal stress, wet strength remained only about half of the dry strength at 600 MPa effective normal stress. The increased coefficient of friction can be correlated with a reduction in the number of loosely bound lubricating surface water layers on the clay platelets due to applied normal stress under saturated conditions. The steady-state rate dependence of friction, a-b, was positive and dependent on normal stress. For saturated samples, a-b increased linearly with applied normal stress from ~0 to 0.004, while for dry samples a-b decreased with increasing normal stress from 0.008 to 0.002. All values were either neutral or rate strengthening, indicating a tendency for stable sliding.

Statistical characterization of a large geochemical database and effect of sample size

USGS Publications Warehouse

Zhang, C.; Manheim, F.T.; Hinde, J.; Grossman, J.N.

2005-01-01

The authors investigated statistical distributions for concentrations of chemical elements from the National Geochemical Survey (NGS) database of the U.S. Geological Survey. At the time of this study, the NGS data set encompasses 48,544 stream sediment and soil samples from the conterminous United States analyzed by ICP-AES following a 4-acid near-total digestion. This report includes 27 elements: Al, Ca, Fe, K, Mg, Na, P, Ti, Ba, Ce, Co, Cr, Cu, Ga, La, Li, Mn, Nb, Nd, Ni, Pb, Sc, Sr, Th, V, Y and Zn. The goal and challenge for the statistical overview was to delineate chemical distributions in a complex, heterogeneous data set spanning a large geographic range (the conterminous United States), and many different geological provinces and rock types. After declustering to create a uniform spatial sample distribution with 16,511 samples, histograms and quantile-quantile (Q-Q) plots were employed to delineate subpopulations that have coherent chemical and mineral affinities. Probability groupings are discerned by changes in slope (kinks) on the plots. Major rock-forming elements, e.g., Al, Ca, K and Na, tend to display linear segments on normal Q-Q plots. These segments can commonly be linked to petrologic or mineralogical associations. For example, linear segments on K and Na plots reflect dilution of clay minerals by quartz sand (low in K and Na). Minor and trace element relationships are best displayed on lognormal Q-Q plots. These sensitively reflect discrete relationships in subpopulations within the wide range of the data. For example, small but distinctly log-linear subpopulations for Pb, Cu, Zn and Ag are interpreted to represent ore-grade enrichment of naturally occurring minerals such as sulfides. None of the 27 chemical elements could pass the test for either normal or lognormal distribution on the declustered data set. Part of the reasons relate to the presence of mixtures of subpopulations and outliers. Random samples of the data set with successively smaller numbers of data points showed that few elements passed standard statistical tests for normality or log-normality until sample size decreased to a few hundred data points. Large sample size enhances the power of statistical tests, and leads to rejection of most statistical hypotheses for real data sets. For large sample sizes (e.g., n > 1000), graphical methods such as histogram, stem-and-leaf, and probability plots are recommended for rough judgement of probability distribution if needed. ?? 2005 Elsevier Ltd. All rights reserved.

Digital-computer normal shock position and restart control of a Mach 2.5 axisymmetric mixed-compression inlet

NASA Technical Reports Server (NTRS)

Neiner, G. H.; Cole, G. L.; Arpasi, D. J.

1972-01-01

Digital computer control of a mixed-compression inlet is discussed. The inlet was terminated with a choked orifice at the compressor face station to dynamically simulate a turbojet engine. Inlet diffuser exit airflow disturbances were used. A digital version of a previously tested analog control system was used for both normal shock and restart control. Digital computer algorithms were derived using z-transform and finite difference methods. Using a sample rate of 1000 samples per second, the digital normal shock and restart controls essentially duplicated the inlet analog computer control results. At a sample rate of 100 samples per second, the control system performed adequately but was less stable.

The Properties of the Massive Star-forming Galaxies with an Outside-in Assembly Mode

NASA Astrophysics Data System (ADS)

Wang, Enci; Kong, Xu; Wang, Huiyuan; Wang, Lixin; Lin, Lin; Gao, Yulong; Liu, Qing

2017-08-01

Previous findings show that massive ({M}* > {10}10 {M}⊙ ) star-forming (SF) galaxies usually have an “inside-out” stellar mass assembly mode. In this paper, we have for the first time selected a sample of 77 massive SF galaxies with an “outside-in” assembly mode (called the “targeted sample”) from the Mapping Nearby Galaxies at the Apache Point Observatory (MaNGA) survey. For comparison, two control samples are constructed from the MaNGA sample matched in stellar mass: a sample of 154 normal SF galaxies and a sample of 62 quiescent galaxies. In contrast to normal SF galaxies, the targeted galaxies appear to be smoother and more bulge-dominated and have a smaller size and higher concentration, star formation rate, and gas-phase metallicity as a whole. However, they have a larger size and lower concentration than quiescent galaxies. Unlike the normal SF sample, the targeted sample exhibits a slightly positive gradient of the 4000 Å break and a pronounced negative gradient of Hα equivalent width. Furthermore, the median surface mass density profile is between those of the normal SF and quiescent samples, indicating that the gas accretion of quiescent galaxies is not likely to be the main approach for the outside-in assembly mode. Our results suggest that the targeted galaxies are likely in the transitional phase from normal SF galaxies to quiescent galaxies, with rapid ongoing central stellar mass assembly (or bulge growth). We discuss several possible formation mechanisms for the outside-in mass assembly mode.

Transcriptome instability as a molecular pan-cancer characteristic of carcinomas.

PubMed

Sveen, Anita; Johannessen, Bjarne; Teixeira, Manuel R; Lothe, Ragnhild A; Skotheim, Rolf I

2014-08-10

We have previously proposed transcriptome instability as a genome-wide, pre-mRNA splicing-related characteristic of colorectal cancer. Here, we explore the hypothesis of transcriptome instability being a general characteristic of cancer. Exon-level microarray expression data from ten cancer datasets were analyzed, including breast cancer, cervical cancer, colorectal cancer, gastric cancer, lung cancer, neuroblastoma, and prostate cancer (555 samples), as well as paired normal tissue samples from the colon, lung, prostate, and stomach (93 samples). Based on alternative splicing scores across the genomes, we calculated sample-wise relative amounts of aberrant exon skipping and inclusion. Strong and non-random (P < 0.001) correlations between these estimates and the expression levels of splicing factor genes (n = 280) were found in most cancer types analyzed (breast-, cervical-, colorectal-, lung- and prostate cancer). This suggests a biological explanation for the splicing variation. Surprisingly, these associations prevailed in pan-cancer analyses. This is in contrast to the tissue and cancer specific patterns observed in comparisons across healthy tissue samples from the colon, lung, prostate, and stomach, and between paired cancer-normal samples from the same four tissue types. Based on exon-level expression profiling and computational analyses of alternative splicing, we propose transcriptome instability as a molecular pan-cancer characteristic. The affected cancers show strong and non-random associations between low expression levels of splicing factor genes, and high amounts of aberrant exon skipping and inclusion, and vice versa, on a genome-wide scale.

Imaging using a supercontinuum laser to assess tumors in patients with breast carcinoma

NASA Astrophysics Data System (ADS)

Sordillo, Laura A.; Sordillo, Peter P.; Alfano, R. R.

2016-03-01

The supercontinuum laser light source has many advantages over other light sources, including broad spectral range. Transmission images of paired normal and malignant breast tissue samples from two patients were obtained using a Leukos supercontinuum (SC) laser light source with wavelengths in the second and third NIR optical windows and an IR- CCD InGaAs camera detector (Goodrich Sensors Inc. high response camera SU320KTSW-1.7RT with spectral response between 900 nm and 1,700 nm). Optical attenuation measurements at the four NIR optical windows were obtained from the samples.

Progress Summaries

DTIC Science & Technology

1973-01-10

nitrogenous urinary metabolites and osmolarity ave been verified and extended to include electrolytes, ketogenic teroids and hydroxysteroids...epidemiological surveys of oral disease for interrelating the effects of climate, diet , oral care motivation and work activity. Oral health factors are monitored...from young rats saturated at 5D FSW days and 60 FSW for 35 days in air while receiving low, normal, and gh calcium diets . Samples from matur8 rats

CPTAC Releases Cancer Proteome Confirmatory Colon Study Data | Office of Cancer Clinical Proteomics Research

Cancer.gov

The National Cancer Institute (NCI) Clinical Proteomic Tumor Analysis Consortium (CPTAC) announces the release of the cancer proteome confirmatory colon study data. The goal of the study is to analyze the proteomes of approximately 100 confirmatory colon tumor patients, which includes tumor and adjacent normal samples, with liquid chromatography-tandem mass spectrometry (LC-MS/MS) global proteomic and phosphoproteomic profiling.

Expression patterns of DLK1 and INSL3 identify stages of Leydig cell differentiation during normal development and in testicular pathologies, including testicular cancer and Klinefelter syndrome.

PubMed

Lottrup, G; Nielsen, J E; Maroun, L L; Møller, L M A; Yassin, M; Leffers, H; Skakkebæk, N E; Rajpert-De Meyts, E

2014-08-01

What is the differentiation stage of human testicular interstitial cells, in particular Leydig cells (LC), within micronodules found in patients with infertility, testicular cancer and Klinefelter syndrome? The Leydig- and peritubular-cell populations in testes with dysgenesis contain an increased proportion of undifferentiated cells when compared with control samples, as demonstrated by increased delta-like homolog 1 (DLK1) and decreased insulin-like peptide 3 (INSL3) expression. Normal LC function is essential for male development and reproduction. Signs of LC failure, including LC micronodules, are often observed in patients with reproductive disorders. In this retrospective study, a panel of markers and factors linked to the differentiation of LCs was investigated in 33 fetal and prepubertal human specimens and in 58 adult testis samples from patients with testicular germ cell tumours, including precursor carcinoma in situ (CIS), infertility or Klinefelter syndrome. The expression patterns of DLK1, INSL3, chicken ovalbumin upstream promoter transcription factor 2 (COUP-TFII), cytochrome P450, family 11, subfamily A, polypeptide 1 (CYP11A1) and smooth muscle actin (SMA) were investigated by immunohistochemistry and quantitative RT-PCR. The percentage of positive LCs was estimated and correlated to total LC numbers and serum levels of reproductive hormones. DLK1, INSL3 and COUP-TFII expression changed during normal development and was linked to different stages of LC differentiation: DLK1 was expressed in all fetal LCs, but only in spindle-shaped progenitor cells and in a small subset of polygonal LCs in the normal adult testis; INSL3 was expressed in a subset of fetal LCs, but in the majority of adult LCs; and COUP-TFII was expressed in peritubular and mesenchymal stroma cells at all ages, in fetal LCs early in gestation and in a subset of adult LCs. CYP11A1 was expressed in the majority of LCs regardless of age and pathology and was the best general LC marker examined here. SMA was weakly expressed in peritubular cells in the fetal and infantile testis, but strongly expressed in the adult testis. In pathological testes, the numbers of DLK1-positive interstitial cells were increased. The proportion of DLK1-positive LCs correlated with total LC numbers (R = 0.53; P < 0.001) and was higher in testis with enlargement of the peritubular layers (P < 0.01), which was also highly associated with DLK1 expression in the peritubular compartment (P < 0.001). INSL3 expression was absent in some, but not all LC micronodules, and in the majority of LCs, it was mutually exclusive of DLK1. The number of samples was relatively small and no true normal adult controls were available. True stereology was not used for LC counting, instead LCs were counted in three fields of 0.5 µm(2) surface for each sample. The population of LCs, especially those clustered in large nodules, are heterogeneous and comprise cells at different stages of differentiation. The study demonstrated that the differentiation and function of LCs, and possibly also peritubular cells, are impaired in adult men with testicular pathologies including testis cancer and Klinefelter syndrome. This work was funded by Rigshospitalet's research funds, the Danish Cancer Society and Kirsten and Freddy Johansen's foundation. The authors have no conflicts of interest. © The Author 2014. Published by Oxford University Press on behalf of the European Society of Human Reproduction and Embryology. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Polyport atmospheric gas sampler

DOEpatents

Guggenheim, S. Frederic

1995-01-01

An atmospheric gas sampler with a multi-port valve which allows for multi, sequential sampling of air through a plurality of gas sampling tubes mounted in corresponding gas inlet ports. The gas sampler comprises a flow-through housing which defines a sampling chamber and includes a gas outlet port to accommodate a flow of gases through the housing. An apertured sample support plate defining the inlet ports extends across and encloses the sampling chamber and supports gas sampling tubes which depend into the sampling chamber and are secured across each of the inlet ports of the sample support plate in a flow-through relation to the flow of gases through the housing during sampling operations. A normally closed stopper means mounted on the sample support plate and operatively associated with each of the inlet ports blocks the flow of gases through the respective gas sampling tubes. A camming mechanism mounted on the sample support plate is adapted to rotate under and selectively lift open the stopper spring to accommodate a predetermined flow of gas through the respective gas sampling tubes when air is drawn from the housing through the outlet port.

Development of the technique of terahertz pulse spectroscopy for diagnostic malignant tumors during gastrointestinal surgeries

NASA Astrophysics Data System (ADS)

Goryachuk, A. A.; Khodzitsky, M. K.; Borovkova, M. A.; Khamid, A. K.; Dutkinskii, P. S.; Shishlo, D. A.

2016-08-01

Samples of fresh excised tissues obtained from patients who had undergone gastric cancer have been investigated. Samples were consisted of cancer zone, normal zone and zone mixed of normal and cancer tissues. Their optical properties and spectral features were investigated by terahertz time-domain spectroscopy (TDS) in reflection mode. It was found that waveforms of reflected signals from normal and cancer tissues were well distinguished so it can be concluded that it is easy to discriminate gastric cancer tissue from normal by using THz TDS.

Nontraditional Families and Childhood Progress Through School

PubMed Central

ROSENFELD, MICHAEL J.

2010-01-01

I use U.S. census data to perform the first large-sample, nationally representative tests of outcomes for children raised by same-sex couples. The results show that children of same-sex couples are as likely to make normal progress through school as the children of most other family structures. Heterosexual married couples are the family type whose children have the lowest rates of grade retention, but the advantage of heterosexual married couples is mostly due to their higher socioeconomic status. Children of all family types (including children of same-sex couples) are far more likely to make normal progress through school than are children living in group quarters (such as orphanages and shelters). PMID:20879687

Interidentity amnesia for neutral, episodic information in dissociative identity disorder.

PubMed

Huntjens, Rafaële J C; Postma, Albert; Peters, Madelon L; Woertman, Liesbeth; van der Hart, Onno

2003-05-01

Interidentity amnesia is considered a hallmark of dissociative identity disorder (DID) in clinical practice. In this study, objective methods of testing episodic memory transfer between identities were used. Tests of both recall (interference paradigm) and recognition were used. A sample of 31 DID patients was included. Additionally, 50 control subjects participated, half functioning as normal controls and the other half simulating interidentity amnesia. Twenty-one patients subjectively reported complete one-way amnesia for the learning episode. However, objectively, neither recall nor recognition scores of patients were different from those of normal controls. It is suggested that clinical models of amnesia in DID may be specified to exclude episodic memory impairments for emotionally neutral material.

High histologic grade and increased relative content of tryptophan in breast cancer using ratios from fingerprint fluorescence spectral peaks

NASA Astrophysics Data System (ADS)

Sordillo, Laura A.; Sordillo, Peter P.; Budansky, Yury; Pu, Yang; Alfano, R. R.

2015-03-01

Histologic grade is a very important, but underappreciated, parameter of breast cancer aggressiveness. Despite its importance, it has historically not been included as one of the criteria for staging of this cancer. In this study, spectral fluorescence profiles from patients with breast carcinoma were acquired. Ratios of emission peaks at 340 over 440,460 nm from biomolecules in malignant and normal samples were calculated. Cancerous over normal ratios (double ratio (DR) method) were evaluated with respect to tumor characteristics. Increased tryptophan content in breast cancer tissues correlates strongly with high grade, but not with lymph node metastases, estrogen receptor, progesterone receptor or Her-2-Neu receptor status.

Beyond stuttering: Speech disfluencies in normally fluent French-speaking children at age 4.

PubMed

Leclercq, Anne-Lise; Suaire, Pauline; Moyse, Astrid

2018-01-01

The aim of this study was to establish normative data on the speech disfluencies of normally fluent French-speaking children at age 4, an age at which stuttering has begun in 95% of children who stutter (Yairi & Ambrose, 2013). Fifty monolingual French-speaking children who do not stutter participated in the study. Analyses of a conversational speech sample comprising 250-550 words revealed an average of 10% total disfluencies, 2% stuttering-like disfluencies and around 8% non-stuttered disfluencies. Possible explanations for these high speech disfluency frequencies are discussed, including explanations linked to French in particular. The results shed light on the importance of normative data specific to each language.

Expression of gap junction protein connexin 43 in bovine urinary bladder tumours.

PubMed

Corteggio, A; Florio, J; Roperto, F; Borzacchiello, G

2011-01-01

The aetiopathogenesis of urinary bladder tumours in cattle involves prolonged ingestion of bracken fern and infection by bovine papillomavirus types 1 or 2 (BPV-1/2). The oncogenic activity of BPV is largely associated with the major oncoprotein E5. Gap junctions are the only communicating junctions found in animal tissues and are composed of proteins known as connexins. Alterations in connexin expression have been associated with oncogenesis. The present study investigated biochemically and immunohistochemically the expression of connexin 43 in samples of normal (n=2), dysplastic (n=3) and neoplastic (n=23) bovine urothelium. The tumours included 10 carcinomas in situ, five papillary urothelial carcinomas and eight invasive urothelial carcinomas. Normal and dysplastic urothelium had membrane expression of connexin 43, but this was reduced in samples of carcinoma in situ. Papillary urothelial carcinomas showed moderate cytoplasmic and membrane labelling, while invasive carcinoma showed loss of connexin 43 expression. Copyright © 2010 Elsevier Ltd. All rights reserved.

Graph Curvature for Differentiating Cancer Networks

PubMed Central

Sandhu, Romeil; Georgiou, Tryphon; Reznik, Ed; Zhu, Liangjia; Kolesov, Ivan; Senbabaoglu, Yasin; Tannenbaum, Allen

2015-01-01

Cellular interactions can be modeled as complex dynamical systems represented by weighted graphs. The functionality of such networks, including measures of robustness, reliability, performance, and efficiency, are intrinsically tied to the topology and geometry of the underlying graph. Utilizing recently proposed geometric notions of curvature on weighted graphs, we investigate the features of gene co-expression networks derived from large-scale genomic studies of cancer. We find that the curvature of these networks reliably distinguishes between cancer and normal samples, with cancer networks exhibiting higher curvature than their normal counterparts. We establish a quantitative relationship between our findings and prior investigations of network entropy. Furthermore, we demonstrate how our approach yields additional, non-trivial pair-wise (i.e. gene-gene) interactions which may be disrupted in cancer samples. The mathematical formulation of our approach yields an exact solution to calculating pair-wise changes in curvature which was computationally infeasible using prior methods. As such, our findings lay the foundation for an analytical approach to studying complex biological networks. PMID:26169480

Potential of non-invasive esophagus cancer detection based on urine surface-enhanced Raman spectroscopy

NASA Astrophysics Data System (ADS)

Huang, Shaohua; Wang, Lan; Chen, Weisheng; Feng, Shangyuan; Lin, Juqiang; Huang, Zufang; Chen, Guannan; Li, Buhong; Chen, Rong

2014-11-01

Non-invasive esophagus cancer detection based on urine surface-enhanced Raman spectroscopy (SERS) analysis was presented. Urine SERS spectra were measured on esophagus cancer patients (n = 56) and healthy volunteers (n = 36) for control analysis. Tentative assignments of the urine SERS spectra indicated some interesting esophagus cancer-specific biomolecular changes, including a decrease in the relative content of urea and an increase in the percentage of uric acid in the urine of esophagus cancer patients compared to that of healthy subjects. Principal component analysis (PCA) combined with linear discriminant analysis (LDA) was employed to analyze and differentiate the SERS spectra between normal and esophagus cancer urine. The diagnostic algorithms utilizing a multivariate analysis method achieved a diagnostic sensitivity of 89.3% and specificity of 83.3% for separating esophagus cancer samples from normal urine samples. These results from the explorative work suggested that silver nano particle-based urine SERS analysis coupled with PCA-LDA multivariate analysis has potential for non-invasive detection of esophagus cancer.

Fatty acid methyl esters are detectable in the plasma and their presence correlates with liver dysfunction.

PubMed

Aleryani, Samir Lutf; Cluette-Brown, Joanne E; Khan, Zia A; Hasaba, Hasan; Lopez de Heredia, Luis; Laposata, Michael

2005-09-01

Methanol is a component of certain alcoholic beverages and is also an endogenously formed product. On this basis, we have proposed that methanol may promote synthesis of fatty acid methyl esters (FAMEs) in the same way that ethanol promotes fatty acid ethyl ester (FAEE) synthesis. We tested the hypothesis that FAMEs appear in the blood after ethanol intake. Patient plasma samples obtained from our laboratory (n=78) were grouped according to blood ethanol concentrations (intoxicated, blood ethanol >800 mg/l) and non-intoxicated. These samples were further subdivided into groups based on whether the patient had normal or abnormal liver function tests (abnormal, defined as > or =1 abnormality of plasma alanine and aspartate aminotransferase, albumin, total bilirubin, and alkaline phosphatase). A separate set of plasma samples were also divided into normal and abnormal groups based on pancreatic function tests (amylase and lipase). There were no patients with detectable ethanol in this group. Patients with abnormalities in pancreatic function tests were included upon recognition of endogenously produced FAMEs by patients with liver function test abnormalities. FAMEs were extracted from plasma and individual species of FAMEs quantified by gas chromatography-mass spectrometry (GC/MS). Increased concentrations of FAME were found in patient samples with evidence of liver dysfunction, regardless of whether or not they were intoxicated (n=21, p=0.01). No significant differences in plasma FAME concentrations were found between patients with normal (n=15) versus abnormal pancreatic function tests (n=22, p=0.72). The presence of FAMEs in human plasma may be related to the existence of liver disease, and not to blood ethanol concentrations or pancreatic dysfunction. The metabolic pathways associated with FAME production in patients with impaired liver function remain to be identified.

Stability of bulk Ba2YCu3O(7-x) in a variety of environments

NASA Technical Reports Server (NTRS)

Gaier, James R.; Hepp, Aloysius F.; Curtis, Henry B.; Schupp, Donald A.; Hambourger, Paul D.; Blue, James W.

1988-01-01

Small bars of ceramic Ba2YCu3O(7-x) were fabricated and subjected to environments similar to those that might be encountered during some NASA missions. These conditions include ambient conditions, high humidity, vacuum, and high fluences of electrons and protrons. The normal state resistivity or critical current density (J sub c) were monitored during these tests to assess the stability of the material. When normal state resistivity is used as a criterion, the ambient stability of these samples was relatively good, exhibiting only a 2 percent degradation over a 3 month period. The humidity stability was shown to be very poor, and to be a steep function of temperature. Samples stored at 50 C for 40 min increased in normal state resistivity by four orders of magnitude. Kinetic analysis indicates that the degradation reaction is second order with water vapor concentration. It is suspected that humidity degradation also accounts for the ambient instability. The samples were stable to vacuum over a period of at least 3 months. Degradation of J sub c in a 1 MeV electron fluence of 9.7 x 10 to the 14th e(-)/sq cm was determined to be no more than about 2 percent. Degradation of J sub c in a 8.7 x 10 to the 14th p(+)/sq cm of 42 MeV protons was found to be grain size dependent. Samples with smaller grain size and initial J sub c of about 240 A/sq cm showed no degradation. while that with larger grain size and an initial J sub c of about 30 A/sq cm degraded to 37 percent of its original value.

Differential Contributions of Intrinsic and Extrinsic Pathways to Thrombin Generation in Adult, Maternal and Cord Plasma Samples

PubMed Central

Rice, Nicklaus T.; Szlam, Fania; Varner, Jeffrey D.; Bernstein, Peter S.; Szlam, Arthur D.; Tanaka, Kenichi A.

2016-01-01

Background Thrombin generation (TG) is a pivotal process in achieving hemostasis. Coagulation profiles during pregnancy and early neonatal period are different from that of normal (non-pregnant) adults. In this ex vivo study, the differences in TG in maternal and cord plasma relative to normal adult plasma were studied. Methods Twenty consented pregnant women and ten consented healthy adults were included in the study. Maternal and cord blood samples were collected at the time of delivery. Platelet-poor plasma was isolated for the measurement of TG. In some samples, anti-FIXa aptamer, RB006, or a TFPI inhibitor, BAX499 were added to elucidate the contribution of intrinsic and extrinsic pathway to TG. Additionally, procoagulant and inhibitor levels were measured in maternal and cord plasma, and these values were used to mathematically simulate TG. Results Peak TG was increased in maternal plasma (393.6±57.9 nM) compared to adult and cord samples (323.2±38.9 nM and 209.9±29.5 nM, respectively). Inhibitory effects of RB006 on TG were less robust in maternal or cord plasma (52% vs. 12% respectively) than in adult plasma (81%). Likewise the effectiveness of BAX499 as represented by the increase in peak TG was much greater in adult (21%) than in maternal (10%) or cord plasma (12%). Further, BAX499 was more effective in reversing RB006 in adult plasma than in maternal or cord plasma. Ex vivo data were reproducible with the results of the mathematical simulation of TG. Conclusion Normal parturient plasma shows a large intrinsic pathway reserve for TG compared to adult and cord plasma, while TG in cord plasma is sustained by extrinsic pathway, and low levels of TFPI and AT. PMID:27196067

Measurement of neutrino and antineutrino oscillations by the T2K experiment including a new additional sample of νe interactions at the far detector

NASA Astrophysics Data System (ADS)

Abe, K.; Amey, J.; Andreopoulos, C.; Antonova, M.; Aoki, S.; Ariga, A.; Ashida, Y.; Ban, S.; Barbi, M.; Barker, G. J.; Barr, G.; Barry, C.; Batkiewicz, M.; Berardi, V.; Berkman, S.; Bhadra, S.; Bienstock, S.; Blondel, A.; Bolognesi, S.; Bordoni, S.; Boyd, S. B.; Brailsford, D.; Bravar, A.; Bronner, C.; Buizza Avanzini, M.; Calland, R. G.; Campbell, T.; Cao, S.; Cartwright, S. L.; Catanesi, M. G.; Cervera, A.; Chappell, A.; Checchia, C.; Cherdack, D.; Chikuma, N.; Christodoulou, G.; Coleman, J.; Collazuol, G.; Coplowe, D.; Cudd, A.; Dabrowska, A.; De Rosa, G.; Dealtry, T.; Denner, P. F.; Dennis, S. R.; Densham, C.; Di Lodovico, F.; Dolan, S.; Drapier, O.; Duffy, K. E.; Dumarchez, J.; Dunne, P.; Emery-Schrenk, S.; Ereditato, A.; Feusels, T.; Finch, A. J.; Fiorentini, G. A.; Fiorillo, G.; Friend, M.; Fujii, Y.; Fukuda, D.; Fukuda, Y.; Garcia, A.; Giganti, C.; Gizzarelli, F.; Golan, T.; Gonin, M.; Hadley, D. R.; Haegel, L.; Haigh, J. T.; Hansen, D.; Harada, J.; Hartz, M.; Hasegawa, T.; Hastings, N. C.; Hayashino, T.; Hayato, Y.; Hillairet, A.; Hiraki, T.; Hiramoto, A.; Hirota, S.; Hogan, M.; Holeczek, J.; Hosomi, F.; Huang, K.; Ichikawa, A. K.; Ikeda, M.; Imber, J.; Insler, J.; Intonti, R. A.; Ishida, T.; Ishii, T.; Iwai, E.; Iwamoto, K.; Izmaylov, A.; Jamieson, B.; Jiang, M.; Johnson, S.; Jonsson, P.; Jung, C. K.; Kabirnezhad, M.; Kaboth, A. C.; Kajita, T.; Kakuno, H.; Kameda, J.; Karlen, D.; Katori, T.; Kearns, E.; Khabibullin, M.; Khotjantsev, A.; Kim, H.; Kim, J.; King, S.; Kisiel, J.; Knight, A.; Knox, A.; Kobayashi, T.; Koch, L.; Koga, T.; Koller, P. P.; Konaka, A.; Kormos, L. L.; Koshio, Y.; Kowalik, K.; Kudenko, Y.; Kurjata, R.; Kutter, T.; Lagoda, J.; Lamont, I.; Lamoureux, M.; Lasorak, P.; Laveder, M.; Lawe, M.; Licciardi, M.; Lindner, T.; Liptak, Z. J.; Litchfield, R. P.; Li, X.; Longhin, A.; Lopez, J. P.; Lou, T.; Ludovici, L.; Lu, X.; Magaletti, L.; Mahn, K.; Malek, M.; Manly, S.; Maret, L.; Marino, A. D.; Martin, J. F.; Martins, P.; Martynenko, S.; Maruyama, T.; Matveev, V.; Mavrokoridis, K.; Ma, W. Y.; Mazzucato, E.; McCarthy, M.; McCauley, N.; McFarland, K. S.; McGrew, C.; Mefodiev, A.; Metelko, C.; Mezzetto, M.; Minamino, A.; Mineev, O.; Mine, S.; Missert, A.; Miura, M.; Moriyama, S.; Morrison, J.; Mueller, Th. A.; Nakadaira, T.; Nakahata, M.; Nakamura, K. G.; Nakamura, K.; Nakamura, K. D.; Nakanishi, Y.; Nakayama, S.; Nakaya, T.; Nakayoshi, K.; Nantais, C.; Nielsen, C.; Nishikawa, K.; Nishimura, Y.; Novella, P.; Nowak, J.; O'Keeffe, H. M.; Okumura, K.; Okusawa, T.; Oryszczak, W.; Oser, S. M.; Ovsyannikova, T.; Owen, R. A.; Oyama, Y.; Palladino, V.; Palomino, J. L.; Paolone, V.; Patel, N. D.; Paudyal, P.; Pavin, M.; Payne, D.; Petrov, Y.; Pickering, L.; Pinzon Guerra, E. S.; Pistillo, C.; Popov, B.; Posiadala-Zezula, M.; Poutissou, J.-M.; Pritchard, A.; Przewlocki, P.; Quilain, B.; Radermacher, T.; Radicioni, E.; Ratoff, P. N.; Rayner, M. A.; Reinherz-Aronis, E.; Riccio, C.; Rodrigues, P. A.; Rondio, E.; Rossi, B.; Roth, S.; Ruggeri, A. C.; Rychter, A.; Sakashita, K.; Sánchez, F.; Scantamburlo, E.; Scholberg, K.; Schwehr, J.; Scott, M.; Seiya, Y.; Sekiguchi, T.; Sekiya, H.; Sgalaberna, D.; Shah, R.; Shaikhiev, A.; Shaker, F.; Shaw, D.; Shiozawa, M.; Shirahige, T.; Smy, M.; Sobczyk, J. T.; Sobel, H.; Steinmann, J.; Stewart, T.; Stowell, P.; Suda, Y.; Suvorov, S.; Suzuki, A.; Suzuki, S. Y.; Suzuki, Y.; Tacik, R.; Tada, M.; Takeda, A.; Takeuchi, Y.; Tamura, R.; Tanaka, H. K.; Tanaka, H. A.; Thakore, T.; Thompson, L. F.; Tobayama, S.; Toki, W.; Tomura, T.; Tsukamoto, T.; Tzanov, M.; Vagins, M.; Vallari, Z.; Vasseur, G.; Vilela, C.; Vladisavljevic, T.; Wachala, T.; Walter, C. W.; Wark, D.; Wascko, M. O.; Weber, A.; Wendell, R.; Wilking, M. J.; Wilkinson, C.; Wilson, J. R.; Wilson, R. J.; Wret, C.; Yamada, Y.; Yamamoto, K.; Yanagisawa, C.; Yano, T.; Yen, S.; Yershov, N.; Yokoyama, M.; Yu, M.; Zalewska, A.; Zalipska, J.; Zambelli, L.; Zaremba, K.; Ziembicki, M.; Zimmerman, E. D.; Zito, M.; T2K Collaboration

2017-11-01

The T2K experiment reports an updated analysis of neutrino and antineutrino oscillations in appearance and disappearance channels. A sample of electron neutrino candidates at Super-Kamiokande in which a pion decay has been tagged is added to the four single-ring samples used in previous T2K oscillation analyses. Through combined analyses of these five samples, simultaneous measurements of four oscillation parameters, |Δ m322 |, sin2θ23, sin2θ13, and δCP and of the mass ordering are made. A set of studies of simulated data indicates that the sensitivity to the oscillation parameters is not limited by neutrino interaction model uncertainty. Multiple oscillation analyses are performed, and frequentist and Bayesian intervals are presented for combinations of the oscillation parameters with and without the inclusion of reactor constraints on sin2θ13. When combined with reactor measurements, the hypothesis of C P conservation (δCP=0 or π ) is excluded at 90% confidence level. The 90% confidence region for δCP is [-2.95 ,-0.44 ] ([-1.47 ,-1.27 ] ) for normal (inverted) ordering. The central values and 68% confidence intervals for the other oscillation parameters for normal (inverted) ordering are Δ m322=2.54 ±0.08 (2.51 ±0.08 )×10-3 eV2/c4 and sin2θ23 =0.5 5-0.09+0.05 (0.5 5-0.08+0.05), compatible with maximal mixing. In the Bayesian analysis, the data weakly prefer normal ordering (Bayes factor 3.7) and the upper octant for sin2θ23 (Bayes factor 2.4).

Psychometrics of chronic liver disease questionnaire in Chinese chronic hepatitis B patients.

PubMed

Zhou, Kai-Na; Zhang, Min; Wu, Qian; Ji, Zhen-Hao; Zhang, Xiao-Mei; Zhuang, Gui-Hua

2013-06-14

To evaluate psychometrics of the Chinese (mainland) chronic liver disease questionnaire (CLDQ) in patients with chronic hepatitis B (CHB). A cross-sectional sample of 460 Chinese patients with CHB was selected from the Outpatient Department of the Eighth Hospital of Xi'an, including CHB (CHB without cirrhosis) (n = 323) and CHB-related cirrhosis (n = 137). The psychometrics includes reliability, validity and sensitivity. Internal consistency reliability was measured using Cronbach's α. Convergent and discriminant validity was evaluated by item-scale correlation. Factorial validity was explored by principal component analysis with varimax rotation. Sensitivity was assessed using Cohen's effect size (ES), and independent sample t test between CHB and CHB-related cirrhosis groups and between alanine aminotransferase (ALT) normal and abnormal groups after stratifying the disease (CHB and CHB-related cirrhosis). Internal consistency reliability of the CLDQ was 0.83 (range: 0.65-0.90). Most of the hypothesized item-scale correlations were 0.40 or over, and all of such hypothesized correlations were higher than the alternative ones, indicating satisfactory convergent and discriminant validity. Six factors were extracted after varimax rotation from the 29 items of CLDQ. The eligible Cohen's ES with statistically significant independent sample t test was found in the overall CLDQ and abdominal, systematic, activity scales (CHB vs CHB-related cirrhosis), and in the overall CLDQ and abdominal scale in the stratification of patients with CHB (ALT normal vs abnormal). The CLDQ has acceptable reliability, validity and sensitivity in Chinese (mainland) patients with CHB.

Normalization to specific gravity prior to analysis improves information recovery from high resolution mass spectrometry metabolomic profiles of human urine.

PubMed

Edmands, William M B; Ferrari, Pietro; Scalbert, Augustin

2014-11-04

Extraction of meaningful biological information from urinary metabolomic profiles obtained by liquid-chromatography coupled to mass spectrometry (MS) necessitates the control of unwanted sources of variability associated with large differences in urine sample concentrations. Different methods of normalization either before analysis (preacquisition normalization) through dilution of urine samples to the lowest specific gravity measured by refractometry, or after analysis (postacquisition normalization) to urine volume, specific gravity and median fold change are compared for their capacity to recover lead metabolites for a potential future use as dietary biomarkers. Twenty-four urine samples of 19 subjects from the European Prospective Investigation into Cancer and nutrition (EPIC) cohort were selected based on their high and low/nonconsumption of six polyphenol-rich foods as assessed with a 24 h dietary recall. MS features selected on the basis of minimum discriminant selection criteria were related to each dietary item by means of orthogonal partial least-squares discriminant analysis models. Normalization methods ranked in the following decreasing order when comparing the number of total discriminant MS features recovered to that obtained in the absence of normalization: preacquisition normalization to specific gravity (4.2-fold), postacquisition normalization to specific gravity (2.3-fold), postacquisition median fold change normalization (1.8-fold increase), postacquisition normalization to urinary volume (0.79-fold). A preventative preacquisition normalization based on urine specific gravity was found to be superior to all curative postacquisition normalization methods tested for discovery of MS features discriminant of dietary intake in these urinary metabolomic datasets.

[Cross-sectional study on high-normal blood pressure and chronic kidney disease in occupational physical examination population in Changsha].

PubMed

Cao, Xia; Xie, Xiumei; Xu, Guo; Yuan, Hong; Chen, Zhiheng

2014-06-01

To investigate the relationship between high-normal blood pressure and chronic kidney disease (CKD) in occupational physical examination population in Changsha. With a convenient sampling method, a cross-sectional survey of representative sample of 11 274 white collar workers was conducted in Changsha between March 2011 and May 2011 in a large comprehensive hospital. All subjects were assigned into 4 groups: a normal blood pressure group, a high-normal blood pressure group, an undiagnosed hypertension group, and a diagnosed hypertension group. Anthropometry, blood pressure, blood sample and urine sample were measured with standard instruments and methodology for all the subjects. Multiple logistic regression analysis was used to identify risk factors for CKD. The prevalence of CKD in the normal blood pressure, high-normal blood pressure, undiagnosed hypertension, and diagnosed hypertension were 3.31%, 6.60%, 11.78%, and 17.35%, respectively. The prevalence of CKD in males was significantly higher than that in females (P<0.01). For males with high-normal blood pressure, the CKD risk was significantly greater (OR, 1.30; 95% CI:1.03 - 1.63) than those with optimal blood pressure. The logistic regression analysis showed that there was an additive effect of hyperuricemia on CKD risk in men with high-normal blood pressure compared with men with optimal blood pressure (OR, 2.25; 95% CI, 1.59 - 3.19; P<0.05). The prevalence of CKD in people with the high-normal blood pressure is 6.60% in occupational physical examination population in Changsha. CKD is a high risk for men with highnormal blood pressure and hyperuricemia is an independent risk factor.

A survey of the concentrations of eleven metals in vaccines, allergenic extracts, toxoids, blood, blood derivatives and other biological products.

PubMed

May, J C; Rains, T C; Maienthal, F J; Biddle, G N; Progar, J J

1986-10-01

Approximately 85 samples of injectable biological products regulated by the Center for Drugs and Biologics of the United States Food and Drug Administration were surveyed for the presence of 11 elements, namely aluminum, arsenic, barium, cadmium, chromium, lead, mercury, selenium, thallium and zinc, by flame and flameless methods of atomic absorption spectrometry and flame emission spectrometry. The range of products tested included whole blood, red cells, plasma, normal serum albumin, antihemophilic factor, and other products derived from blood; allergenic extracts including honey bee venom and house dust allergenic extracts; vaccines such as measles virus vaccine and typhoid vaccine; and tetanus toxoid. The metal concentrations found in the majority of these products were low or undetectable. The metal levels varied from manufacturer to manufacturer, product and lot-to-lot of the same manufacturer's products. House dust allergenic extracts had the highest concentrations of arsenic (2.4 ppm), cadmium (0.28 ppm), chromium (0.6 ppm) and lead (1.5 ppm) found in the study. A high zinc concentration (24 ppm) in an immune serum globulin was attributed to the zinc-containing rubber stopper in contact with the product. A range of 0.36-3.30 ppm aluminum was found for seven 25% normal serum albumin samples from seven manufacturers. Values of 8.2, 17 and 18 ppm aluminum were found in one manufacturer's 25% normal serum albumin. These aluminum values appeared to be the result of an anomaly in this manufacturer's production that has not been repeated to date.

A NASTRAN primer for the analysis of rotating flexible blades

NASA Technical Reports Server (NTRS)

Lawrence, Charles; Aiello, Robert A.; Ernst, Michael A.; Mcgee, Oliver G.

1987-01-01

This primer provides documentation for using MSC NASTRAN in analyzing rotating flexible blades. The analysis of these blades includes geometrically nonlinear (large displacement) analysis under centrifugal loading, and frequency and mode shape (normal modes) determination. The geometrically nonlinear analysis using NASTRAN Solution sequence 64 is discussed along with the determination of frequencies and mode shapes using Solution Sequence 63. A sample problem with the complete NASTRAN input data is included. Items unique to rotating blade analyses, such as setting angle and centrifugal softening effects are emphasized.

Characterization of airborne particles in an open pit mining region.

PubMed

Huertas, José I; Huertas, María E; Solís, Dora A

2012-04-15

We characterized airborne particle samples collected from 15 stations in operation since 2007 in one of the world's largest opencast coal mining regions. Using gravimetric, scanning electron microscopy (SEM-EDS), and X-ray photoelectron spectroscopy (XPS) analysis the samples were characterized in terms of concentration, morphology, particle size distribution (PSD), and elemental composition. All of the total suspended particulate (TSP) samples exhibited a log-normal PSD with a mean of d=5.46 ± 0.32 μm and σ(ln d)=0.61 ± 0.03. Similarly, all particles with an equivalent aerodynamic diameter less than 10 μm (PM(10)) exhibited a log-normal type distribution with a mean of d=3.6 ± 0.38 μm and σ(ln d)=0.55 ± 0.03. XPS analysis indicated that the main elements present in the particles were carbon, oxygen, potassium, and silicon with average mass concentrations of 41.5%, 34.7%, 11.6%, and 5.7% respectively. In SEM micrographs the particles appeared smooth-surfaced and irregular in shape, and tended to agglomerate. The particles were typically clay minerals, including limestone, calcite, quartz, and potassium feldspar. Copyright © 2012 Elsevier B.V. All rights reserved.

Pattern of somatostatin receptors expression in normal and bladder cancer tissue samples.

PubMed

Karavitakis, Markos; Msaouel, Pavlos; Michalopoulos, Vassilis; Koutsilieris, Michael

2014-06-01

Known risks factors for bladder cancer progression and recurrence are limited regarding their prognostic ability. Therefore identification of molecular determinants of disease progression could provide with more specific prognostic information and could be translated into new approaches for biomarker development. In the present study we evaluated, the expression patterns of somatostatin receptors 1-5 (SSTRs) in normal and tumor bladder tissues. The expression of SSTR1-5 was characterized in 45 normal and bladder cancer tissue samples using reverse transcriptase-polymerase chain reaction (RT-PCR). SSTR1 was expressed in 24 samples, SSTR2 in 15, SSTR3 in 23, SSTR4 in 16 and SSTR5 in all but one sample. Bladder cancer tissue samples expressed lower levels of SSTR3. Co-expression of SSTRs was associated with superficial disease. Our results demonstrate, for the first time, that there is expression of SSTR in normal and bladder cancer urothelium. Further studies are required to evaluate the prognostic and therapeutic significance of these findings. Copyright© 2014 International Institute of Anticancer Research (Dr. John G. Delinassios), All rights reserved.

Creatinine as a normalization factor to estimate the representativeness of urine sample - Intra-subject and inter-subject variability studies.

PubMed

Sawant, Pramilla D; Kumar, Suja Arun; Wankhede, Sonal; Rao, D D

2018-06-01

In-vitro bioassay monitoring generally involves analysis of overnight urine samples (~12 h) collected from radiation workers to estimate the excretion rate of radionuclides from the body. The unknown duration of sample collection (10-16 h) adds to the overall uncertainty in computation of internal dose. In order to minimize this, IAEA recommends measurement of specific gravity or creatinine excretion rate in urine. Creatinine is excreted at a steady rate with normally functioning kidneys therefore, can be used as a normalization factor to infer the duration of collection and/or dilution of the sample, if any. The present study reports the chemical procedure standardized and its application for the estimation of creatinine as well as creatinine co-efficient in normal healthy individuals. Observations indicate higher inter-subject variability and lower constancy in daily excretion of creatinine for the same subject. Thus creatinine excretion rate may not be a useful indicator for extrapolating to 24 h sample collection. Copyright © 2018 Elsevier Ltd. All rights reserved.

Primary cilia are increased in number and demonstrate structural abnormalities in human cancer.

PubMed

Yasar, Binnaz; Linton, Kim; Slater, Christian; Byers, Richard

2017-07-01

Primary cilia play an important role in the regulation of cell signalling pathways and are thought to have a role in cancer but have seldom been studied in human cancer samples. Primary cilia were visualised by dual immunofluorescence for anti-CROCC (ciliary rootlet coiled-coil) and anti-tubulin in a range of human cancers (including carcinomas of stomach, pancreas, prostate, lung and colon, lobular and ductal breast cancers and follicular lymphoma) and in matched normal tissue (stomach, pancreas, lung, large and small intestines, breast and reactive lymph nodes) samples using a tissue microarray; their frequency, association with proliferation, was measured by Ki-67 staining and their structure was analysed. Compared with normal tissues, primary cilia frequency was significantly elevated in adenocarcinoma of the lung (2.75% vs 1.85%, p=0.016), adenocarcinoma of the colon (3.80% vs 2.43%, respectively, p=0.017), follicular lymphoma (1.18% vs 0.83%, p=0.003) and pancreatic adenocarcinoma (7.00% vs 5.26%, p=0.002); there was no statistically significant difference compared with normal control tissue for gastric and prostatic adenocarcinomas or for lobular and ductal breast cancers. Additionally, structural abnormalities of primary cilia were identified in cancer tissues, including elongation of the axoneme, multiple basal bodies and branching of the axoneme. Ki-67 scores ranged from 0.7% to 78.4% and showed no statistically significant correlation with primary cilia frequency across all tissues (p=0.1501). The results show upregulation of primary cilia and the presence of structural defects in a wide range of human cancer tissue samples demonstrating association of dysregulation of primary cilia with human cancer. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

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.

Detection of human papillomavirus and Epstein-Barr virus DNA sequences in oral mucosa of HIV-infected patients by the polymerase chain reaction.

PubMed Central

Snijders, P. J.; Schulten, E. A.; Mullink, H.; ten Kate, R. W.; Jiwa, M.; van der Waal, I.; Meijer, C. J.; Walboomers, J. M.

1990-01-01

The presence of human papillomavirus (HPV) and Epstein-Barr virus (EBV) was analyzed in 21 oral biopsy specimens of HIV-infected patients using the polymerase chain reaction (PCR) method. Biopsies were categorized as hairy leukoplakia (HL) (n = 12), candidiasis (n = 3), oral warts (n = 2), and clinically normal epithelium (n = 4). For HPV detection a modified general primer-mediated PCR method (GP-PCR), which detects a broad spectrum of HPV genotypes at sub-picogram levels, was used. Human papillomavirus DNA was only found in two oral warts and was identified as HPV type 32. Epstein-Barr virus DNA was detected in 16 biopsy specimens, including the 12 HLs, 2 cases of candidiasis, and 2 samples of normal epithelium. Epstein-Barr virus positivity in HL could be confirmed by Southern blot analysis and DNA in situ hybridization using biotinylated DNA probes (bio-DISH). Epstein-Barr virus bio-DISH was also positive in one sample of normal epithelium from a patient with HL. The results indicate that HL is strongly associated with EBV and not with any of the common HPV types that react with general HPV primers in the PCR. However the detection of EBV in normal oral epithelium by PCR and bio-DISH suggests that the presence of this virus is not exclusively related to HL. Images Figure 1 Figure 2 Figure 3 Figure 4 PMID:2169191

Positron Spectroscopy Investigation of Normal Brain Section and Brain Section with Glioma Derived from a Rat Glioma Model

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

Yang, SH.; Ballmann, C.; Quarles, C. A.

2009-03-10

The application of positron annihilation lifetime spectroscopy (PALS) and Doppler broadening spectroscopy (DBS) to the study of animal or human tissue has only recently been reported [G. Liu, et al. phys. stat. sol. (C) 4, Nos. 10, 3912-3915 (2007)]. We have initiated a study of normal brain section and brain section with glioma derived from a rat glioma model. For the rat glioma model, 200,000 C6 cells were implanted in the basal ganglion of adult Sprague Dawley rats. The rats were sacrificed at 21 days after implantation. The brains were harvested, sliced into 2 mm thick coronal sections, and fixedmore » in 4% formalin. PALS lifetime runs were made with the samples soaked in formalin, and there was not significant evaporation of formalin during the runs. The lifetime spectra were analyzed into two lifetime components. While early results suggested a small decrease in ortho-Positronium (o-Ps) pickoff lifetime between the normal brain section and brain section with glioma, further runs with additional samples have showed no statistically significant difference between the normal and tumor tissue for this type of tumor. The o-Ps lifetime in formalin alone was lower than either the normal tissue or glioma sample. So annihilation in the formalin absorbed in the samples would lower the o-Ps lifetime and this may have masked any difference due to the glioma itself. DBS was also used to investigate the difference in positronium formation between tumor and normal tissue. Tissue samples are heterogeneous and this needs to be carefully considered if PALS and DBS are to become useful tools in distinguishing tissue samples.« less

Strain partitioning and deformation mode analysis of the normal faults at Red Mountain, Birmingham, Alabama

NASA Astrophysics Data System (ADS)

Wu, Schuman

1989-12-01

In a low-temperature environment, the thin-section scale rock-deformation mode is primarily a function of confining pressure and total strain at geological strain rates. A deformation mode diagram is constructed from published experimental data by plotting the deformation mode on a graph of total strain versus the confining pressure. Four deformation modes are shown on the diagram: extensional fracturing, mesoscopic faulting, incipient faulting, and uniform flow. By determining the total strain and the deformation mode of a naturally deformed sample, the confining pressure and hence the depth at which the rock was deformed can be evaluated. The method is applied to normal faults exposed on the gently dipping southeast limb of the Birmingham anticlinorium in the Red Mountain expressway cut in Birmingham, Alabama. Samples of the Ordovician Chickamauga Limestone within and adjacent to the faults contain brittle structures, including mesoscopic faults and veins, and ductile deformation features including calcite twins, intergranular and transgranular pressure solution, and deformed burrows. During compaction, a vertical shortening of about 45 to 80% in shale is indicated by deformed burrows and relative compaction of shale to burrows, about 6% in limestone by stylolites. The normal faults formed after the Ordovician rocks were consolidated because the faults and associated veins truncate the deformed burrows and stylolites, which truncate the calcite cement. A total strain of 2.0% was caused by mesoscopic faults during normal faulting. A later homogenous deformation, indicated by the calcite twins in veins, cement and fossil fragments, has its major principal shortening strain in the dip direction at a low angle (about 22°) to bedding. The strain magnitude is about 2.6%. By locating the observed data on the deformation mode diagram, it is found that the normal faulting characterized by brittle deformation occurred under low confining pressure (< 18 MPa) at shallow depth (< 800 m), and the homogenous horizontal compression characterized by uniform flow occurred under higher confining pressure (at least 60 MPa) at greater depth (> 2.5 km).

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.

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.

Correlation between Na/K ratio and electron densities in blood samples of breast cancer patients.

PubMed

Topdağı, Ömer; Toker, Ozan; Bakırdere, Sezgin; Bursalıoğlu, Ertuğrul Osman; Öz, Ersoy; Eyecioğlu, Önder; Demir, Mustafa; İçelli, Orhan

2018-05-31

The main purpose of this study was to investigate the relationship between the electron densities and Na/K ratio which has important role in breast cancer disease. Determinations of sodium and potassium concentrations in blood samples performed with inductive coupled plasma-atomic emission spectrometry. Electron density values of blood samples were determined via ZXCOM. Statistical analyses were performed for electron densities and Na/K ratio including Kolmogorov-Smirnov normality tests, Spearman's rank correlation test and Mann-Whitney U test. It was found that the electron densities significantly differ between control and breast cancer groups. In addition, statistically significant positive correlation was found between the electron density and Na/K ratios in breast cancer group.

The impact of obesity on specific airway resistance and conductance among schoolchildren.

PubMed

Parraguez Arévalo, Andrea; Rojas Navarro, Francisco; Ruz Céspedes, Macarena; Medina González, Paul; Escobar Cabello, Máximo; Muñoz Cofré, Rodrigo

2018-04-01

Child and adolescent obesity is an epidemiological problem in developing countries. Its prevalence among preschoolers and schoolchildren is over 30%. It has been associated with a wide range of health complications, including rapid loss of lung function leading to changes in physiology and ventilatory mechanics. The objective of this study was to analyze the association between obesity and the increase in specific airway resistance (sRaw) in a sample of obese children and adolescents from the district of Talca. In a sample of 36 subjects with an average age of 9.38 ± 1.99 years, divided into 2 groups (normal weight and obese), the tricipital, subscapular, and abdominal skinfolds and lung volumes were measured. For the statistical analysis, data normality was determined and then the Student's t test or the Mann-Whitney U test and Pearson's or Spearman's correlations were used, as applicable. A value of p < 0.05 was considered statistically significant. When comparing normal weight and obese subjects, a significant increase in sRaw and a significant reduction in specific airway conductance (sGaw) were observed in obese subjects. In addition, an adequate and significant correlation was observed between sRaw and fat percentage. Obese subjects showed an increased sRaw and a reduced sGaw. Sociedad Argentina de Pediatría.

Pilot Study: The Role of the Hemispheric Lateralization in Mental Disorders by Use of the Limb (Eye, Hand, Foot) Dominance.

PubMed

Goodarzi, Naser; Dabbaghi, Parviz; Valipour, Habib; Vafadari, Behnam

2015-04-01

Based on the previous studies, we know that the hemispheric lateralization defects, increase the probability of psychological disorders. We also know that dominant limb is controlled by dominant hemisphere and limb preference is used as an indicator for hemisphere dominance. In this study we attempted to explore the hemispheric dominance by the use of three limbs (hand, foot and eye). We performed this survey on two samples, psychiatric patients compared with normal population. For this purpose, knowing that the organ dominance is stabilized in adolescence, and age has no effect on the people above 15, we used 48 high school girls and 65 boys as the final samples of normal population. The patient group included 57 male and 26 female who were chronic psychiatric patients. The result shows that left-eye dominance is more in patients than the normal group (P=0.000) but the handedness and footedness differences are not significance. In psychotic, bipolar and depressive disorders, eye dominance had significant difference (P=0.018). But this is not true about hand and foot dominance. Our findings proved that generally in psychiatric patients, left-eye dominance is more common, left-eye dominance is also more in psychotic and depressive disorders. It is less common in bipolar disorders.

Dye-enhanced multimodal confocal imaging as a novel approach to intraoperative diagnosis of brain tumors.

PubMed

Snuderl, Matija; Wirth, Dennis; Sheth, Sameer A; Bourne, Sarah K; Kwon, Churl-Su; Ancukiewicz, Marek; Curry, William T; Frosch, Matthew P; Yaroslavsky, Anna N

2013-01-01

Intraoperative diagnosis plays an important role in accurate sampling of brain tumors, limiting the number of biopsies required and improving the distinction between brain and tumor. The goal of this study was to evaluate dye-enhanced multimodal confocal imaging for discriminating gliomas from nonglial brain tumors and from normal brain tissue for diagnostic use. We investigated a total of 37 samples including glioma (13), meningioma (7), metastatic tumors (9) and normal brain removed for nontumoral indications (8). Tissue was stained in 0.05 mg/mL aqueous solution of methylene blue (MB) for 2-5 minutes and multimodal confocal images were acquired using a custom-built microscope. After imaging, tissue was formalin fixed and paraffin embedded for standard neuropathologic evaluation. Thirteen pathologists provided diagnoses based on the multimodal confocal images. The investigated tumor types exhibited distinctive and complimentary characteristics in both the reflectance and fluorescence responses. Images showed distinct morphological features similar to standard histology. Pathologists were able to distinguish gliomas from normal brain tissue and nonglial brain tumors, and to render diagnoses from the images in a manner comparable to haematoxylin and eosin (H&E) slides. These results confirm the feasibility of multimodal confocal imaging for intravital intraoperative diagnosis. © 2012 The Authors; Brain Pathology © 2012 International Society of Neuropathology.

Bioimaging of metals in brain tissue by laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) and metallomics.

PubMed

Becker, J Sabine; Matusch, Andreas; Palm, Christoph; Salber, Dagmar; Morton, Kathryn A; Becker, J Susanne

2010-02-01

Laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) has been developed and established as an emerging technique in the generation of quantitative images of metal distributions in thin tissue sections of brain samples (such as human, rat and mouse brain), with applications in research related to neurodegenerative disorders. A new analytical protocol is described which includes sample preparation by cryo-cutting of thin tissue sections and matrix-matched laboratory standards, mass spectrometric measurements, data acquisition, and quantitative analysis. Specific examples of the bioimaging of metal distributions in normal rodent brains are provided. Differences to the normal were assessed in a Parkinson's disease and a stroke brain model. Furthermore, changes during normal aging were studied. Powerful analytical techniques are also required for the determination and characterization of metal-containing proteins within a large pool of proteins, e.g., after denaturing or non-denaturing electrophoretic separation of proteins in one-dimensional and two-dimensional gels. LA-ICP-MS can be employed to detect metalloproteins in protein bands or spots separated after gel electrophoresis. MALDI-MS can then be used to identify specific metal-containing proteins in these bands or spots. The combination of these techniques is described in the second section.

YALE NATURAL RADIOCARBON MEASUREMENTS. PART VI

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

Stuiver, M.; Deevey, E.S.

1961-01-01

Most of the measurements made since publication of Yale V are included; some measurements, such as a series collected in Greenland, are withneld pending additional information or field work that will make better interpretations possible. In addition to radiocarbon dates of geologic and/or archaeologic interest, recent assays are given of C/sup 14/ in lake waters and other lacustrine materials, now normalized for C/sup 13/ content. The newly accepted convention is followed in expressing normalized C/sup 14/ values as DELTA = delta C/sup 14/ (2 delta C/sup 13/ + 50)STAl + ( delta C/sup 14//1000)! where DELTA is the per milmore » deviation of the C/sup 14/ if the sample from any contemporary standard (whether organic or a carbonate) after correction of sample and/or standard for real age, for the Suess effect, for normal isotopic fractionation, and for deviations of C/sup 14/ content of the age- and pollution- corrected l9th-century wood standard from that of 95% of the NBS oxalic acid standard; delta C/sup 14/ is the measured deviation from 95% of the NBS standard, and delta C/sup 13/ is the deviation from the NBS limestone standard, both in per mil. These assays are variously affected by artificial C/sup 14/ resulting from nuclear tests. (auth)« less

Development of algorithms for detecting citrus canker based on hyperspectral reflectance imaging.

PubMed

Li, Jiangbo; Rao, Xiuqin; Ying, Yibin

2012-01-15

Automated discrimination of fruits with canker from other fruit with normal surface and different type of peel defects has become a helpful task to enhance the competitiveness and profitability of the citrus industry. Over the last several years, hyperspectral imaging technology has received increasing attention in the agricultural products inspection field. This paper studied the feasibility of classification of citrus canker from other peel conditions including normal surface and nine peel defects by hyperspectal imaging. A combination algorithm based on principal component analysis and the two-band ratio (Q(687/630)) method was proposed. Since fewer wavelengths were desired in order to develop a rapid multispectral imaging system, the canker classification performance of the two-band ratio (Q(687/630)) method alone was also evaluated. The proposed combination approach and two-band ratio method alone resulted in overall classification accuracy for training set samples and test set samples of 99.5%, 84.5% and 98.2%, 82.9%, respectively. The proposed combination approach was more efficient for classifying canker against various conditions under reflectance hyperspectral imagery. However, the two-band ratio (Q(687/630)) method alone also demonstrated effectiveness in discriminating citrus canker from normal fruit and other peel diseases except for copper burn and anthracnose. Copyright © 2011 Society of Chemical Industry.

Frictional properties of low-angle normal fault gouges and implications for low-angle normal fault slip

NASA Astrophysics Data System (ADS)

Haines, Samuel; Marone, Chris; Saffer, Demian

2014-12-01

The mechanics of slip on low-angle normal faults (LANFs) remain an enduring problem in structural geology and fault mechanics. In most cases, new faults should form rather than having slip occur on LANFs, assuming values of fault friction consistent with Byerlee's Law. We present results of laboratory measurements on the frictional properties of natural clay-rich gouges from low-angle normal faults (LANF) in the American Cordillera, from the Whipple Mts. Detachment, the Panamint range-front detachment, and the Waterman Hills detachment. These clay-rich gouges are dominated by neoformed clay minerals and are an integral part of fault zones in many LANFs, yet their frictional properties under in situ conditions remain relatively unknown. We conducted measurements under saturated and controlled pore pressure conditions at effective normal stresses ranging from 20 to 60 MPa (corresponding to depths of 0.9-2.9 km), on both powdered and intact wafers of fault rock. For the Whipple Mountains detachment, friction coefficient (μ) varies depending on clast content, with values ranging from 0.40 to 0.58 for clast-rich material, and 0.29-0.30 for clay-rich gouge. Samples from the Panamint range-front detachment were clay-rich, and exhibit friction values of 0.28 to 0.38, significantly lower than reported from previous studies on fault gouges tested under room humidity (nominally dry) conditions, including samples from the same exposure. Samples from the Waterman Hills detachment are slightly stronger, with μ ranging from 0.38 to 0.43. The neoformed gouge materials from all three localities exhibits velocity-strengthening frictional behavior under almost all of the experimental conditions we explored, with values of the friction rate parameter (a - b) ranging from -0.001 to +0.025. Clast-rich samples exhibited frictional healing (strength increases with hold time), whereas clay-rich samples do not. Our results indicate that where clay-rich neoformed gouges are present along LANFs, they provide a mechanically viable explanation for slip on faults with dips <20°, requiring only moderate (Pf <σ3) overpressures and/or correcting for ∼5° of footwall tilting. Furthermore, the low rates of frictional strength recovery and velocity-strengthening frictional behavior we observe provide an explanation for the lack of observed seismicity on these structures. We suggest that LANFs in the upper crust (depth <8 km) slip via a combination of a) reaction-weakening of initially high-angle fault zones by the formation of neoformed clay-rich gouges, and b) regional tectonic accommodation of rotating fault blocks.

High wavenumber Raman spectroscopy in the characterization of urinary metabolites of normal subjects, oral premalignant and malignant patients

NASA Astrophysics Data System (ADS)

Brindha, Elumalai; Rajasekaran, Ramu; Aruna, Prakasarao; Koteeswaran, Dornadula; Ganesan, Singaravelu

2017-01-01

Urine has emerged as one of the diagnostically potential bio fluids, as it has many metabolites. As the concentration and the physiochemical properties of the urinary metabolites may vary under pathological transformation, Raman spectroscopic characterization of urine has been exploited as a significant tool in identifying several diseased conditions, including cancers. In the present study, an attempt was made to study the high wavenumber (HWVN) Raman spectroscopic characterization of urine samples of normal subjects, oral premalignant and malignant patients. It is concluded that the urinary metabolites flavoproteins, tryptophan and phenylalanine are responsible for the observed spectral variations between the normal and abnormal groups. Principal component analysis-based linear discriminant analysis was carried out to verify the diagnostic potentiality of the present technique. The discriminant analysis performed across normal and oral premalignant subjects classifies 95.6% of the original and 94.9% of the cross-validated grouped cases correctly. In the second analysis performed across normal and oral malignant groups, the accuracy of the original and cross-validated grouped cases was 96.4% and 92.1% respectively. Similarly, the third analysis performed across three groups, normal, oral premalignant and malignant groups, classifies 93.3% and 91.2% of the original and cross-validated grouped cases correctly.

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.

DNA methylation markers for diagnosis and prognosis of common cancers

PubMed Central

Hao, Xiaoke; Luo, Huiyan; Krawczyk, Michal; Wei, Wei; Wang, Wenqiu; Wang, Juan; Flagg, Ken; Hou, Jiayi; Zhang, Heng; Yi, Shaohua; Jafari, Maryam; Lin, Danni; Chung, Christopher; Caughey, Bennett A.; Li, Gen; Dhar, Debanjan; Shi, William; Zheng, Lianghong; Hou, Rui; Zhu, Jie; Zhao, Liang; Fu, Xin; Zhang, Edward; Zhang, Charlotte; Zhu, Jian-Kang; Karin, Michael; Xu, Rui-Hua; Zhang, Kang

2017-01-01

The ability to identify a specific cancer using minimally invasive biopsy holds great promise for improving the diagnosis, treatment selection, and prediction of prognosis in cancer. Using whole-genome methylation data from The Cancer Genome Atlas (TCGA) and machine learning methods, we evaluated the utility of DNA methylation for differentiating tumor tissue and normal tissue for four common cancers (breast, colon, liver, and lung). We identified cancer markers in a training cohort of 1,619 tumor samples and 173 matched adjacent normal tissue samples. We replicated our findings in a separate TCGA cohort of 791 tumor samples and 93 matched adjacent normal tissue samples, as well as an independent Chinese cohort of 394 tumor samples and 324 matched adjacent normal tissue samples. The DNA methylation analysis could predict cancer versus normal tissue with more than 95% accuracy in these three cohorts, demonstrating accuracy comparable to typical diagnostic methods. This analysis also correctly identified 29 of 30 colorectal cancer metastases to the liver and 32 of 34 colorectal cancer metastases to the lung. We also found that methylation patterns can predict prognosis and survival. We correlated differential methylation of CpG sites predictive of cancer with expression of associated genes known to be important in cancer biology, showing decreased expression with increased methylation, as expected. We verified gene expression profiles in a mouse model of hepatocellular carcinoma. Taken together, these findings demonstrate the utility of methylation biomarkers for the molecular characterization of cancer, with implications for diagnosis and prognosis. PMID:28652331

A Monte Carlo Study of Levene's Test of Homogeneity of Variance: Empirical Frequencies of Type I Error in Normal Distributions.

ERIC Educational Resources Information Center

Neel, John H.; Stallings, William M.

An influential statistics test recommends a Levene text for homogeneity of variance. A recent note suggests that Levene's test is upwardly biased for small samples. Another report shows inflated Alpha estimates and low power. Neither study utilized more than two sample sizes. This Monte Carlo study involved sampling from a normal population for…

Multivariate normality

NASA Technical Reports Server (NTRS)

Crutcher, H. L.; Falls, L. W.

1976-01-01

Sets of experimentally determined or routinely observed data provide information about the past, present and, hopefully, future sets of similarly produced data. An infinite set of statistical models exists which may be used to describe the data sets. The normal distribution is one model. If it serves at all, it serves well. If a data set, or a transformation of the set, representative of a larger population can be described by the normal distribution, then valid statistical inferences can be drawn. There are several tests which may be applied to a data set to determine whether the univariate normal model adequately describes the set. The chi-square test based on Pearson's work in the late nineteenth and early twentieth centuries is often used. Like all tests, it has some weaknesses which are discussed in elementary texts. Extension of the chi-square test to the multivariate normal model is provided. Tables and graphs permit easier application of the test in the higher dimensions. Several examples, using recorded data, illustrate the procedures. Tests of maximum absolute differences, mean sum of squares of residuals, runs and changes of sign are included in these tests. Dimensions one through five with selected sample sizes 11 to 101 are used to illustrate the statistical tests developed.

Alterable Magnetic Gratings for Fiber Optic Switching.

DTIC Science & Technology

1982-12-01

monotonically decreasing function as X moves into the infrared from the visible. The Faraday rotation of bismuth garnet samples including the new large... photodector giving as fast a response as possible while still providing usable signal levels, measure the detector response * using the electro-optic...icity. Normally a stripe domain array is configured as a linear grating. In-plane magnetic fields can rotate the grating as well as alter the periodicity

[The Amsterdam Dementia Screening Test in cognitively healthy and clinical samples. An update of normative data].

PubMed

van Toutert, Meta; Diesfeldt, Han; Hoek, Dirk

2016-10-01

The six tests in the Amsterdam Dementia Screening Test (ADST) examine the cognitive domains of episodic memory (delayed picture recognition, word learning), orientation, category fluency (animals and occupations), constructional ability (figure copying) and executive function (alternating sequences). New normative data were collected in a sample of 102 elderly volunteers (aged 65-94), including subjects with medical or other health conditions, except dementia or frank cognitive impairment (MMSE > 24). Included subjects were independent in complex instrumental activities of daily living.Fluency, not the other tests, needed adjustment for age and education. A deficit score (0-1) was computed for each test. Summation (range 0-6) proved useful in differentiating patients with dementia (N = 741) from normal elderly (N = 102).Positive and negative predictive power across a range of summed deficit scores and base rates are displayed in Bayesian probability tables.In the normal elderly, delayed recall for eight words was tested and adjusted for initial recall. A recognition test mixed the target words with eight distractors. Delayed recognition was adjusted for immediate and delayed recall.The ADST and the normative data in this paper help the clinical neuropsychologist to make decisions concerning the presence or absence of neurocognitive disorder in individual elderly examinees.

Physio-chemical reactions in recycle aggregate concrete.

PubMed

Tam, Vivian W Y; Gao, X F; Tam, C M; Ng, K M

2009-04-30

Concrete waste constitutes the major proportion of construction waste at about 50% of the total waste generated. An effective way to reduce concrete waste is to reuse it as recycled aggregate (RA) for the production of recycled aggregate concrete (RAC). This paper studies the physio-chemical reactions of cement paste around aggregate for normal aggregate concrete (NAC) and RAC mixed with normal mixing approach (NMA) and two-stage mixing approach (TSMA) by differential scanning calorimetry (DSC) and scanning electron microscopy (SEM). Four kinds of physio-chemical reactions have been recorded from the concrete samples, including the dehydration of C(3)S(2)H(3), iron-substituted ettringite, dehydroxylation of CH and development of C(6)S(3)H at about 90 degrees C, 135 degrees C, 441 degrees C and 570 degrees C, respectively. From the DSC results, it is confirmed that the concrete samples with RA substitution have generated less amount of strength enhancement chemical products when compared to those without RA substitution. However, the results from the TSMA are found improving the RAC quality. The pre-mix procedure of the TSMA can effectively develop some strength enhancing chemical products including, C(3)S(2)H(3), ettringite, CH and C(6)S(3)H, which shows that RAC made from the TSMA can improve the hydration processes.

Siderophile-element Anomalies in CK Carbonaceous Chondrites: Implications for Parent-body Aqueous Alteration and Terrestrial Weathering of Sulfides

NASA Technical Reports Server (NTRS)

Huber, Heinz; Rubin, Alan E.; Kallemeyn, Gregory W.; Wasson, John T.

2006-01-01

CK chondrites constitute the most oxidized anhydrous carbonaceous chondrite group; most of the Fe occurs in magnetite and in FeO-rich mafic silicates. The two observed CK falls (Karoonda and Kobe), along with thirteen relatively unweathered CK finds, have unfractionated siderophile-element abundance patterns. In contrast, a sizable fraction of CK finds (9 of 24 investigated) shows fractionated siderophile abundance patterns including low abundances of Ni, Co, Se and Au; the most extreme depletions are in Ni (0.24 of normal CK) and Au (0.14 of normal CK). This depletion pattern has not been found in other chondrite groups. Out of the 74 CK chondrites listed in the Meteoritical Bulletin Database (2006; excluded considerably paired specimens; see http://tin.er.usgs.gov/meteor/ metbull.php) we analyzed 24 and subclassified the CK chondrites in terms of their chemical composition and sulfide mineralogy: sL (siderophiles low; six samples) for large depletions in Ni, Co, Se and Au (>50% of sulfides lost); sM (siderophiles medium; two CKs) for moderately low Ni and Co abundances (sulfides are highly altered or partly lost); sH (siderophiles high; one specimen) for enrichments in Ni, Co, Se and Au; 'normal' for unfractionated samples (13 samples). The sole sH sample may have obtained additional sulfide from impact redistribution in the parent asteroid. We infer that these elements became incorporated into sulfides after asteroidal aqueous processes oxidized nebular metal; thermal metamorphism probably also played a role in their mineral siting. The siderophile losses in the SL and sM samples are mainly the result of oxidation of pentlandite, pyrite and violarite by terrestrial alteration followed by leaching of the resulting phases. Some Antarctic CK chondrites have lost most of their sulfides but retained Ni, Co, Se and Au, presumably as insoluble weathering products.

Metabolic phenotype and risk of colorectal cancer in normal-weight postmenopausal women

PubMed Central

Liang, Xiaoyun; Margolis, Karen L.; Hendryx, Michael; Rohan, Thomas; Groessl, Erik J.; Thomson, Cynthia A.; Kroenke, Candyce H.; Simon, Michael; Lane, Dorothy; Stefanick, Marcia; Luo, Juhua

2016-01-01

Background The prevalence of metabolically unhealthy phenotype in normal-weight adults is 30%, and few studies have explored the association between metabolic phenotype and colorectal cancer incidence in normal-weight individuals. Our aim was to compare the risk of colorectal cancer in normal-weight postmenopausal women who were characterized by either the metabolically healthy phenotype or the metabolically unhealthy phenotype. Methods A large prospective cohort, the Women’s Health Initiative (WHI), was used. The analytical sample included 5,068 postmenopausal women with BMI 18.5–<25 kg/m2. Metabolic phenotype was defined using the Adult Treatment Panel-III (ATP-III) definition, excluding waist circumference; therefore, women with one or none of the four components (elevated triglycerides, low HDL-C, elevated blood pressure, and elevated fasting glucose) were classified as metabolically healthy. Multivariable Cox proportional hazards regression was used to estimate adjusted hazard ratios for the association between metabolic phenotype and risk of colorectal cancer. Results Among normal-weight women, those who were metabolically unhealthy had higher risks of colorectal cancer (HR: 1.49, 95% CI: 1.02–2.18) compared to those who were metabolically healthy. Conclusions A metabolically unhealthy phenotype was associated with higher risk of colorectal cancer among normal-weight women. Impact Normal-weight women should still be evaluated for metabolic health and appropriate steps taken to reduce their risk of colorectal cancer. PMID:28148595

Impact of dietary fiber fermentation from cereal grains on metabolite production by the fecal microbiota from normal weight and obese individuals.

PubMed

Yang, Junyi; Keshavarzian, Ali; Rose, Devin J

2013-09-01

Gut bacteria may influence obesity through the metabolites produced by dietary fiber fermentation (mainly, short-chain fatty acids [SCFA]). Five cereal grain samples (wheat, rye, maize [corn], rice, and oats) were subjected to in vitro digestion and fermentation using fecal samples from 10 obese and nine normal weight people. No significant differences in total SCFA production between the normal weight and obese groups were observed [279 (12) vs. 280 (12), mean (standard error), respectively; P=.935]. However, the obese microbiota resulted in elevated propionate production compared with that of normal weight [24.8(2.2) vs. 17.8(1.9), respectively; P=.008]. Rye appeared to be particularly beneficial among grain samples due to the lowest propionate production and highest butyrate production during fermentation. These data suggest that the dietary fibers from cereal grains affect bacterial metabolism differently in obese and normal weight classes and that certain grains may be particularly beneficial for promoting gut health in obese states.

Relative expression of rRNA transcripts and 45S rDNA promoter methylation status are dysregulated in tumors in comparison with matched-normal tissues in breast cancer.

PubMed

Karahan, Gurbet; Sayar, Nilufer; Gozum, Gokcen; Bozkurt, Betul; Konu, Ozlen; Yulug, Isik G

2015-06-01

Ribosomal RNA (rRNA) expression, one of the most important factors regulating ribosome production, is primarily controlled by a CG-rich 45 S rDNA promoter. However, the DNA methylation state of the 45 S rDNA promoter, as well as its effect on rRNA gene expression in types of human cancers is controversial. In the present study we analyzed the methylation status of the rDNA promoter (-380 to +53 bp) as well as associated rRNA expression levels in breast cancer cell lines and breast tumor-normal tissue pairs. We found that the aforementioned regulatory region was extensively methylated (74-96%) in all cell lines and in 68% (13/19 tumor-normal pairs) of the tumors. Expression levels of rRNA transcripts 18 S, 28 S, 5.8 S and 45 S external transcribed spacer (45 S ETS) greatly varied in the breast cancer cell lines regardless of their methylation status. Analyses of rRNA transcript expression levels in the breast tumor and normal matched tissues showed no significant difference when normalized with TBP. On the other hand, using the geometric mean of the rRNA expression values (GM-rRNA) as reference enabled us to identify significant changes in the relative expression of rRNAs in the tissue samples. We propose GM-rRNA normalization as a novel strategy to analyze expression differences between rRNA transcripts. Accordingly, the 18S rRNA/GM-rRNA ratio was significantly higher whereas the 5.8S rRNA/GM-rRNA ratio was significantly lower in breast tumor samples than this ratio in the matched normal samples. Moreover, the 18S rRNA/GM-rRNA ratio was negatively correlated with the 45 S rDNA promoter methylation level in the normal breast tissue samples, yet not in the breast tumors. Significant correlations observed between the expression levels of rRNA transcripts in the normal samples were lost in the tumor samples. We showed that the expression of rRNA transcripts may not be based solely on promoter methylation. Carcinogenesis may cause dysregulation of the correlation between spliced rRNA expression levels, possibly due to changes in rRNA processing, which requires further investigation.

Food and waste management biotechnology for the space shuttle

NASA Technical Reports Server (NTRS)

Murray, R. W.; Schelkopf, J. D.; Hunt, S. R.; Sauer, R. L.

1979-01-01

Space-crew facilities for preparation, eating, personal hygiene and waste management are contained in one small area of the Shuttle Orbiter Mid-Deck, all the functional systems being interconnected. The paper discusses three major systems: (1) the Galley, which includes the personal hygiene station and food packages; (2) the Waste Collector, which includes provisions for male and female users, urine, feces and emesis collection in both a normal and contigency mode of operation; and (3) Biowaste Monitoring, which includes mass measurement and sampling. The technology improvement continues by assuring that the Orbiter systems have sufficient design flexibility to permit later improvements in operation and in function.

Concordant 241Pu-241Am Dating of Environmental Samples: Results from Forest Fire Ash

NASA Astrophysics Data System (ADS)

Goldstein, S. J.; Oldham, W. J.; Murrell, M. T.; Katzman, D.

2010-12-01

We have measured the Pu, 237Np, 241Am, and 151Sm isotopic systematics for a set of forest fire ash samples from various locations in the western U.S. including Montana, Wyoming, Idaho, and New Mexico. The goal of this study is to develop a concordant 241Pu (t1/2 = 14.4 y)-241Am dating method for environmental collections. Environmental samples often contain mixtures of components including global fallout. There are a number of approaches for subtracting the global fallout component for such samples. One approach is to use 242Pu/239Pu as a normalizing isotope ratio in a three-isotope plot, where this ratio for the non-global fallout component can be estimated or assumed to be small. This study investigates a new, complementary method of normalization using the long-lived fission product, 151Sm (t1/2 = 90 y). We find that forest fire ash concentrates actinides and fission products with ~1E10 atoms 239Pu/g and ~1E8 atoms 151Sm/g, allowing us to measure these nuclides by mass spectrometric (MIC-TIMS) and radiometric (liquid scintillation counting) methods. The forest fire ash samples are characterized by a western U.S. regional isotopic signature representing varying mixtures of global fallout with a local component from atmospheric testing of nuclear weapons at the Nevada Test Site (NTS). Our results also show that 151Sm is well correlated with the Pu nuclides in the forest fire ash, suggesting that these nuclides have similar geochemical behavior in the environment. Results of this correlation indicate that the 151Sm/239Pu atom ratio for global fallout is ~0.164, in agreement with an independent estimate of 0.165 based on 137Cs fission yields for atmospheric weapons tests at the NTS. 241Pu-241Am dating of the non-global fallout component in the forest fire ash samples yield ages in the late 1950’s-early 1960’s, consistent with a peak in NTS weapons testing at that time. The age results for this component are in agreement using both 242Pu and 151Sm normalizations, although the errors for the 151Sm correction are currently larger due to the greater uncertainty of their measurements. Additional efforts to develop a concordant 241Pu-241Am dating method for environmental collections are underway with emphasis on soil cores.

Concordant plutonium-241-americium-241 dating of environmental samples: results from forest fire ash

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

Goldstein, Steven J; Oldham, Warren J; Murrell, Michael T

2010-12-07

We have measured the Pu, {sup 237}Np, {sup 241}Am, and {sup 151}Sm isotopic systematics for a set of forest fire ash samples from various locations in the western U.S. including Montana, Wyoming, Idaho, and New Mexico. The goal of this study is to develop a concordant {sup 241}Pu (t{sub 1/2} = 14.4 y)-{sup 241}Am dating method for environmental collections. Environmental samples often contain mixtures of components including global fallout. There are a number of approaches for subtracting the global fallout component for such samples. One approach is to use {sup 242}/{sup 239}Pu as a normalizing isotope ratio in a three-isotopemore » plot, where this ratio for the nonglobal fallout component can be estimated or assumed to be small. This study investigates a new, complementary method of normalization using the long-lived fission product, {sup 151}Sm (t{sub 1/2} = 90 y). We find that forest fire ash concentrates actinides and fission products with {approx}1E10 atoms {sup 239}Pu/g and {approx}1E8 atoms {sup 151}Sm/g, allowing us to measure these nuclides by mass spectrometric (MIC-TIMS) and radiometric (liquid scintillation counting) methods. The forest fire ash samples are characterized by a western U.S. regional isotopic signature representing varying mixtures of global fallout with a local component from atmospheric testing of nuclear weapons at the Nevada Test Site (NTS). Our results also show that {sup 151}Sm is well correlated with the Pu nuclides in the forest fire ash, suggesting that these nuclides have similar geochemical behavior in the environment. Results of this correlation indicate that the {sup 151}Sm/{sup 239}Pu atom ratio for global fallout is {approx}0.164, in agreement with an independent estimate of 0.165 based on {sup 137}Cs fission yields for atmospheric weapons tests at the NTS. {sup 241}Pu-{sup 241}Am dating of the non-global fallout component in the forest fire ash samples yield ages in the late 1950's-early 1960's, consistent with a peak in NTS weapons testing at that time. The age results for this component are in agreement using both {sup 242}Pu and {sup 151}Sm normalizations, although the errors for the {sup 151}Sm correction are currently larger due to the greater uncertainty of their measurements. Additional efforts to develop a concordant {sup 241}Pu-{sup 241}Am dating method for environmental collections are underway with emphasis on soil cores.« less

A direct comparison of popular models of normal memory loss and Alzheimer's disease in samples of African Americans, Mexican Americans, and refugees and immigrants from the former Soviet Union.

PubMed

Schrauf, Robert W; Iris, Madelyn

2011-04-01

To understand how people differentiate normal memory loss from Alzheimer's disease (AD) by investigating cultural models of these conditions. Ethnographic interviews followed by a survey. Cultural consensus analysis was used to test for the presence of group models, derive the "culturally correct" set of beliefs, and compare models of normal memory loss and AD. Chicago, Illinois. One hundred eight individuals from local neighborhoods: African Americans, Mexican Americans, and refugees and immigrants from the former Soviet Union. Participants responded to yes-or-no questions about the nature and causes of normal memory loss and AD and provided information on ethnicity, age, sex, acculturation, and experience with AD. Groups held a common model of AD as a brain-based disease reflecting irreversible cognitive decline. Higher levels of acculturation predicted greater knowledge of AD. Russian speakers favored biological over psychological models of the disease. Groups also held a common model of normal memory loss, including the important belief that "normal" forgetting involves eventual recall of the forgotten material. Popular models of memory loss and AD confirm that patients and clinicians are speaking the same "language" in their discussions of memory loss and AD. Nevertheless, the presence of coherent models of memory loss and AD, and the unequal distribution of that knowledge across groups, suggests that clinicians should include wider circles of patients' families and friends in their consultations. These results frame knowledge as distributed across social groups rather than simply the possession of individual minds. © 2011, Copyright the Authors. Journal compilation © 2011, The American Geriatrics Society.

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

PubMed

Wang, Zuozhen

2018-01-01

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

Incidence of Fanconi anaemia in phenotypically normal aplastic anaemia patients in West Bengal.

PubMed

Dutta, Atreyee; De, Rajib; Dolai, Tuphan Kanti; Pal, Pritha; Ghosh, Shanoli; Mitra, Pradip Kumar; Halder, Ajanta

2018-01-07

Fanconi anaemia (FA) is a rare inherited bone marrow failure and autosomal recessive blood disorder. FA patients have a higher risk of cancer, including acute myeloid leukaemia and squamous cell carcinoma. Maximum, but not all, affected individuals have one or more somatic abnormalities, including skin, skeletal, genitourinary, gastrointestinal, cardiac and neurological anomalies, etc. Positive stress cytogenetics has immense implications for the treatment and management of FA. The aim of our study was to find out the incidence of FA in the population of phenotypically normal aplastic anaemia (AA) patients in West Bengal. Ethical clearances were obtained from the corresponding institutional committees. A total of 117 AA cases was selected. Stress cytogenetics was performed from peripheral venous blood (PVB) samples of 63 AA patients (age ≤ 50 years) and 63 age- and sex-matched healthy individual (control) using Mitomycin C (MMC). Out of 63 AA patients, 6 (9.25%) cases showed positive stress cytogenetics suggestive of FA, which is statistically significant (p-value - 0.000532), analysed by chi-square test. A considerable percentage of patients showing sensitivity towards MMC, even if they are phenotypically normal and did not have any distinguishable features which are generally found in FA. This observation may indicate that stress cytogenetics analysis of phenotypically normal AA patients (≤50 years) is essential for the improvement of the treatment procedure.

Lewis x is highly expressed in normal tissues: a comparative immunohistochemical study and literature revision.

PubMed

Croce, María V; Isla-Larrain, Marina; Rabassa, Martín E; Demichelis, Sandra; Colussi, Andrea G; Crespo, Marina; Lacunza, Ezequiel; Segal-Eiras, Amada

2007-01-01

An immunohistochemical analysis was employed to determine the expression of carbohydrate antigens associated to mucins in normal epithelia. Tissue samples were obtained as biopsies from normal breast (18), colon (35) and oral cavity mucosa (8). The following carbohydrate epitopes were studied: sialyl-Lewis x, Lewis x, Lewis y, Tn hapten, sialyl-Tn and Thomsen-Friedenreich antigen. Mucins were also studied employing antibodies against MUC1, MUC2, MUC4, MUC5AC, MUC6 and also normal colonic glycolipid. Statistical analysis was performed and Kendall correlations were obtained. Lewis x showed an apical pattern mainly at plasma membrane, although cytoplasmic staining was also found in most samples. TF, Tn and sTn haptens were detected in few specimens, while sLewis x was found in oral mucosa and breast tissue. Also, normal breast expressed MUC1 at a high percentage, whereas MUC4 was observed in a small number of samples. Colon specimens mainly expressed MUC2 and MUC1, while most oral mucosa samples expressed MUC4 and MUC1. A positive correlation between MUC1VNTR and TF epitope (r=0.396) was found in breast samples, while in colon specimens MUC2 and colonic glycolipid versus Lewis x were statistically significantly correlated (r=0.28 and r=0.29, respectively). As a conclusion, a defined carbohydrate epitope expression is not exclusive of normal tissue or a determined localization, and it is possible to assume that different glycoproteins and glycolipids may be carriers of carbohydrate antigens depending on the tissue localization considered.

Analysis of the variability of human normal urine by 2D-GE reveals a "public" and a "private" proteome.

PubMed

Molina, Laurence; Salvetat, Nicolas; Ameur, Randa Ben; Peres, Sabine; Sommerer, Nicolas; Jarraya, Fayçal; Ayadi, Hammadi; Molina, Franck; Granier, Claude

2011-12-10

The characterization of the normal urinary proteome is steadily progressing and represents a major interest in the assessment of clinical urinary biomarkers. To estimate quantitatively the variability of the normal urinary proteome, urines of 20 healthy people were collected. We first evaluated the impact of the sample conservation temperature on urine proteome integrity. Keeping the urine sample at RT or at +4°C until storage at -80°C seems the best way for long-term storage of samples for 2D-GE analysis. The quantitative variability of the normal urinary proteome was estimated on the 20 urines mapped by 2D-GE. The occurrence of the 910 identified spots was analysed throughout the gels and represented in a virtual 2D gel. Sixteen percent of the spots were found to occur in all samples and 23% occurred in at least 90% of urines. About 13% of the protein spots were present only in 10% or less of the samples, thus representing the most variable part of the normal urinary proteome. Twenty proteins corresponding to a fraction of the fully conserved spots were identified by mass spectrometry. In conclusion, a "public" urinary proteome, common to healthy individuals, seems to coexist with a "private" urinary proteome, which is more specific to each individual. Copyright © 2011 Elsevier B.V. All rights reserved.

Predicting ambient aerosol Thermal Optical Reflectance (TOR) measurements from infrared spectra: organic carbon

NASA Astrophysics Data System (ADS)

Dillner, A. M.; Takahama, S.

2014-11-01

Organic carbon (OC) can constitute 50% or more of the mass of atmospheric particulate matter. Typically, the organic carbon concentration is measured using thermal methods such as Thermal-Optical Reflectance (TOR) from quartz fiber filters. Here, methods are presented whereby Fourier Transform Infrared (FT-IR) absorbance spectra from polytetrafluoroethylene (PTFE or Teflon) filters are used to accurately predict TOR OC. Transmittance FT-IR analysis is rapid, inexpensive, and non-destructive to the PTFE filters. To develop and test the method, FT-IR absorbance spectra are obtained from 794 samples from seven Interagency Monitoring of PROtected Visual Environment (IMPROVE) sites sampled during 2011. Partial least squares regression is used to calibrate sample FT-IR absorbance spectra to artifact-corrected TOR OC. The FTIR spectra are divided into calibration and test sets by sampling site and date which leads to precise and accurate OC predictions by FT-IR as indicated by high coefficient of determination (R2; 0.96), low bias (0.02 μg m-3, all μg m-3 values based on the nominal IMPROVE sample volume of 32.8 m-3), low error (0.08 μg m-3) and low normalized error (11%). These performance metrics can be achieved with various degrees of spectral pretreatment (e.g., including or excluding substrate contributions to the absorbances) and are comparable in precision and accuracy to collocated TOR measurements. FT-IR spectra are also divided into calibration and test sets by OC mass and by OM / OC which reflects the organic composition of the particulate matter and is obtained from organic functional group composition; this division also leads to precise and accurate OC predictions. Low OC concentrations have higher bias and normalized error due to TOR analytical errors and artifact correction errors, not due to the range of OC mass of the samples in the calibration set. However, samples with low OC mass can be used to predict samples with high OC mass indicating that the calibration is linear. Using samples in the calibration set that have a different OM / OC or ammonium / OC distributions than the test set leads to only a modest increase in bias and normalized error in the predicted samples. We conclude that FT-IR analysis with partial least squares regression is a robust method for accurately predicting TOR OC in IMPROVE network samples; providing complementary information to the organic functional group composition and organic aerosol mass estimated previously from the same set of sample spectra (Ruthenburg et al., 2014).

Minimally-invasive biomarker studies in eosinophilic esophagitis: a systematic review.

PubMed

Hines, Brittany T; Rank, Matthew A; Wright, Benjamin L; Marks, Lisa A; Hagan, John B; Straumann, Alex; Greenhawt, Matthew; Dellon, Evan S

2018-05-10

Eosinophilic esophagitis (EoE) is a chronic, inflammatory disease of the esophagus which currently requires repeated endoscopic biopsies for diagnosis and monitoring as no reliable non-invasive markers have been identified. To identify promising minimally-invasive EoE biomarkers and remaining gaps in biomarker validation. We performed a systematic review of EMBASE, Ovid Medline, PubMed, and Web of Science from inception to June 6, 2017. Studies were included if subjects met the 2007 consensus criteria for EoE diagnosis, a minimally-invasive biomarker was assessed, and the study included at least 1 control for comparison. The search identified 2094 studies, with 234 reviewed at full text level, and 49 included in the analysis (20 adult, 19 pediatric, 7 pediatric and adult, and 3 not stated). The majority (26 of 49) were published after 2014. Thirty-five studies included normal controls, 9 analyzed atopic controls, and 29 compared samples from subjects with active and inactive EoE. Minimally-invasive biomarkers were obtained from peripheral blood (n=41 studies), sponge/string samples (3), oral/throat swab secretions (2), breath condensate (2), stool (2), and urine (2). The most commonly reported biomarkers were peripheral blood eosinophils (16), blood and string eosinophil granule proteins (14), and eosinophil surface or intracellular markers (12). EoE biomarkers distinguished active EoE from normal controls in 23 studies, atopic controls in 2 studies, and inactive EoE controls in 20 studies. Several promising minimally-invasive biomarkers for EoE have emerged; however, few are able to differentiate EoE from other atopic diseases. Copyright © 2018. Published by Elsevier Inc.

Self-Monitoring of Listening Abilities in Normal-Hearing Children, Normal-Hearing Adults, and Children with Cochlear Implants

PubMed Central

Rothpletz, Ann M.; Wightman, Frederic L.; Kistler, Doris J.

2012-01-01

Background Self-monitoring has been shown to be an essential skill for various aspects of our lives, including our health, education, and interpersonal relationships. Likewise, the ability to monitor one’s speech reception in noisy environments may be a fundamental skill for communication, particularly for those who are often confronted with challenging listening environments, such as students and children with hearing loss. Purpose The purpose of this project was to determine if normal-hearing children, normal-hearing adults, and children with cochlear implants can monitor their listening ability in noise and recognize when they are not able to perceive spoken messages. Research Design Participants were administered an Objective-Subjective listening task in which their subjective judgments of their ability to understand sentences from the Coordinate Response Measure corpus presented in speech spectrum noise were compared to their objective performance on the same task. Study Sample Participants included 41 normal-hearing children, 35 normal-hearing adults, and 10 children with cochlear implants. Data Collection and Analysis On the Objective-Subjective listening task, the level of the masker noise remained constant at 63 dB SPL, while the level of the target sentences varied over a 12 dB range in a block of trials. Psychometric functions, relating proportion correct (Objective condition) and proportion perceived as intelligible (Subjective condition) to target/masker ratio (T/M), were estimated for each participant. Thresholds were defined as the T/M required to produce 51% correct (Objective condition) and 51% perceived as intelligible (Subjective condition). Discrepancy scores between listeners’ threshold estimates in the Objective and Subjective conditions served as an index of self-monitoring ability. In addition, the normal-hearing children were administered tests of cognitive skills and academic achievement, and results from these measures were compared to findings on the Objective-Subjective listening task. Results Nearly half of the children with normal hearing significantly overestimated their listening in noise ability on the Objective-Subjective listening task, compared to less than 9% of the adults. There was a significant correlation between age and results on the Objective-Subjective task, indicating that the younger children in the sample (age 7–12 yr) tended to overestimate their listening ability more than the adolescents and adults. Among the children with cochlear implants, eight of the 10 participants significantly overestimated their listening ability (as compared to 13 of the 24 normal-hearing children in the same age range). We did not find a significant relationship between results on the Objective-Subjective listening task and performance on the given measures of academic achievement or intelligence. Conclusions Findings from this study suggest that many children with normal hearing and children with cochlear implants often fail to recognize when they encounter conditions in which their listening ability is compromised. These results may have practical implications for classroom learning, particularly for children with hearing loss in mainstream settings. PMID:22436118

The childhood executive function inventory: confirmatory factor analyses and cross-cultural clinical validity in a sample of 8- to 11-year-old children.

PubMed

Catale, Corinne; Meulemans, Thierry; Thorell, Lisa B

2015-06-01

The aim was to investigate the psychometric characteristics of the French adaptation of the Childhood Executive Functioning Inventory (CHEXI) in children and to explore the cross-cultural validity of the CHEXI in discriminating between children with ADHD and controls in two culturally different samples (Belgian and Swedish). Study I included normally developing children (n = 242), whereas Study II included both children diagnosed with ADHD (n = 87) and controls (n = 87). CHEXI ratings were collected from parents. Confirmatory factor analyses replicated the two-factor solution, referred to as inhibition and working memory, which had been identified previously. Both subscales had good psychometric properties. Furthermore, the CHEXI was found to discriminate, with high sensitivity and specificity, between children with ADHD and controls in both cultural samples. The CHEXI can be considered as a valuable screening measure for ADHD in children, but the cross-cultural clinical implications of ratings have to be considered. © 2013 SAGE Publications.

Identification and Characterization of Post-Translational Modifications on EAF1 and EAF2 in Prostate Cancer

DTIC Science & Technology

2013-04-01

1nM R1881). All samples were normalized to renilla . B) Activity of PSA- luciferase in the presence of FOXA1 when EAF2 is over-expressed. All...samples performed in the presence of 1nM R1881. All samples were normalized to renilla . *=pɘ.05 All experiments were performed in C4-2 cells. FOXA1

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%.

Fetal scalp pH testing

MedlinePlus

... such as HIV/AIDS or hepatitis C. Normal Results Normal fetal blood sample results are: Normal pH: ... meaning of your specific test results. What Abnormal Results Mean A fetal scalp blood pH level of ...

Is Coefficient Alpha Robust to Non-Normal Data?

PubMed Central

Sheng, Yanyan; Sheng, Zhaohui

2011-01-01

Coefficient alpha has been a widely used measure by which internal consistency reliability is assessed. In addition to essential tau-equivalence and uncorrelated errors, normality has been noted as another important assumption for alpha. Earlier work on evaluating this assumption considered either exclusively non-normal error score distributions, or limited conditions. In view of this and the availability of advanced methods for generating univariate non-normal data, Monte Carlo simulations were conducted to show that non-normal distributions for true or error scores do create problems for using alpha to estimate the internal consistency reliability. The sample coefficient alpha is affected by leptokurtic true score distributions, or skewed and/or kurtotic error score distributions. Increased sample sizes, not test lengths, help improve the accuracy, bias, or precision of using it with non-normal data. PMID:22363306

Mouse mammary tumor virus-like RNA transcripts and DNA are found in affected cells of human breast cancer.

PubMed

Ford, Caroline E; Faedo, Margaret; Rawlinson, William D

2004-11-01

Identifiable risk factors for the development of breast cancer include age, diet, family history, and lifetime estrogen exposure. An infectious agent (mouse mammary tumor virus; MMTV) is known to cause murine breast tumors and may be involved in the pathogenesis of human disease. Multiple studies have detected MMTV-like sequences in 30 to 60% of breast cancer samples and up to 1.8% of samples from normal breast. Using in situ PCR of MMTV-like sequences of formalin-fixed, paraffin-embedded breast tissue, viral sequences have been located in cancerous epithelial cells in breast acini of male and female breast tumors, but not in adjacent nonmalignant cells. MMTV-like sequences were also located in the epithelial cells of male gynecomastia samples. Using reverse transcriptase in situ PCR, RNA transcripts from the env gene were also detected within cancerous epithelial cells of 78% of DNA-positive tumors, 80% of gynecomastia samples, and 0% of normal tissues screened. This suggests the virus may be replicating in these cells. The epidemiologic and histopathological data are consistent with the association of an MMTV-like virus with breast cancers in men and women. The association with gynecomastia, a benign, possibly premalignant condition suggests hormonal influences, rather than cancer per se, may be the dominant factor in determining viral presence and replication.

Analyzing gene expression profiles in dilated cardiomyopathy via bioinformatics methods.

PubMed

Wang, Liming; Zhu, L; Luan, R; Wang, L; Fu, J; Wang, X; Sui, L

2016-10-10

Dilated cardiomyopathy (DCM) is characterized by ventricular dilatation, and it is a common cause of heart failure and cardiac transplantation. This study aimed to explore potential DCM-related genes and their underlying regulatory mechanism using methods of bioinformatics. The gene expression profiles of GSE3586 were downloaded from Gene Expression Omnibus database, including 15 normal samples and 13 DCM samples. The differentially expressed genes (DEGs) were identified between normal and DCM samples using Limma package in R language. Pathway enrichment analysis of DEGs was then performed. Meanwhile, the potential transcription factors (TFs) and microRNAs (miRNAs) of these DEGs were predicted based on their binding sequences. In addition, DEGs were mapped to the cMap database to find the potential small molecule drugs. A total of 4777 genes were identified as DEGs by comparing gene expression profiles between DCM and control samples. DEGs were significantly enriched in 26 pathways, such as lymphocyte TarBase pathway and androgen receptor signaling pathway. Furthermore, potential TFs (SP1, LEF1, and NFAT) were identified, as well as potential miRNAs (miR-9, miR-200 family, and miR-30 family). Additionally, small molecules like isoflupredone and trihexyphenidyl were found to be potential therapeutic drugs for DCM. The identified DEGs (PRSS12 and FOXG1), potential TFs, as well as potential miRNAs, might be involved in DCM.

Analyzing gene expression profiles in dilated cardiomyopathy via bioinformatics methods

PubMed Central

Wang, Liming; Zhu, L.; Luan, R.; Wang, L.; Fu, J.; Wang, X.; Sui, L.

2016-01-01

Dilated cardiomyopathy (DCM) is characterized by ventricular dilatation, and it is a common cause of heart failure and cardiac transplantation. This study aimed to explore potential DCM-related genes and their underlying regulatory mechanism using methods of bioinformatics. The gene expression profiles of GSE3586 were downloaded from Gene Expression Omnibus database, including 15 normal samples and 13 DCM samples. The differentially expressed genes (DEGs) were identified between normal and DCM samples using Limma package in R language. Pathway enrichment analysis of DEGs was then performed. Meanwhile, the potential transcription factors (TFs) and microRNAs (miRNAs) of these DEGs were predicted based on their binding sequences. In addition, DEGs were mapped to the cMap database to find the potential small molecule drugs. A total of 4777 genes were identified as DEGs by comparing gene expression profiles between DCM and control samples. DEGs were significantly enriched in 26 pathways, such as lymphocyte TarBase pathway and androgen receptor signaling pathway. Furthermore, potential TFs (SP1, LEF1, and NFAT) were identified, as well as potential miRNAs (miR-9, miR-200 family, and miR-30 family). Additionally, small molecules like isoflupredone and trihexyphenidyl were found to be potential therapeutic drugs for DCM. The identified DEGs (PRSS12 and FOXG1), potential TFs, as well as potential miRNAs, might be involved in DCM. PMID:27737314

A comparative review of methods for comparing means using partially paired data.

PubMed

Guo, Beibei; Yuan, Ying

2017-06-01

In medical experiments with the objective of testing the equality of two means, data are often partially paired by design or because of missing data. The partially paired data represent a combination of paired and unpaired observations. In this article, we review and compare nine methods for analyzing partially paired data, including the two-sample t-test, paired t-test, corrected z-test, weighted t-test, pooled t-test, optimal pooled t-test, multiple imputation method, mixed model approach, and the test based on a modified maximum likelihood estimate. We compare the performance of these methods through extensive simulation studies that cover a wide range of scenarios with different effect sizes, sample sizes, and correlations between the paired variables, as well as true underlying distributions. The simulation results suggest that when the sample size is moderate, the test based on the modified maximum likelihood estimator is generally superior to the other approaches when the data is normally distributed and the optimal pooled t-test performs the best when the data is not normally distributed, with well-controlled type I error rates and high statistical power; when the sample size is small, the optimal pooled t-test is to be recommended when both variables have missing data and the paired t-test is to be recommended when only one variable has missing data.

The 1064 nm laser-induced breakdown spectroscopy (LIBS) inspection to detect the nutrient elements in freshly cut carrot samples

NASA Astrophysics Data System (ADS)

Yudasari, N.; Prasetyo, S.; Suliyanti, M. M.

2018-03-01

The laser-induced breakdown spectroscopy (LIBS) technique was applied to detect the nutrient elements contained in fresh carrot. Nd:YAG laser the wavelength of 1064 nm was employed in the experiments for ablation. Employing simple set-up of LIBS and preparing the sample with less step method, we are able to detect 18 chemical elements including some fundamental element of carrot, i.e Mg, Al, Fe, Mn, Ti, Ca, and Mn. By applying normalized profiles calculation on some of the element, we are able to compare the concentration level of each element of the outer and inner part of carrot.

Using Single Drop Microextraction for Headspace Analysis with Gas Chromatography

NASA Astrophysics Data System (ADS)

Riccio, Daniel; Wood, Derrick C.; Miller, James M.

2008-07-01

Headspace (HS) gas chromatography (GC) is commonly used to analyze samples that contain non-volatiles. In 1996, a new sampling technique called single drop microextraction, SDME, was introduced, and in 2001 it was applied to HS analysis. It is a simple technique that uses equipment normally found in the undergraduate laboratory, making it ideal for instructional use, especially to illustrate HS analysis or as an alternative to solid-phase microextraction (SPME) to which it is very similar. The basic principles and practice of HS-GC using SDME are described, including a complete review of the literature. Some possible experiments are suggested using water and N -methylpyrrolidone (NMP) as solvents.

Point-of-Care Quantitative Measure of Glucose-6-Phosphate Dehydrogenase Enzyme Deficiency.

PubMed

Bhutani, Vinod K; Kaplan, Michael; Glader, Bertil; Cotten, Michael; Kleinert, Jairus; Pamula, Vamsee

2015-11-01

Widespread newborn screening on a point-of-care basis could prevent bilirubin neurotoxicity in newborns with glucose-6-phosphate dehydrogenase (G6PD) deficiency. We evaluated a quantitative G6PD assay on a digital microfluidic platform by comparing its performance with standard clinical methods. G6PD activity was measured quantitatively by using digital microfluidic fluorescence and the gold standard fluorescence biochemical test on a convenience sample of 98 discarded blood samples. Twenty-four samples were designated as G6PD deficient. Mean ± SD G6PD activity for normal samples using the digital microfluidic method and the standard method, respectively, was 9.7 ± 2.8 and 11.1 ± 3.0 U/g hemoglobin (Hb), respectively; for G6PD-deficient samples, it was 0.8 ± 0.7 and 1.4 ± 0.9 U/g Hb. Bland-Altman analysis determined a mean difference of -0.96 ± 1.8 U/g Hb between the digital microfluidic fluorescence results and the standard biochemical test results. The lower and upper limits for the digital microfluidic platform were 4.5 to 19.5 U/g Hb for normal samples and 0.2 to 3.7 U/g Hb for G6PD-deficient samples. The lower and upper limits for the Stanford method were 5.5 to 20.7 U/g Hb for normal samples and 0.1 to 2.8 U/g Hb for G6PD-deficient samples. The measured activity discriminated between G6PD-deficient samples and normal samples with no overlap. Pending further validation, a digital microfluidics platform could be an accurate point-of-care screening tool for rapid newborn G6PD screening. Copyright © 2015 by the American Academy of Pediatrics.

Evaluation of the repeatability of a crude adult indirect Ostertagia ostertagi ELISA and methods of expressing test results.

PubMed

Sanchez, J; Dohoo, I R; Markham, F; Leslie, K; Conboy, G

2002-10-16

An indirect enzyme-linked immunosorbent assay (ELISA) for the detection of antibodies against Ostertagia ostertagi using a crude adult worm antigen was evaluated using serum and milk samples from adult cows, as well as from bulk tank milk. Within and between plate repeatabilities were determined. In addition, the effects of factors such as antigen batch, freezing, preserving of the samples and somatic cell counts (SCCs) of the samples were evaluated. Raw optical densities (ODs) and normalized values were compared using the concordance correlation coefficient (CCC), the coefficient of variation (CV), Bland-Altman plots (BA). Based on raw OD values, there was a high repeatability within a plate (CCC approximately 0.96 and CV<10%). Repeatability between plates was evaluated following normalization of OD values by four methods. Computing normalized values as (OD-Nt)/(Pst-Nt), gave the most repeatable results, with the CCC being approximately 0.95 and the CV approximately 11%. When the OD values were higher than 1.2 and 0.3 for the positive and the negative controls, respectively, none of the normalization methods evaluated provided highly repeatable results and it was necessary to repeat the test. Two batches of the crude antigen preparation were evaluated for repeatability, and no difference was found (CCC=0.96). The use of preservative (bronopol) did not affect test results, nor did freezing the samples for up to 8 months. A significant positive relationship between ELISA OD for milk samples and SCC score was found. Therefore, the use of composite milk samples, which have less variable SCC than samples taken from each quarter, would be more suitable when the udder health status is unknown. The analytical methods used to evaluate repeatability provided a practical way to select among normalization procedures.

Low levels of nasal nitric oxide (NO) correlate to impaired mucociliary function in the upper airways.

PubMed

Lindberg, S; Cervin, A; Runer, T

1997-09-01

Findings in previous studies have suggested nitric oxide (NO) to be a regulator of mucociliary activity in the upper airways. The aim of the present investigation was to study whether a correlation exists between the nasal NO concentration and mucociliary function in patients suffering from respiratory tract diseases such as chronic sinusitis or recurrent pneumonia. Nasal NO was measured with a chemiluminescence analyser, 100 ppb (parts per billion) being adopted as the lower limit of the normal range on the basis of findings in an earlier study of healthy subjects. Mucociliary function was evaluated by measurements of ciliary beat frequency (CBF) in nasal brush samples, and the saccharin transport test. A subnormal level of nasal NO was found in 50% (9/18) of the patients. This correlated with a significantly impaired mucociliary function, regarding both CBF and the saccharin transport time. The median CBF was 10.6 Hz in the group with normal levels of nasal NO, as compared to 8.4 Hz in the subnormal NO group. All patients with a normal nasal NO concentration had a mean CBF of > or = 9.0 Hz in their nasal brush samples, but in the subnormal group the same measurements yielded a CBF of > or = 9.0 Hz in only 22% (2/9) of the cases. As measured with the saccharin test, mucociliary transport was normal in 78% (7/9) in the normal nasal NO group, but the saccharin test was normal only in 11% (1/9) of the subnormal nasal NO group. Nasal NO levels were found to correlate with both CBF measurements (Spearman's rho, 0.80) and the saccharin transport test results (Spearman's rho, -0.61). The results of the present study provide further support for the view that NO is an important regulator of mucociliary function in the upper airways, and that measurements of the nasal NO concentration should be included in investigations of the mucociliary system.

Normalized inverse characterization of sound absorbing rigid porous media.

PubMed

Zieliński, Tomasz G

2015-06-01

This paper presents a methodology for the inverse characterization of sound absorbing rigid porous media, based on standard measurements of the surface acoustic impedance of a porous sample. The model parameters need to be normalized to have a robust identification procedure which fits the model-predicted impedance curves with the measured ones. Such a normalization provides a substitute set of dimensionless (normalized) parameters unambiguously related to the original model parameters. Moreover, two scaling frequencies are introduced, however, they are not additional parameters and for different, yet reasonable, assumptions of their values, the identification procedure should eventually lead to the same solution. The proposed identification technique uses measured and computed impedance curves for a porous sample not only in the standard configuration, that is, set to the rigid termination piston in an impedance tube, but also with air gaps of known thicknesses between the sample and the piston. Therefore, all necessary analytical formulas for sound propagation in double-layered media are provided. The methodology is illustrated by one numerical test and by two examples based on the experimental measurements of the acoustic impedance and absorption of porous ceramic samples of different thicknesses and a sample of polyurethane foam.

Association between oral lichen planus and Epstein–Barr virus in Iranian patients

PubMed Central

Shariati, Matin; Mokhtari, Mojgan; Masoudifar, Aria

2018-01-01

Background: Oral lichen planus (OLP) is a common mucocutaneous disease with malignant transformation potential. Several etiologies such as humoral, autoimmunity, and viral infections might play a role, but still there is no definite etiology for this disease. The aim of this study was to investigate the presence of Epstein–Barr virus (EBV) genome in Iranian patients with OLP as compared to people with normal mucosa. Materials and Methods: The study was carried out on a case group including 38 tissue specimens of patients with histopathological confirmation of OLP and a control group including 38 samples of healthy mucosa. All samples were examined by nested polymerase chain reaction (PCR) method to determine the DNA of EBV. Results: Twenty-two (57.9%) female samples and 16 (42.1%) male samples with OLP were randomly selected as the case group, and 20 (52.6%) female samples and 18 (47.4%) male samples with healthy mucosa as the control group. There was a statistically significant difference in the percentage of EBV positivity between the case (15.8%) and the control groups (P < 0.05); in the case group, three female samples (13.6%) and three male samples (18.8%) were infected with EBV; the difference between the genders was not statistically significant (P = 0.50). Conclusion: Results emphasized that EBV genome was significantly higher among Iranian patients with OLP so antiviral therapy might be helpful. PMID:29692821

Association between oral lichen planus and Epstein-Barr virus in Iranian patients.

PubMed

Shariati, Matin; Mokhtari, Mojgan; Masoudifar, Aria

2018-01-01

Oral lichen planus (OLP) is a common mucocutaneous disease with malignant transformation potential. Several etiologies such as humoral, autoimmunity, and viral infections might play a role, but still there is no definite etiology for this disease. The aim of this study was to investigate the presence of Epstein-Barr virus (EBV) genome in Iranian patients with OLP as compared to people with normal mucosa. The study was carried out on a case group including 38 tissue specimens of patients with histopathological confirmation of OLP and a control group including 38 samples of healthy mucosa. All samples were examined by nested polymerase chain reaction (PCR) method to determine the DNA of EBV. Twenty-two (57.9%) female samples and 16 (42.1%) male samples with OLP were randomly selected as the case group, and 20 (52.6%) female samples and 18 (47.4%) male samples with healthy mucosa as the control group. There was a statistically significant difference in the percentage of EBV positivity between the case (15.8%) and the control groups ( P < 0.05); in the case group, three female samples (13.6%) and three male samples (18.8%) were infected with EBV; the difference between the genders was not statistically significant ( P = 0.50). Results emphasized that EBV genome was significantly higher among Iranian patients with OLP so antiviral therapy might be helpful.

Sample size calculation for stepped wedge and other longitudinal cluster randomised trials.

PubMed

Hooper, Richard; Teerenstra, Steven; de Hoop, Esther; Eldridge, Sandra

2016-11-20

The sample size required for a cluster randomised trial is inflated compared with an individually randomised trial because outcomes of participants from the same cluster are correlated. Sample size calculations for longitudinal cluster randomised trials (including stepped wedge trials) need to take account of at least two levels of clustering: the clusters themselves and times within clusters. We derive formulae for sample size for repeated cross-section and closed cohort cluster randomised trials with normally distributed outcome measures, under a multilevel model allowing for variation between clusters and between times within clusters. Our formulae agree with those previously described for special cases such as crossover and analysis of covariance designs, although simulation suggests that the formulae could underestimate required sample size when the number of clusters is small. Whether using a formula or simulation, a sample size calculation requires estimates of nuisance parameters, which in our model include the intracluster correlation, cluster autocorrelation, and individual autocorrelation. A cluster autocorrelation less than 1 reflects a situation where individuals sampled from the same cluster at different times have less correlated outcomes than individuals sampled from the same cluster at the same time. Nuisance parameters could be estimated from time series obtained in similarly clustered settings with the same outcome measure, using analysis of variance to estimate variance components. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Establishment of Protocols for Global Metabolomics by LC-MS for Biomarker Discovery.

PubMed

Saigusa, Daisuke; Okamura, Yasunobu; Motoike, Ikuko N; Katoh, Yasutake; Kurosawa, Yasuhiro; Saijyo, Reina; Koshiba, Seizo; Yasuda, Jun; Motohashi, Hozumi; Sugawara, Junichi; Tanabe, Osamu; Kinoshita, Kengo; Yamamoto, Masayuki

2016-01-01

Metabolomics is a promising avenue for biomarker discovery. Although the quality of metabolomic analyses, especially global metabolomics (G-Met) using mass spectrometry (MS), largely depends on the instrumentation, potential bottlenecks still exist at several basic levels in the metabolomics workflow. Therefore, we established a precise protocol initially for the G-Met analyses of human blood plasma to overcome some these difficulties. In our protocol, samples are deproteinized in a 96-well plate using an automated liquid-handling system, and conducted either using a UHPLC-QTOF/MS system equipped with a reverse phase column or a LC-FTMS system equipped with a normal phase column. A normalization protocol of G-Met data was also developed to compensate for intra- and inter-batch differences, and the variations were significantly reduced along with our normalization, especially for the UHPLC-QTOF/MS data with a C18 reverse-phase column for positive ions. Secondly, we examined the changes in metabolomic profiles caused by the storage of EDTA-blood specimens to identify quality markers for the evaluation of the specimens' pre-analytical conditions. Forty quality markers, including lysophospholipids, dipeptides, fatty acids, succinic acid, amino acids, glucose, and uric acid were identified by G-Met for the evaluation of plasma sample quality and established the equation of calculating the quality score. We applied our quality markers to a small-scale study to evaluate the quality of clinical samples. The G-Met protocols and quality markers established here should prove useful for the discovery and development of biomarkers for a wider range of diseases.

The fabrication of a multi-spectral lens array and its application in assisting color blindness

NASA Astrophysics Data System (ADS)

Di, Si; Jin, Jian; Tang, Guanrong; Chen, Xianshuai; Du, Ruxu

2016-01-01

This article presents a compact multi-spectral lens array and describes its application in assisting color-blindness. The lens array consists of 9 microlens, and each microlens is coated with a different color filter. Thus, it can capture different light bands, including red, orange, yellow, green, cyan, blue, violet, near-infrared, and the entire visible band. First, the fabrication process is described in detail. Second, an imaging system is setup and a color blindness testing card is selected as the sample. By the system, the vision results of normal people and color blindness can be captured simultaneously. Based on the imaging results, it is possible to be used for helping color-blindness to recover normal vision.

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

PubMed

Almonte, Lisa; Colchero, Jaime

2017-02-23

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

Multivariate Bayesian analysis of Gaussian, right censored Gaussian, ordered categorical and binary traits using Gibbs sampling

PubMed Central

Korsgaard, Inge Riis; Lund, Mogens Sandø; Sorensen, Daniel; Gianola, Daniel; Madsen, Per; Jensen, Just

2003-01-01

A fully Bayesian analysis using Gibbs sampling and data augmentation in a multivariate model of Gaussian, right censored, and grouped Gaussian traits is described. The grouped Gaussian traits are either ordered categorical traits (with more than two categories) or binary traits, where the grouping is determined via thresholds on the underlying Gaussian scale, the liability scale. Allowances are made for unequal models, unknown covariance matrices and missing data. Having outlined the theory, strategies for implementation are reviewed. These include joint sampling of location parameters; efficient sampling from the fully conditional posterior distribution of augmented data, a multivariate truncated normal distribution; and sampling from the conditional inverse Wishart distribution, the fully conditional posterior distribution of the residual covariance matrix. Finally, a simulated dataset was analysed to illustrate the methodology. This paper concentrates on a model where residuals associated with liabilities of the binary traits are assumed to be independent. A Bayesian analysis using Gibbs sampling is outlined for the model where this assumption is relaxed. PMID:12633531

75 FR 64411 - Lowering Miners' Exposure to Respirable Coal Mine Dust, Including Continuous Personal Dust Monitors

Federal Register 2010, 2011, 2012, 2013, 2014

2010-10-19

...The Mine Safety and Health Administration (MSHA) proposes to lower miners' exposure to respirable coal mine dust by revising the Agency's existing standards on miners' occupational exposure to respirable coal mine dust. The major provisions of the proposal would lower the existing exposure limit; provide for full-shift sampling; redefine the term ``normal production shift; '' and add reexamination and decertification requirements for persons certified to sample, and maintain and calibrate sampling devices. In addition, the proposed rule would provide for single shift compliance sampling under the mine operator and MSHA's inspector sampling programs, and would establish sampling requirements for use of the Continuous Personal Dust Monitor (CPDM) and expanded requirements for medical surveillance. The proposed rule would significantly improve health protections for this Nation's coal miners by reducing their occupational exposure to respirable coal mine dust and lowering the risk that they will suffer material impairment of health or functional capacity over their working lives.

Preanalytical considerations in detection of colorectal cancer in blood serum using Raman molecular imaging (Conference Presentation)

NASA Astrophysics Data System (ADS)

Treado, Patrick J.; Stewart, Shona D.; Smith, Aaron; Kirschner, Heather; Post, Christopher; Overholt, Bergein F.

2016-03-01

Colorectal cancer (CRC) is the third most common cancer in men and women in the United States. Raman Molecular Imaging (RMI) is an effective technique to evaluate human tissue, cells and bodily fluids, including blood serum for disease diagnosis. ChemImage Corporation, in collaboration with clinicians, has been engaged in development of an in vitro diagnostic Raman assay focused on CRC detection. The Raman Assay for Colorectal Cancer (RACC) exploits the high specificity of Raman imaging to distinguish diseased from normal dried blood serum droplets without additional reagents. Pilot Study results from testing of hundreds of biobank patient samples have demonstrated that RACC detects CRC with high sensitivity and specificity. However, expanded clinical trials, which are ongoing, are revealing a host of important preanalytical considerations associated with sample collection, sample storage and stability, sample shipping, sample preparation and sample interferents, which impact detection performance. Results from recent clinical studies will be presented.

Mineralogy and Geochemistry of Granitic rocks within Lichen Hills, Outback Nunatak, Northern Victoria Land, Antarctica

NASA Astrophysics Data System (ADS)

KIM, T.; KIM, Y.; Lee, I.; Lee, J.; Woo, J.

2015-12-01

The study areas, Lichen Hills and Outback Nunatak are located in the Northern Victoria Land which is close to Pacific Ocean side of Transantarctic Mountain (TAM), Antarctica. According to the study of Zeller and Dreschoff (1990), the radioactivity values of Lichen hills and Frontier Mt. area in the Victoria Land were very high. To identify the geochemical characteristics of granitic rocks in these areas, 13 samples of Lichen Hills rocks and 4 samples of Outback Nunatak rocks are analyzed. For mineralogical study, samples were observed in macroscale as well as microscale including microscope electron probe analysis. Rock samples of Lichen Hills, Outback Nunatak are mainly leucogranite and granitic pegmatite. These rock samples are composed of quartz, k-feldspar, plagioclase, muscovite, garnet, tourmaline like granite. In SEM-EDS analysis, the observed light colored minerals show relatively high Th, U, Dy, Ce, Nb concentration. This suggests that rock samples may contain minerals such as fergusonite, monazite, thorite, allanite, karnasurtite which are considered to be REE-bearing minerals. Samples of related rocks have been analyzed in terms of major, trace and rare earth element (REE) concentrations using X-ray fluorescence (XRF) spectrometer and Inductively Coupled Plasma Mass Spectrometer (ICP-MS). As concentration of SiO2 increase, Al2O3, TiO2, Fe2O3, MgO, P2O5 concentration decrease and Na2O, K2O, MnO concentration increase. Analyzed trace elements and REE are normalized using CI Chondrite, Primitive mantle. The normalized data show that LREE are enriched compared to HREE. The distinct negative anomalies of Eu, Sr are observed, indicating that rock-forming melts are fairly processed state of fractional crystallization. It means that Th, U, Nb, Ta are much enriched in the melts.

Skeletal maturation in obese patients.

PubMed

Giuca, Maria Rita; Pasini, Marco; Tecco, Simona; Marchetti, Enrico; Giannotti, Laura; Marzo, Giuseppe

2012-12-01

The objective of this study was to compare skeletal maturation in obese patients and in subjects of normal weight to evaluate the best timing for orthopedic and orthodontic treatment. The null hypothesis was that obese and normal-weight patients show similar degrees of skeletal maturation. The sample for this retrospective study consisted of 50 white patients (28 boys, 22 girls) whose x-rays (hand-wrist and lateral cephalometric radiographs) were already available. The test group included 25 obese patients (11 girls, 14 boys; average age, 9.8 ± 2.11 years), and the control group included 25 subjects of normal weight (11 girls, 14 boys; average age, 9.9 ± 2.5 years). Skeletal maturation was determined by using the carpal analysis method and the cervical vertebral maturation method. According to the carpal analysis, there was a significant difference between skeletal and chronologic ages between the test group (11.8 ± 11.4 months) and the control group (-2.9 ± 3.1 months). Furthermore, the obese subjects exhibited a significantly higher mean cervical vertebral maturation score (2.8 ± 0.7) than did the control subjects (2 ± 0.6) (P <0.05). Compared with the normal-weight subjects, the obese subjects showed a higher mean discrepancy between skeletal and chronologic ages according to the carpal analysis and had a significantly higher cervical vertebral maturation score. Thus, to account for the growth in obese patients with skeletal discrepancies, it might be necessary to perform examinations and dentofacial and orthopedic treatments earlier than in normal-weight subjects. Copyright © 2012 American Association of Orthodontists. Published by Mosby, Inc. All rights reserved.

Photoacoustic physio-chemical analysis for prostate cancer diagnosis (Conference Presentation)

NASA Astrophysics Data System (ADS)

Xu, Guan; Cheng, Qian; Huang, Shengsong; Qin, Ming; Hopkins, Thomas; Lee, Chang H.; Kopelman, Raoul; Chao, Wan-yu; Keller, Evan T.; Wu, Denglong; Wang, Xueding

2017-03-01

Photoacoustic physio-chemical analysis (PAPCA) is a recently developed technology capable of simultaneously quantifying the content of molecular components and the corresponding microarchitectures in biological tissue. We have successfully quantified the diagnostic information in livers with PAPCA. In this study, we implemented PAPCA to the diagnosis of prostate cancers. 4 human prostates were scanned ex vivo. The PA signals from normal and cancerous regions in the prostates were acquired by an interstitial needle PA probe. A total of 14 interstitial measurements, including 6 within the normal regions and 8 in the cancerous regions, were acquired. The observed changes in molecular components, including lipid, collagen and hemoglobin were consistent with the findings by other research groups. The changes were quantified by PA spectral analysis (PASA) at wavelengths where strong optical absorption of the relevant molecular components was found. Statistically significant differences among the PASA parameters were observed (p=0.025 at significance of 0.05). A support vector machine model for differentiating the normal and cancerous tissue was established. With the limited number of samples, an 85% diagnostic accuracy was found. The diagnostic information in the PCPCA can be further enriched by targeted optical contrast agents visualizing the microarchitecture in PCa tissues. F3 PAA-PEG nanoparticles was employed to stain the PCa cells in a transgenic mouse model, in which the microarchitectures of normal and cancerous prostate tissues are comparable to that in human. Statistically significant differences were observed between the contrast-enhanced normal and cancerous regions (p=0.038 at a significance of 0.05).

Sample entropy analysis of cervical neoplasia gene-expression signatures

PubMed Central

Botting, Shaleen K; Trzeciakowski, Jerome P; Benoit, Michelle F; Salama, Salama A; Diaz-Arrastia, Concepcion R

2009-01-01

Background We introduce Approximate Entropy as a mathematical method of analysis for microarray data. Approximate entropy is applied here as a method to classify the complex gene expression patterns resultant of a clinical sample set. Since Entropy is a measure of disorder in a system, we believe that by choosing genes which display minimum entropy in normal controls and maximum entropy in the cancerous sample set we will be able to distinguish those genes which display the greatest variability in the cancerous set. Here we describe a method of utilizing Approximate Sample Entropy (ApSE) analysis to identify genes of interest with the highest probability of producing an accurate, predictive, classification model from our data set. Results In the development of a diagnostic gene-expression profile for cervical intraepithelial neoplasia (CIN) and squamous cell carcinoma of the cervix, we identified 208 genes which are unchanging in all normal tissue samples, yet exhibit a random pattern indicative of the genetic instability and heterogeneity of malignant cells. This may be measured in terms of the ApSE when compared to normal tissue. We have validated 10 of these genes on 10 Normal and 20 cancer and CIN3 samples. We report that the predictive value of the sample entropy calculation for these 10 genes of interest is promising (75% sensitivity, 80% specificity for prediction of cervical cancer over CIN3). Conclusion The success of the Approximate Sample Entropy approach in discerning alterations in complexity from biological system with such relatively small sample set, and extracting biologically relevant genes of interest hold great promise. PMID:19232110

An enzyme-linked immunosorbent assay for the evaluation of thrombocytopenia induced by heparin.

PubMed

Howe, S E; Lynch, D M

1985-05-01

Five patients with heparin-associated thrombocytopenia (HAT) were evaluated by platelet aggregation and quantitation of immunoglobulin binding to intact target platelets in both the presence and absence of heparin. These patients developed thrombocytopenia (12,000 to 70,000 platelets/microliter) 7 to 15 days and embolic and hemorrhagic complications 9 to 15 days after the initiation of heparin therapy. Platelet aggregation after the addition of heparin was demonstrated in two of four HAT serum samples, whereas normal serum samples showed no significant platelet aggregation. The five HAT serum samples showed normal to elevated baseline serum platelet-bindable immunoglobulin (SPBIg) with a range of 4.3 to 11.4 fg/platelet (normal less than or equal to 1.0 to 6.5 fg/platelet). When HAT sera were incubated with target platelets and heparin (5 U/ml), the SPBIg increased to 8.5 to 37.5 fg/platelet, a mean increase of 148% in the presence of heparin. Normal and control serum samples (from 10 normal laboratory volunteers, nine patients without thrombocytopenia receiving heparin, nine patients with autoimmune thrombocytopenic purpura, and nine patients with nonimmune thrombocytopenia not receiving heparin) showed only a slight increase in SPBIg of 0 to 2.8 fg/platelet above baseline, a mean increase of 15% after heparin incubation with the serum samples. The measurement of SPBIg of washed platelets incubated with test serum samples in the presence and absence of heparin is potentially a specific and sensitive in vitro test for the diagnosis of HAT and may prove more sensitive than platelet aggregation studies with heparin.

Characterization of DNA isolated from normal and cancerous ovarian tissues by ultraviolet resonance Raman spectroscopy

NASA Astrophysics Data System (ADS)

Zhao, Xiaojie; Vinson, Michael A.; Malins, Donald C.; Spiro, Thomas G.

2000-05-01

We report significant differences in UV resonance Raman (UVRR) spectra of DNA samples from normal and cancerous tissues. The four bases of DNA, adenosine, thymine, guanosine and cytidine, can be enhanced in UVRR spectra, and their intensities are very sensitive to base stacking and DNA H-bonding. 14 DNA samples from patients at different stages of ovarian cancer, 5 from normal, 2 from primary, 3 from metastasis primary and 4 from distant metastasis tumor tissues, were characterized by 257, 238, 229, 220 and 210 nm-excited UVRR spectra. Raman spectral difference between normal and tumor DNA could be readily detected.

A comparative study on the mechanical energy of the normal, ACL, osteoarthritis, and Parkinson subjects.

PubMed

Bahreinizad, Hossein; Salimi Bani, Milad; Hasani, Mojtaba; Karimi, Mohammad Taghi; Sharifmoradi, Keyvan; Karimi, Alireza

2017-08-09

The influence of various musculoskeletal disorders has been evaluated using different kinetic and kinematic parameters. But the efficiency of walking can be evaluated by measuring the effort of the subject, or by other words the energy that is required to walk. The aim of this study was to identify mechanical energy differences between the normal and pathological groups. Four groups of 15 healthy subjects, 13 Parkinson subjects, 4 osteoarthritis subjects, and 4 ACL reconstructed subjects have participated in this study. The motions of foot, shank and thigh were recorded using a three dimensional motion analysis system. The kinetic, potential and total mechanical energy of each segment was calculated using 3D markers positions and anthropometric measurements. Maximum value and sample entropy of energies was compared between the normal and abnormal subjects. Maximum value of potential energy of OA subjects was lower than the normal subjects. Furthermore, sample entropy of mechanical energy for Parkinson subjects was low in comparison to the normal subjects while sample entropy of mechanical energy for the ACL subjects was higher than that of the normal subjects. Findings of this study suggested that the subjects with different abilities show different mechanical energy during walking.

Long Non-Coding RNAs Differentially Expressed between Normal versus Primary Breast Tumor Tissues Disclose Converse Changes to Breast Cancer-Related Protein-Coding Genes

PubMed Central

Reiche, Kristin; Kasack, Katharina; Schreiber, Stephan; Lüders, Torben; Due, Eldri U.; Naume, Bjørn; Riis, Margit; Kristensen, Vessela N.; Horn, Friedemann; Børresen-Dale, Anne-Lise; Hackermüller, Jörg; Baumbusch, Lars O.

2014-01-01

Breast cancer, the second leading cause of cancer death in women, is a highly heterogeneous disease, characterized by distinct genomic and transcriptomic profiles. Transcriptome analyses prevalently assessed protein-coding genes; however, the majority of the mammalian genome is expressed in numerous non-coding transcripts. Emerging evidence supports that many of these non-coding RNAs are specifically expressed during development, tumorigenesis, and metastasis. The focus of this study was to investigate the expression features and molecular characteristics of long non-coding RNAs (lncRNAs) in breast cancer. We investigated 26 breast tumor and 5 normal tissue samples utilizing a custom expression microarray enclosing probes for mRNAs as well as novel and previously identified lncRNAs. We identified more than 19,000 unique regions significantly differentially expressed between normal versus breast tumor tissue, half of these regions were non-coding without any evidence for functional open reading frames or sequence similarity to known proteins. The identified non-coding regions were primarily located in introns (53%) or in the intergenic space (33%), frequently orientated in antisense-direction of protein-coding genes (14%), and commonly distributed at promoter-, transcription factor binding-, or enhancer-sites. Analyzing the most diverse mRNA breast cancer subtypes Basal-like versus Luminal A and B resulted in 3,025 significantly differentially expressed unique loci, including 682 (23%) for non-coding transcripts. A notable number of differentially expressed protein-coding genes displayed non-synonymous expression changes compared to their nearest differentially expressed lncRNA, including an antisense lncRNA strongly anticorrelated to the mRNA coding for histone deacetylase 3 (HDAC3), which was investigated in more detail. Previously identified chromatin-associated lncRNAs (CARs) were predominantly downregulated in breast tumor samples, including CARs located in the protein-coding genes for CALD1, FTX, and HNRNPH1. In conclusion, a number of differentially expressed lncRNAs have been identified with relation to cancer-related protein-coding genes. PMID:25264628

Long non-coding RNAs differentially expressed between normal versus primary breast tumor tissues disclose converse changes to breast cancer-related protein-coding genes.

PubMed

Reiche, Kristin; Kasack, Katharina; Schreiber, Stephan; Lüders, Torben; Due, Eldri U; Naume, Bjørn; Riis, Margit; Kristensen, Vessela N; Horn, Friedemann; Børresen-Dale, Anne-Lise; Hackermüller, Jörg; Baumbusch, Lars O

2014-01-01

Breast cancer, the second leading cause of cancer death in women, is a highly heterogeneous disease, characterized by distinct genomic and transcriptomic profiles. Transcriptome analyses prevalently assessed protein-coding genes; however, the majority of the mammalian genome is expressed in numerous non-coding transcripts. Emerging evidence supports that many of these non-coding RNAs are specifically expressed during development, tumorigenesis, and metastasis. The focus of this study was to investigate the expression features and molecular characteristics of long non-coding RNAs (lncRNAs) in breast cancer. We investigated 26 breast tumor and 5 normal tissue samples utilizing a custom expression microarray enclosing probes for mRNAs as well as novel and previously identified lncRNAs. We identified more than 19,000 unique regions significantly differentially expressed between normal versus breast tumor tissue, half of these regions were non-coding without any evidence for functional open reading frames or sequence similarity to known proteins. The identified non-coding regions were primarily located in introns (53%) or in the intergenic space (33%), frequently orientated in antisense-direction of protein-coding genes (14%), and commonly distributed at promoter-, transcription factor binding-, or enhancer-sites. Analyzing the most diverse mRNA breast cancer subtypes Basal-like versus Luminal A and B resulted in 3,025 significantly differentially expressed unique loci, including 682 (23%) for non-coding transcripts. A notable number of differentially expressed protein-coding genes displayed non-synonymous expression changes compared to their nearest differentially expressed lncRNA, including an antisense lncRNA strongly anticorrelated to the mRNA coding for histone deacetylase 3 (HDAC3), which was investigated in more detail. Previously identified chromatin-associated lncRNAs (CARs) were predominantly downregulated in breast tumor samples, including CARs located in the protein-coding genes for CALD1, FTX, and HNRNPH1. In conclusion, a number of differentially expressed lncRNAs have been identified with relation to cancer-related protein-coding genes.

Using a Six Sigma Fishbone Analysis Approach To Evaluate the Effect of Extreme Weather Events on Salmonella Positives in Young Chicken Slaughter Establishments.

PubMed

Linville, John W; Schumann, Douglas; Aston, Christopher; Defibaugh-Chavez, Stephanie; Seebohm, Scott; Touhey, Lucy

2016-12-01

A six sigma fishbone analysis approach was used to develop a machine learning model in SAS, Version 9.4, by using stepwise linear regression. The model evaluated the effect of a wide variety of variables, including slaughter establishment operational measures, normal (30-year average) weather, and extreme weather events on the rate of Salmonella -positive carcasses in young chicken slaughter establishments. Food Safety and Inspection Service (FSIS) verification carcass sampling data, as well as corresponding data from the National Oceanographic and Atmospheric Administration and the Federal Emergency Management Agency, from September 2011 through April 2015, were included in the model. The results of the modeling show that in addition to basic establishment operations, normal weather patterns, differences from normal and disaster events, including time lag weather and disaster variables, played a role in explaining the Salmonella percent positive that varied by slaughter volume quartile. Findings show that weather and disaster events should be considered as explanatory variables when assessing pathogen-related prevalence analysis or research and slaughter operational controls. The apparent significance of time lag weather variables suggested that at least some of the impact on Salmonella rates occurred after the weather events, which may offer opportunities for FSIS or the poultry industry to implement interventions to mitigate those effects.

Frontiers of Two-Dimensional Correlation Spectroscopy. Part 1. New concepts and noteworthy developments

NASA Astrophysics Data System (ADS)

Noda, Isao

2014-07-01

A comprehensive survey review of new and noteworthy developments, which are advancing forward the frontiers in the field of 2D correlation spectroscopy during the last four years, is compiled. This review covers books, proceedings, and review articles published on 2D correlation spectroscopy, a number of significant conceptual developments in the field, data pretreatment methods and other pertinent topics, as well as patent and publication trends and citation activities. Developments discussed include projection 2D correlation analysis, concatenated 2D correlation, and correlation under multiple perturbation effects, as well as orthogonal sample design, predicting 2D correlation spectra, manipulating and comparing 2D spectra, correlation strategy based on segmented data blocks, such as moving-window analysis, features like determination of sequential order and enhanced spectral resolution, statistical 2D spectroscopy using covariance and other statistical metrics, hetero-correlation analysis, and sample-sample correlation technique. Data pretreatment operations prior to 2D correlation analysis are discussed, including the correction for physical effects, background and baseline subtraction, selection of reference spectrum, normalization and scaling of data, derivatives spectra and deconvolution technique, and smoothing and noise reduction. Other pertinent topics include chemometrics and statistical considerations, peak position shift phenomena, variable sampling increments, computation and software, display schemes, such as color coded format, slice and power spectra, tabulation, and other schemes.

Role of sampling times and serum cortisol cut-off concentrations on the routine assessment of adrenal function using the standard cosyntropin test in an academic hospital from Spain: a retrospective chart review.

PubMed

Ortiz-Flores, Andrés E; Santacruz, Elisa; Jiménez-Mendiguchia, Lucía; García-Cano, Ana; Nattero-Chávez, Lia; Escobar-Morreale, Héctor F; Luque-Ramírez, Manuel

2018-05-05

Aiming to validate the use of a single poststimulus sampling protocol for cosyntropin test short standard high-dose test (SST) in our institution, our primary objectives were (1) to determine the concordance between 30 and 60 min serum cortisol (SC) measurements during SST; and (2) to evaluate the diagnostic agreement between both sampling times when using classic or assay-specific and sex-specific SC cut-off values. The secondary objectives included (1) estimating the specificity and positive predictive value of 30 and 60 min sampling times while considering the suspected origin of adrenal insufficiency (AI); and (2) obtaining assay-specific cut-off values for SC after SST in a group of subjects with normal hypothalamic-pituitary-adrenal (HPA) axis. This is a retrospective chart review study conducted at a Spanish academic hospital from 2011 to 2015. Two groups were evaluated: (1) a main study group including 370 patients in whom SC was measured at 30 and 60 min during SST; and (2) a confirmative group that included 150 women presenting with a normal HPA axis in whom SST was conducted to rule out late-onset congenital adrenal hyperplasia. Diagnostic agreement between both sampling times was assessed by considering both classic (500 nmol/L) and assay-specific SC cut-off concentrations. Diagnostic agreement between both sampling times was greater when applying sex-specific and assay-specific cut-off values instead of the classic cut-off values. For suspected primary AI, 30 min SC determination was enough to establish a diagnosis in over 95% of cases, without missing any necessary treatment. When central AI is suspected, 60 min SC measurement was more specific, establishing a diagnosis in over 97% of cases. Sex-specific and assay-specific SC cut-off values improve the diagnostic accuracy of SST. For primary disease, a subnormal SC response at 30 min is a reliable marker of adrenal dysfunction. On the contrary, when central AI is suspected, 60 min SC measurement improves the diagnostic accuracy of the test. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Optimizing fish sampling for fish - mercury bioaccumulation factors

USGS Publications Warehouse

Scudder Eikenberry, Barbara C.; Riva-Murray, Karen; Knightes, Christopher D.; Journey, Celeste A.; Chasar, Lia C.; Brigham, Mark E.; Bradley, Paul M.

2015-01-01

Fish Bioaccumulation Factors (BAFs; ratios of mercury (Hg) in fish (Hgfish) and water (Hgwater)) are used to develop Total Maximum Daily Load and water quality criteria for Hg-impaired waters. Both applications require representative Hgfish estimates and, thus, are sensitive to sampling and data-treatment methods. Data collected by fixed protocol from 11 streams in 5 states distributed across the US were used to assess the effects of Hgfish normalization/standardization methods and fish sample numbers on BAF estimates. Fish length, followed by weight, was most correlated to adult top-predator Hgfish. Site-specific BAFs based on length-normalized and standardized Hgfish estimates demonstrated up to 50% less variability than those based on non-normalized Hgfish. Permutation analysis indicated that length-normalized and standardized Hgfish estimates based on at least 8 trout or 5 bass resulted in mean Hgfish coefficients of variation less than 20%. These results are intended to support regulatory mercury monitoring and load-reduction program improvements.

The Role of the Sonic Hedgehog Pathway for Prostate Cancer Progression

DTIC Science & Technology

2006-02-01

were reviewed to determine the nature of the disease and the tumor histology . In addition, immunohistochemistry with keratin antibodies was used to...cell carcinomas. This study also includes specimens for normal stomach tissues (n ¼ 11), gastritis (n ¼ 4) and other stomach tissues (n ¼ 3) (see...nature of the disease and the tumor histology [24]. The randomly sorted samples with masked identity were evaluated by at least two independent

Universal aspects of adhesion and atomic force microscopy

NASA Technical Reports Server (NTRS)

Banerjea, Amitava; Smith, John R.; Ferrante, John

1990-01-01

Adhesive energies are computed for flat and atomically sharp tips as a function of the normal distance to the substrate. The dependence of binding energies on tip shape is investigated. The magnitudes of the binding energies for the atomic force microscope are found to depend sensitively on tip material, tip shape and the sample site being probed. The form of the energy-distance curve, however, is universal and independent of these variables, including tip shape.

Pressure induced ageing of polymers

NASA Technical Reports Server (NTRS)

Emri, I.; Knauss, W. G.

1988-01-01

The nonlinearly viscoelastic response of an amorphous homopolymer is considered under aspects of time dependent free volume behavior. In contrast to linearly viscoelastic solids, this model couples shear and volume deformation through a shift function which influences the rate of molecular relaxation or creep. Sample computations produce all those qualitative features one observes normally in uniaxial tension including the rate dependent formation of a yield point as a consequence of the history of an imposed pressure.

A basic introduction to statistics for the orthopaedic surgeon.

PubMed

Bertrand, Catherine; Van Riet, Roger; Verstreken, Frederik; Michielsen, Jef

2012-02-01

Orthopaedic surgeons should review the orthopaedic literature in order to keep pace with the latest insights and practices. A good understanding of basic statistical principles is of crucial importance to the ability to read articles critically, to interpret results and to arrive at correct conclusions. This paper explains some of the key concepts in statistics, including hypothesis testing, Type I and Type II errors, testing of normality, sample size and p values.

Analytical methods for the assessment of endocrine disrupting chemical exposure during human fetal and lactation stages: a review.

PubMed

Jiménez-Díaz, I; Vela-Soria, F; Rodríguez-Gómez, R; Zafra-Gómez, A; Ballesteros, O; Navalón, A

2015-09-10

In the present work, a review of the analytical methods developed in the last 15 years for the determination of endocrine disrupting chemicals (EDCs) in human samples related with children, including placenta, cord blood, amniotic fluid, maternal blood, maternal urine and breast milk, is proposed. Children are highly vulnerable to toxic chemicals in the environment. Among these environmental contaminants to which children are at risk of exposure are EDCs -substances able to alter the normal hormone function of wildlife and humans-. The work focuses mainly on sample preparation and instrumental techniques used for the detection and quantification of the analytes. The sample preparation techniques include, not only liquid-liquid extraction (LLE) and solid-phase extraction (SPE), but also modern microextraction techniques such as extraction with molecular imprinted polymers (MIPs), stir-bar sorptive extraction (SBSE), hollow-fiber liquid-phase microextraction (HF-LPME), dispersive liquid-liquid microextraction (DLLME), matrix solid phase dispersion (MSPD) or ultrasound-assisted extraction (UAE), which are becoming alternatives in the analysis of human samples. Most studies focus on minimizing the number of steps and using the lowest solvent amounts in the sample treatment. The usual instrumental techniques employed include liquid chromatography (LC), gas chromatography (GC) mainly coupled to tandem mass spectrometry. Multiresidue methods are being developed for the determination of several families of EDCs with one extraction step and limited sample preparation. Copyright © 2015 Elsevier B.V. All rights reserved.

Human papillomavirus genotype distribution in Madrid and correlation with cytological data.

PubMed

Martín, Paloma; Kilany, Linah; García, Diego; López-García, Ana M; Martín-Azaña, Ma José; Abraira, Victor; Bellas, Carmen

2011-11-15

Cervical cancer is the second most common cancer in women worldwide. Infection with certain human papillomavirus (HPV) genotypes is the most important risk factor associated with cervical cancer. This study analysed the distribution of type-specific HPV infection among women with normal and abnormal cytology, to assess the potential benefit of prophylaxis with anti-HPV vaccines. Cervical samples of 2,461 women (median age 34 years; range 15-75) from the centre of Spain were tested for HPV DNA. These included 1,656 samples with normal cytology (NC), 336 with atypical squamous cells of undetermined significance (ASCUS), 387 low-grade squamous intraepithelial lesions (LSILs), and 82 high-grade squamous intraepithelial lesions (HSILs). HPV detection and genotyping were performed by PCR using 5'-biotinylated MY09/11 consensus primers, and reverse dot blot hybridisation. HPV infection was detected in 1,062 women (43.2%). Out of these, 334 (31%) samples had normal cytology and 728 (69%) showed some cytological abnormality: 284 (27%) ASCUS, 365 (34%) LSILs, and 79 (8%) HSILs. The most common genotype found was HPV 16 (28%) with the following distribution: 21% in NC samples, 31% in ASCUS, 26% in LSILs, and 51% in HSILs. HPV 53 was the second most frequent (16%): 16% in NC, 16% in ASCUS, 19% in LSILs, and 5% in HSILs. The third genotype was HPV 31 (12%): 10% in NC, 11% in ASCUS, 14% in LSILs, and 11% in HSILs. Co-infections were found in 366 samples (34%). In 25%, 36%, 45% and 20% of samples with NC, ASCUS, LSIL and HSIL, respectively, more than one genotype was found. HPV 16 was the most frequent genotype in our area, followed by HPV 53 and 31, with a low prevalence of HPV 18 even in HSILs. The frequency of genotypes 16, 52 and 58 increased significantly from ASCUS to HSILs. Although a vaccine against HPV 16 and 18 could theoretically prevent approximately 50% of HSILs, genotypes not covered by the vaccine are frequent in our population. Knowledge of the epidemiological distribution is necessary to predict the effect of vaccines on incidence of infection and evaluate cross-protection from current vaccines against infection with other types.

Neighborhood Greenness and Chronic Health Conditions in Medicare Beneficiaries.

PubMed

Brown, Scott C; Lombard, Joanna; Wang, Kefeng; Byrne, Margaret M; Toro, Matthew; Plater-Zyberk, Elizabeth; Feaster, Daniel J; Kardys, Jack; Nardi, Maria I; Perez-Gomez, Gianna; Pantin, Hilda M; Szapocznik, José

2016-07-01

Prior studies suggest that exposure to the natural environment may impact health. The present study examines the association between objective measures of block-level greenness (vegetative presence) and chronic medical conditions, including cardiometabolic conditions, in a large population-based sample of Medicare beneficiaries in Miami-Dade County, Florida. The sample included 249,405 Medicare beneficiaries aged ≥65 years whose location (ZIP+4) within Miami-Dade County, Florida, did not change, from 2010 to 2011. Data were obtained in 2013 and multilevel analyses conducted in 2014 to examine relationships between greenness, measured by mean Normalized Difference Vegetation Index from satellite imagery at the Census block level, and chronic health conditions in 2011, adjusting for neighborhood median household income, individual age, gender, race, and ethnicity. Higher greenness was significantly associated with better health, adjusting for covariates: An increase in mean block-level Normalized Difference Vegetation Index from 1 SD less to 1 SD more than the mean was associated with 49 fewer chronic conditions per 1,000 individuals, which is approximately similar to a reduction in age of the overall study population by 3 years. This same level of increase in mean Normalized Difference Vegetation Index was associated with a reduced risk of diabetes by 14%, hypertension by 13%, and hyperlipidemia by 10%. Planned post-hoc analyses revealed stronger and more consistently positive relationships between greenness and health in lower- than higher-income neighborhoods. Greenness or vegetative presence may be effective in promoting health in older populations, particularly in poor neighborhoods, possibly due to increased time outdoors, physical activity, or stress mitigation. Copyright © 2016 American Journal of Preventive Medicine. Published by Elsevier Inc. All rights reserved.

Mössbauer Spectra of Mouse Hearts Reveal Age-dependent Changes in Mitochondrial and Ferritin Iron Levels.

PubMed

Wofford, Joshua D; Chakrabarti, Mrinmoy; Lindahl, Paul A

2017-03-31

Cardiac function requires continuous high levels of energy, and so iron, a critical player in mitochondrial respiration, is an important component of the heart. Hearts from 57 Fe-enriched mice were evaluated by Mössbauer spectroscopy. Spectra consisted of a sextet and two quadrupole doublets. One doublet was due to residual blood, whereas the other was due to [Fe 4 S 4 ] 2+ clusters and low-spin Fe II hemes, most of which were associated with mitochondrial respiration. The sextet was due to ferritin; there was no evidence of hemosiderin, a ferritin decomposition product. Iron from ferritin was nearly absent in young hearts, but increased steadily with age. EPR spectra exhibited signals similar to those of brain, liver, and human cells. No age-dependent EPR trends were apparent. Hearts from HFE -/- mice with hemochromatosis contained slightly more iron overall than controls, including more ferritin and less mitochondrial iron; these differences typify slightly older hearts, perhaps reflecting the burden due to this disease. HFE -/- livers were overloaded with ferritin but had low mitochondrial iron levels. IRP2 -/- hearts contained less ferritin than controls but normal levels of mitochondrial iron. Hearts of young mice born to an iron-deficient mother contained normal levels of mitochondrial iron and no ferritin; the heart from the mother contained low ferritin and normal levels of mitochondrial iron. High-spin Fe II ions were nearly undetectable in heart samples; these were evident in brains, livers, and human cells. Previous Mössbauer spectra of unenriched diseased human hearts lacked mitochondrial and blood doublets and included hemosiderin features. This suggests degradation of iron-containing species during sample preparation. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Genomic profiling of 766 cancer-related genes in archived esophageal normal and carcinoma tissues.

PubMed

Chen, Jing; Guo, Liping; Peiffer, Daniel A; Zhou, Lixin; Chan, Owen Tsan Mo; Bibikova, Marina; Wickham-Garcia, Eliza; Lu, Shih-Hsin; Zhan, Qimin; Wang-Rodriguez, Jessica; Jiang, Wei; Fan, Jian-Bing

2008-05-15

We employed the BeadArraytrade mark technology to perform a genetic analysis in 33 formalin-fixed, paraffin-embedded (FFPE) human esophageal carcinomas, mostly squamous-cell-carcinoma (ESCC), and their adjacent normal tissues. A total of 1,432 single nucleotide polymorphisms (SNPs) derived from 766 cancer-related genes were genotyped with partially degraded genomic DNAs isolated from these samples. This directly targeted genomic profiling identified not only previously reported somatic gene amplifications (e.g., CCND1) and deletions (e.g., CDKN2A and CDKN2B) but also novel genomic aberrations. Among these novel targets, the most frequently deleted genomic regions were chromosome 3p (including tumor suppressor genes FANCD2 and CTNNB1) and chromosome 5 (including tumor suppressor gene APC). The most frequently amplified genomic region was chromosome 3q (containing DVL3, MLF1, ABCC5, BCL6, AGTR1 and known oncogenes TNK2, TNFSF10, FGF12). The chromosome 3p deletion and 3q amplification occurred coincidently in nearly all of the affected cases, suggesting a molecular mechanism for the generation of somatic chromosomal aberrations. We also detected significant differences in germline allele frequency between the esophageal cohort of our study and normal control samples from the International HapMap Project for 10 genes (CSF1, KIAA1804, IL2, PMS2, IRF7, FLT3, NTRK2, MAP3K9, ERBB2 and PRKAR1A), suggesting that they might play roles in esophageal cancer susceptibility and/or development. Taken together, our results demonstrated the utility of the BeadArray technology for high-throughput genetic analysis in FFPE tumor tissues and provided a detailed genetic profiling of cancer-related genes in human esophageal cancer. (c) 2008 Wiley-Liss, Inc.

Psychometrics of chronic liver disease questionnaire in Chinese chronic hepatitis B patients

PubMed Central

Zhou, Kai-Na; Zhang, Min; Wu, Qian; Ji, Zhen-Hao; Zhang, Xiao-Mei; Zhuang, Gui-Hua

2013-01-01

AIM: To evaluate psychometrics of the Chinese (mainland) chronic liver disease questionnaire (CLDQ) in patients with chronic hepatitis B (CHB). METHODS: A cross-sectional sample of 460 Chinese patients with CHB was selected from the Outpatient Department of the Eighth Hospital of Xi’an, including CHB (CHB without cirrhosis) (n = 323) and CHB-related cirrhosis (n = 137). The psychometrics includes reliability, validity and sensitivity. Internal consistency reliability was measured using Cronbach’s α. Convergent and discriminant validity was evaluated by item-scale correlation. Factorial validity was explored by principal component analysis with varimax rotation. Sensitivity was assessed using Cohen’s effect size (ES), and independent sample t test between CHB and CHB-related cirrhosis groups and between alanine aminotransferase (ALT) normal and abnormal groups after stratifying the disease (CHB and CHB-related cirrhosis). RESULTS: Internal consistency reliability of the CLDQ was 0.83 (range: 0.65-0.90). Most of the hypothesized item-scale correlations were 0.40 or over, and all of such hypothesized correlations were higher than the alternative ones, indicating satisfactory convergent and discriminant validity. Six factors were extracted after varimax rotation from the 29 items of CLDQ. The eligible Cohen’s ES with statistically significant independent sample t test was found in the overall CLDQ and abdominal, systematic, activity scales (CHB vs CHB-related cirrhosis), and in the overall CLDQ and abdominal scale in the stratification of patients with CHB (ALT normal vs abnormal). CONCLUSION: The CLDQ has acceptable reliability, validity and sensitivity in Chinese (mainland) patients with CHB. PMID:23801844

Identification of Reliable Reference Genes for Quantification of MicroRNAs in Serum Samples of Sulfur Mustard-Exposed Veterans.

PubMed

Gharbi, Sedigheh; Shamsara, Mehdi; Khateri, Shahriar; Soroush, Mohammad Reza; Ghorbanmehr, Nassim; Tavallaei, Mahmood; Nourani, Mohammad Reza; Mowla, Seyed Javad

2015-01-01

In spite of accumulating information about pathological aspects of sulfur mustard (SM), the precise mechanism responsible for its effects is not well understood. Circulating microRNAs (miRNAs) are promising biomarkers for disease diagnosis and prognosis. Accurate normalization using appropriate reference genes, is a critical step in miRNA expression studies. In this study, we aimed to identify appropriate reference gene for microRNA quantification in serum samples of SM victims. In this case and control experimental study, using quantitative real-time polymerase chain reaction (qRT-PCR), we evaluated the suitability of a panel of small RNAs including SNORD38B, SNORD49A, U6, 5S rRNA, miR-423-3p, miR-191, miR-16 and miR-103 in sera of 28 SM-exposed veterans of Iran-Iraq war (1980-1988) and 15 matched control volunteers. Different statistical algorithms including geNorm, Normfinder, best-keeper and comparative delta-quantification cycle (Cq) method were employed to find the least variable reference gene. miR-423-3p was identified as the most stably expressed reference gene, and miR- 103 and miR-16 ranked after that. We demonstrate that non-miRNA reference genes have the least stabil- ity in serum samples and that some house-keeping miRNAs may be used as more reliable reference genes for miRNAs in serum. In addition, using the geometric mean of two reference genes could increase the reliability of the normalizers.

Determination of Zn/Cu ratio and oligoelements in serum samples by total reflection X-ray fluorescence spectrometry for cancer diagnosis

NASA Astrophysics Data System (ADS)

Marcó P., L. M.; Jiménez, E.; Hernández C., E. A.; Rojas, A.; Greaves, E. D.

2001-11-01

The method of quantification using the Compton peak as an internal standard, developed in a previous work, was applied to the routine determination of Fe, Cu, Zn and Se in serum samples from normal individuals and cancer patients by total reflection X-ray fluorescence spectrometry. Samples were classified according to age and sex of the donor, in order to determine reference values for normal individuals. Results indicate that the Zn/Cu ratio and the Cu concentration could prove to be useful tools for cancer diagnosis. Significant differences in these parameters between the normal and cancer group were found for all age ranges. The multielemental character of the technique, coupled with the small amounts of sample required and the short analysis time make it a valuable tool in clinical analysis.

Geochemical fingerprinting and source discrimination in soils at the continental scale

NASA Astrophysics Data System (ADS)

Negrel, Philippe; Sadeghi, Martiya; Ladenberger, Anna; Birke, Manfred; Reimann, Clemens

2014-05-01

Agricultural soil (Ap-horizon, 0-20 cm) samples were collected from a large part of Europe (33 countries, 5.6 million km2) at an average density of 1 sample site per 2500 km2. The resulting 2108 soil samples were air dried, sieved to <2 mm, milled and analysed for their major and trace element concentrations by wavelength dispersive X-ray fluorescence spectrometry (WD-XRF). The main goal of this study is to provide a global view of element mobility and source rocks at the continent scale, either by reference to crustal evolution or normalized patterns of element mobility during weathering processes. The survey area includes several sedimentary basins with different geological history, developed in different climate zones and landscapes and with different land use. In order to normalize the chemical composition of soils, mean values and standard deviation of the selected elements have been checked against values for the upper continental crust (UCC). Some elements turned out to be enriched relative to the UCC (Al, P, Zr, Pb) whereas others, like Mg, Na, Sr and Pb were depleted with regards to the variation represented by the standard deviation. The concept of UCC extended normalization patterns have been further used for the selected elements. The mean value of Rb, K, Y, Ti, Al, Si, Zr, Ce and Fe are very close to the UCC model even if standard deviation suggests slight enrichment or depletion, and Zr shows the best fit with the UCC model using both mean value and standard deviation. Lead and Cr are enriched in European soils when compared to UCC but their standard deviation values show very large variations, particularly towards very low values, which can be interpreted as a lithological effect. Element variability has been explored by looking at the variations using indicator elements. Soil data have been converted into Al-normalized enrichment factors and Na was applied as normalizing element for studying provenance source taking into account the main lithologies of the UCC. This latter normalization highlighted variations related to the soluble and insoluble behavior of some elements (K, Rb versus Ti, Al, Si, V, Y, Zr, Ba, and La, respectively), their reactivity (Fe, Mn, Zn), association with carbonates (Ca and Sr) and with phosphates (P and Ce). The maps of normalized composition revealed some problems with use of classical element ratios due to genetical differences in composition of parent material reflected, for example, in large differences in titanium content in bedrock and soil throughout the Europe.

Technical note: An improved approach to determining background aerosol concentrations with PILS sampling on aircraft

NASA Astrophysics Data System (ADS)

Fukami, Christine S.; Sullivan, Amy P.; Ryan Fulgham, S.; Murschell, Trey; Borch, Thomas; Smith, James N.; Farmer, Delphine K.

2016-07-01

Particle-into-Liquid Samplers (PILS) have become a standard aerosol collection technique, and are widely used in both ground and aircraft measurements in conjunction with off-line ion chromatography (IC) measurements. Accurate and precise background samples are essential to account for gas-phase components not efficiently removed and any interference in the instrument lines, collection vials or off-line analysis procedures. For aircraft sampling with PILS, backgrounds are typically taken with in-line filters to remove particles prior to sample collection once or twice per flight with more numerous backgrounds taken on the ground. Here, we use data collected during the Front Range Air Pollution and Photochemistry Éxperiment (FRAPPÉ) to demonstrate that not only are multiple background filter samples are essential to attain a representative background, but that the chemical background signals do not follow the Gaussian statistics typically assumed. Instead, the background signals for all chemical components analyzed from 137 background samples (taken from ∼78 total sampling hours over 18 flights) follow a log-normal distribution, meaning that the typical approaches of averaging background samples and/or assuming a Gaussian distribution cause an over-estimation of background samples - and thus an underestimation of sample concentrations. Our approach of deriving backgrounds from the peak of the log-normal distribution results in detection limits of 0.25, 0.32, 3.9, 0.17, 0.75 and 0.57 μg m-3 for sub-micron aerosol nitrate (NO3-), nitrite (NO2-), ammonium (NH4+), sulfate (SO42-), potassium (K+) and calcium (Ca2+), respectively. The difference in backgrounds calculated from assuming a Gaussian distribution versus a log-normal distribution were most extreme for NH4+, resulting in a background that was 1.58× that determined from fitting a log-normal distribution.

Bayesian evidence computation for model selection in non-linear geoacoustic inference problems.

PubMed

Dettmer, Jan; Dosso, Stan E; Osler, John C

2010-12-01

This paper applies a general Bayesian inference approach, based on Bayesian evidence computation, to geoacoustic inversion of interface-wave dispersion data. Quantitative model selection is carried out by computing the evidence (normalizing constants) for several model parameterizations using annealed importance sampling. The resulting posterior probability density estimate is compared to estimates obtained from Metropolis-Hastings sampling to ensure consistent results. The approach is applied to invert interface-wave dispersion data collected on the Scotian Shelf, off the east coast of Canada for the sediment shear-wave velocity profile. Results are consistent with previous work on these data but extend the analysis to a rigorous approach including model selection and uncertainty analysis. The results are also consistent with core samples and seismic reflection measurements carried out in the area.

Estimating the sample mean and standard deviation from the sample size, median, range and/or interquartile range.

PubMed

Wan, Xiang; Wang, Wenqian; Liu, Jiming; Tong, Tiejun

2014-12-19

In systematic reviews and meta-analysis, researchers often pool the results of the sample mean and standard deviation from a set of similar clinical trials. A number of the trials, however, reported the study using the median, the minimum and maximum values, and/or the first and third quartiles. Hence, in order to combine results, one may have to estimate the sample mean and standard deviation for such trials. In this paper, we propose to improve the existing literature in several directions. First, we show that the sample standard deviation estimation in Hozo et al.'s method (BMC Med Res Methodol 5:13, 2005) has some serious limitations and is always less satisfactory in practice. Inspired by this, we propose a new estimation method by incorporating the sample size. Second, we systematically study the sample mean and standard deviation estimation problem under several other interesting settings where the interquartile range is also available for the trials. We demonstrate the performance of the proposed methods through simulation studies for the three frequently encountered scenarios, respectively. For the first two scenarios, our method greatly improves existing methods and provides a nearly unbiased estimate of the true sample standard deviation for normal data and a slightly biased estimate for skewed data. For the third scenario, our method still performs very well for both normal data and skewed data. Furthermore, we compare the estimators of the sample mean and standard deviation under all three scenarios and present some suggestions on which scenario is preferred in real-world applications. In this paper, we discuss different approximation methods in the estimation of the sample mean and standard deviation and propose some new estimation methods to improve the existing literature. We conclude our work with a summary table (an Excel spread sheet including all formulas) that serves as a comprehensive guidance for performing meta-analysis in different situations.

Scanning transmission ion microscopy mass measurements for quantitative trace element analysis within biological samples and validation using atomic force microscopy thickness measurements

NASA Astrophysics Data System (ADS)

Devès, Guillaume; Cohen-Bouhacina, Touria; Ortega, Richard

2004-10-01

We used the nuclear microprobe techniques, micro-PIXE (particle-induced X-ray emission), micro-RBS (Rutherford backscattering spectrometry) and scanning transmission ion microscopy (STIM) in order to perform the characterization of trace element content and spatial distribution within biological samples (dehydrated cultured cells, tissues). The normalization of PIXE results was usually expressed in terms of sample dry mass as determined by micro-RBS recorded simultaneously to micro-PIXE. However, the main limit of RBS mass measurement is the sample mass loss occurring during irradiation and which could be up to 30% of the initial sample mass. We present here a new methodology for PIXE normalization and quantitative analysis of trace element within biological samples based on dry mass measurement performed by mean of STIM. The validation of STIM cell mass measurements was obtained in comparison with AFM sample thickness measurements. Results indicated the reliability of STIM mass measurement performed on biological samples and suggested that STIM should be performed for PIXE normalization. Further information deriving from direct confrontation of AFM and STIM analysis could as well be obtained, like in situ measurements of cell specific gravity within cells compartment (nucleolus and cytoplasm).

Gene Expression Analysis of Early Stage Endometrial Cancers Reveals Unique Transcripts Associated with Grade and Histology but Not Depth of Invasion

PubMed Central

Risinger, John I.; Allard, Jay; Chandran, Uma; Day, Roger; Chandramouli, Gadisetti V. R.; Miller, Caela; Zahn, Christopher; Oliver, Julie; Litzi, Tracy; Marcus, Charlotte; Dubil, Elizabeth; Byrd, Kevin; Cassablanca, Yovanni; Becich, Michael; Berchuck, Andrew; Darcy, Kathleen M.; Hamilton, Chad A.; Conrads, Thomas P.; Maxwell, G. Larry

2013-01-01

Endometrial cancer is the most common gynecologic malignancy in the United States but it remains poorly understood at the molecular level. This investigation was conducted to specifically assess whether gene expression changes underlie the clinical and pathologic factors traditionally used for determining treatment regimens in women with stage I endometrial cancer. These include the effect of tumor grade, depth of myometrial invasion and histotype. We utilized oligonucleotide microarrays to assess the transcript expression profile in epithelial glandular cells laser microdissected from 79 endometrioid and 12 serous stage I endometrial cancers with a heterogeneous distribution of grade and depth of myometrial invasion, along with 12 normal post-menopausal endometrial samples. Unsupervised multidimensional scaling analyses revealed that serous and endometrioid stage I cancers have similar transcript expression patterns when compared to normal controls where 900 transcripts were identified to be differentially expressed by at least fourfold (univariate t-test, p < 0.001) between the cancers and normal endometrium. This analysis also identified transcript expression differences between serous and endometrioid cancers and tumor grade, but no apparent differences were identified as a function of depth of myometrial invasion. Four genes were validated by quantitative PCR on an independent set of cancer and normal endometrium samples. These findings indicate that unique gene expression profiles are associated with histologic type and grade, but not myometrial invasion among early stage endometrial cancers. These data provide a comprehensive perspective on the molecular alterations associated with stage I endometrial cancer, particularly those subtypes that have the worst prognosis. PMID:23785665

An analytical approach to reduce between-plate variation in multiplex assays that measure antibodies to Plasmodium falciparum antigens.

PubMed

Fang, Rui; Wey, Andrew; Bobbili, Naveen K; Leke, Rose F G; Taylor, Diane Wallace; Chen, John J

2017-07-17

Antibodies play an important role in immunity to malaria. Recent studies show that antibodies to multiple antigens, as well as, the overall breadth of the response are associated with protection from malaria. Yet, the variability and reliability of antibody measurements against a combination of malarial antigens using multiplex assays have not been well characterized. A normalization procedure for reducing between-plate variation using replicates of pooled positive and negative controls was investigated. Sixty test samples (30 from malaria-positive and 30 malaria-negative individuals), together with five pooled positive-controls and two pooled negative-controls, were screened for antibody levels to 9 malarial antigens, including merozoite antigens (AMA1, EBA175, MSP1, MSP2, MSP3, MSP11, Pf41), sporozoite CSP, and pregnancy-associated VAR2CSA. The antibody levels were measured in triplicate on each of 3 plates, and the experiments were replicated on two different days by the same technician. The performance of the proposed normalization procedure was evaluated with the pooled controls for the test samples on both the linear and natural-log scales. Compared with data on the linear scale, the natural-log transformed data were less skewed and reduced the mean-variance relationship. The proposed normalization procedure using pooled controls on the natural-log scale significantly reduced between-plate variation. For malaria-related research that measure antibodies to multiple antigens with multiplex assays, the natural-log transformation is recommended for data analysis and use of the normalization procedure with multiple pooled controls can improve the precision of antibody measurements.

Localization of hypericin-induced fluorescence after Hypericum perforatum polar fraction instillation in normal rat urinary bladder

NASA Astrophysics Data System (ADS)

Stavropoulos, Nikos E.; Skalkos, Dimitris; Tsimaris, Ioannis; Kalogeras, D.; Nseyo, Unyime O.; Batistatou, A.; Agnantis, N. J.

2005-04-01

The photodynamic action of the Hypericum perforatum L. extract, mainly its polar methanolic fraction (PMF) has recently been substantiated by our group. The herb contains a number of naphthodianthrones - photosensitizers mainly hypericin and pseudohypericin. The concentration of hypericins in PMF was found to be 1.37 %. The distribution of hypericins fluorescence in sections of normal rat bladder tissues after the intravesical instillation of the polar methanolic fraction of hypericum (PMF) was studied by the use of fluorescence microscopy. PMF was dissolved in normal saline containing 0.5 μg/ml concentration of hypericins, and was then instilled in rat bladder for 15, 30, 60 and 120 minutes respectively. PMF solutions were withdrawn, bladders were rinsed through the catheter with normal saline and rats were sacrificed. Bladders were then removed, cut open and immediately mounted in medium, and immersed in liquid nitrogen. Two consecutive 3-μm frozen sections were cut with a cryostat. The first section was examined by fluorescence microscopy and the second section was stained with hematoxylin and eosin. For fluorescence imaging the filter set used included a 535/50 nm bandpass excitation filter and a 610/75 nm emission filter. Fluorescence images were acquired and documented using photography. Fluorescene could be detected in bladder samples after only 15 minutes of instillation with the above described solution. The urothelium / muscle fluorescence ratio ranged from 5/1 to 11/1 in various sites of the samples examined. No fluorescence originating from the muscle could be detected. PMF should be further studied towards the direction of its use in photodynamic therapy.

Leveraging increased cytoplasmic nucleoside kinase activity to target mtDNA and oxidative phosphorylation in AML.

PubMed

Liyanage, Sanduni U; Hurren, Rose; Voisin, Veronique; Bridon, Gaëlle; Wang, Xiaoming; Xu, ChangJiang; MacLean, Neil; Siriwardena, Thirushi P; Gronda, Marcela; Yehudai, Dana; Sriskanthadevan, Shrivani; Avizonis, Daina; Shamas-Din, Aisha; Minden, Mark D; Bader, Gary D; Laposa, Rebecca; Schimmer, Aaron D

2017-05-11

Mitochondrial DNA (mtDNA) biosynthesis requires replication factors and adequate nucleotide pools from the mitochondria and cytoplasm. We performed gene expression profiling analysis of 542 human acute myeloid leukemia (AML) samples and identified 55% with upregulated mtDNA biosynthesis pathway expression compared with normal hematopoietic cells. Genes that support mitochondrial nucleotide pools, including mitochondrial nucleotide transporters and a subset of cytoplasmic nucleoside kinases, were also increased in AML compared with normal hematopoietic samples. Knockdown of cytoplasmic nucleoside kinases reduced mtDNA levels in AML cells, demonstrating their contribution in maintaining mtDNA. To assess cytoplasmic nucleoside kinase pathway activity, we used a nucleoside analog 2'3'-dideoxycytidine (ddC), which is phosphorylated to the activated antimetabolite, 2'3'-dideoxycytidine triphosphate by cytoplasmic nucleoside kinases. ddC is a selective inhibitor of the mitochondrial DNA polymerase γ. ddC was preferentially activated in AML cells compared with normal hematopoietic progenitor cells. ddC treatment inhibited mtDNA replication, oxidative phosphorylation, and induced cytotoxicity in a panel of AML cell lines. Furthermore, ddC preferentially inhibited mtDNA replication in a subset of primary human leukemia cells and selectively targeted leukemia cells while sparing normal progenitor cells. In animal models of human AML, treatment with ddC decreased mtDNA, electron transport chain proteins, and induced tumor regression without toxicity. ddC also targeted leukemic stem cells in secondary AML xenotransplantation assays. Thus, AML cells have increased cytidine nucleoside kinase activity that regulates mtDNA biogenesis and can be leveraged to selectively target oxidative phosphorylation in AML. © 2017 by The American Society of Hematology.

Leveraging increased cytoplasmic nucleoside kinase activity to target mtDNA and oxidative phosphorylation in AML

PubMed Central

Liyanage, Sanduni U.; Hurren, Rose; Voisin, Veronique; Bridon, Gaëlle; Wang, Xiaoming; Xu, ChangJiang; MacLean, Neil; Siriwardena, Thirushi P.; Gronda, Marcela; Yehudai, Dana; Sriskanthadevan, Shrivani; Avizonis, Daina; Shamas-Din, Aisha; Minden, Mark D.; Bader, Gary D.; Laposa, Rebecca

2017-01-01

Mitochondrial DNA (mtDNA) biosynthesis requires replication factors and adequate nucleotide pools from the mitochondria and cytoplasm. We performed gene expression profiling analysis of 542 human acute myeloid leukemia (AML) samples and identified 55% with upregulated mtDNA biosynthesis pathway expression compared with normal hematopoietic cells. Genes that support mitochondrial nucleotide pools, including mitochondrial nucleotide transporters and a subset of cytoplasmic nucleoside kinases, were also increased in AML compared with normal hematopoietic samples. Knockdown of cytoplasmic nucleoside kinases reduced mtDNA levels in AML cells, demonstrating their contribution in maintaining mtDNA. To assess cytoplasmic nucleoside kinase pathway activity, we used a nucleoside analog 2′3′-dideoxycytidine (ddC), which is phosphorylated to the activated antimetabolite, 2′3′-dideoxycytidine triphosphate by cytoplasmic nucleoside kinases. ddC is a selective inhibitor of the mitochondrial DNA polymerase γ. ddC was preferentially activated in AML cells compared with normal hematopoietic progenitor cells. ddC treatment inhibited mtDNA replication, oxidative phosphorylation, and induced cytotoxicity in a panel of AML cell lines. Furthermore, ddC preferentially inhibited mtDNA replication in a subset of primary human leukemia cells and selectively targeted leukemia cells while sparing normal progenitor cells. In animal models of human AML, treatment with ddC decreased mtDNA, electron transport chain proteins, and induced tumor regression without toxicity. ddC also targeted leukemic stem cells in secondary AML xenotransplantation assays. Thus, AML cells have increased cytidine nucleoside kinase activity that regulates mtDNA biogenesis and can be leveraged to selectively target oxidative phosphorylation in AML. PMID:28283480

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

Normalization of RNA-seq data using factor analysis of control genes or samples

PubMed Central

Risso, Davide; Ngai, John; Speed, Terence P.; Dudoit, Sandrine

2015-01-01

Normalization of RNA-seq data has proven essential to ensure accurate inference of expression levels. Here we show that usual normalization approaches mostly account for sequencing depth and fail to correct for library preparation and other more-complex unwanted effects. We evaluate the performance of the External RNA Control Consortium (ERCC) spike-in controls and investigate the possibility of using them directly for normalization. We show that the spike-ins are not reliable enough to be used in standard global-scaling or regression-based normalization procedures. We propose a normalization strategy, remove unwanted variation (RUV), that adjusts for nuisance technical effects by performing factor analysis on suitable sets of control genes (e.g., ERCC spike-ins) or samples (e.g., replicate libraries). Our approach leads to more-accurate estimates of expression fold-changes and tests of differential expression compared to state-of-the-art normalization methods. In particular, RUV promises to be valuable for large collaborative projects involving multiple labs, technicians, and/or platforms. PMID:25150836

Experiments with central-limit properties of spatial samples from locally covariant random fields

USGS Publications Warehouse

Barringer, T.H.; Smith, T.E.

1992-01-01

When spatial samples are statistically dependent, the classical estimator of sample-mean standard deviation is well known to be inconsistent. For locally dependent samples, however, consistent estimators of sample-mean standard deviation can be constructed. The present paper investigates the sampling properties of one such estimator, designated as the tau estimator of sample-mean standard deviation. In particular, the asymptotic normality properties of standardized sample means based on tau estimators are studied in terms of computer experiments with simulated sample-mean distributions. The effects of both sample size and dependency levels among samples are examined for various value of tau (denoting the size of the spatial kernel for the estimator). The results suggest that even for small degrees of spatial dependency, the tau estimator exhibits significantly stronger normality properties than does the classical estimator of standardized sample means. ?? 1992.

Total and regional brain volumes in a population-based normative sample from 4 to 18 years: the NIH MRI Study of Normal Brain Development.

PubMed

2012-01-01

Using a population-based sampling strategy, the National Institutes of Health (NIH) Magnetic Resonance Imaging Study of Normal Brain Development compiled a longitudinal normative reference database of neuroimaging and correlated clinical/behavioral data from a demographically representative sample of healthy children and adolescents aged newborn through early adulthood. The present paper reports brain volume data for 325 children, ages 4.5-18 years, from the first cross-sectional time point. Measures included volumes of whole-brain gray matter (GM) and white matter (WM), left and right lateral ventricles, frontal, temporal, parietal and occipital lobe GM and WM, subcortical GM (thalamus, caudate, putamen, and globus pallidus), cerebellum, and brainstem. Associations with cross-sectional age, sex, family income, parental education, and body mass index (BMI) were evaluated. Key observations are: 1) age-related decreases in lobar GM most prominent in parietal and occipital cortex; 2) age-related increases in lobar WM, greatest in occipital, followed by the temporal lobe; 3) age-related trajectories predominantly curvilinear in females, but linear in males; and 4) small systematic associations of brain tissue volumes with BMI but not with IQ, family income, or parental education. These findings constitute a normative reference on regional brain volumes in children and adolescents.

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

PubMed

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

2015-12-29

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

Vitrification of neat semen alters sperm parameters and DNA integrity.

PubMed

Khalili, Mohammad Ali; Adib, Maryam; Halvaei, Iman; Nabi, Ali

2014-05-06

Our aim was to evaluate the effect of neat semen vitrification on human sperm vital parameters and DNA integrity in men with normal and abnormal sperm parameters. Semen samples were 17 normozoospermic samples and 17 specimens with abnormal sperm parameters. Semen analysis was performed according to World Health Organization (WHO) criteria. Then, the smear was provided from each sample and fixed for terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) staining. Vitrification of neat semen was done by plunging cryoloops directly into liquid nitrogen and preserved for 7 days. The samples were warmed and re-evaluated for sperm parameters as well as DNA integrity. Besides, the correlation between sperm parameters and DNA fragmentation was assessed pre- and post vitrification. Cryopreserved spermatozoa showed significant decrease in sperm motility, viability and normal morphology after thawing in both normal and abnormal semen. Also, the rate of sperm DNA fragmentation was significantly higher after vitrification compared to fresh samples in normal (24.76 ± 5.03 and 16.41 ± 4.53, P = .002) and abnormal (34.29 ± 10.02 and 23.5 ± 8.31, P < .0001), respectively. There was negative correlation between sperm motility and sperm DNA integrity in both groups after vitrification. Vitrification of neat ejaculates has negative impact on sperm parameters as well as DNA integrity, particularly among abnormal semen subjects. It is, therefore, recommend to process semen samples and vitrify the sperm pellets.

Photoacoustic study on the possible components of total suspended particles

NASA Astrophysics Data System (ADS)

Wang, Xidong; Huang, Zuohua; Tang, Zhilie

2006-02-01

Total suspended particles (TSP) are one of the main atmospheric pollutants. The ingredients are very complex, mainly including black carbon (C),organic compound, inorganic compound and biologic component, which will do great harm to human's health. During environmental monitoring, the airborne suspended particle always is an index for evaluating the quality of atmosphere. In this article, possible mixture of TSP is proposed to determine its ingredients and content by photoacoustic spectroscopy. The normalized photoacoustic (PA) signal of the sulfur powder, mixtures of sulfur and black carbon in different proportions are obtained respectively. Simulation with linear equation says that the PA signal has a certain relationship with the content of sample. The normalized PA spectroscopy of various materials is acquired via examining the sample of the powder of cupric sulfate mixed with nitro compound (2, 5 -methoxybenzoic-4nitro-dehyde), Portland cement, residual particles of automobile exhaust pipe, ash of power plant's stocks. The experimental results have important reference value to the practical analysis of TSP, it also provides new possible methodology to the environmental monitoring.

Longitudinal Stability and Predictors of Poor Oral Comprehenders and Poor Decoders

PubMed Central

Elwér, Åsa; Keenan, Janice M.; Olson, Richard K.; Byrne, Brian; Samuelsson, Stefan

2012-01-01

Two groups of 4th grade children were selected from a population sample (N= 926) to either be Poor Oral Comprehenders (poor oral comprehension but normal word decoding), or Poor Decoders (poor decoding but normal oral comprehension). By examining both groups in the same study with varied cognitive and literacy predictors, and examining them both retrospectively and prospectively, we could assess how distinctive and stable the predictors of each deficit are. Predictors were assessed retrospectively at preschool, at the end of kindergarten, 1st, and 2nd grades. Group effects were significant at all test occasions, including those for preschool vocabulary (worse in poor oral comprehenders) and rapid naming (RAN) (worse in poor decoders). Preschool RAN and Vocabulary prospectively predicted grade 4 group membership (77–79% correct classification) within the selected samples. Reselection in preschool of at-risk poor decoder and poor oral comprehender subgroups based on these variables led to significant but relatively weak prediction of subtype membership at grade 4. Implications of the predictive stability of our results for identification and intervention of these important subgroups are discussed. PMID:23528975

A comparison of protein profiles of cervical tissue homogenate, exfoliated cells from cervix and serum in normal and cervical malignancy conditions.

PubMed

Bhat, Sujatha; Kartha, Vasudevan Bhaskaran; Rai, Lavanya; Chidangil, Santhosh

2015-01-01

Cervical cancer, the second most common cancer in women, progresses silently over long periods before producing any clinical manifestation. Research in early detection of this condition using proteomic techniques is of very recent origin. We used high-performance liquid chromatography combined with laser-induced fluorescence method in our lab to record the protein profiles of tissue homogenate, cell lysate and serum samples of normal and different stages of malignant conditions of the cervix. Information on protein markers in the protein profiles was derived using various data processing methods including curve resolution. The variations in relative intensities of different peaks with respect to peak height, width and area under the curve from different sample types were compared to get information regarding the concentration of the various proteins and their significance in the induction and metastasis of cervical cancer. The method can be used in diagnosis, follow-up with respect to the progression, remission and effective therapy, in cervical malignancy. © The Author [2014]. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Considerations for potency equivalent calculations in the Ah receptor-based CALUX bioassay: Normalization of superinduction results for improved sample potency estimation

PubMed Central

Baston, David S.; Denison, Michael S.

2011-01-01

The chemically activated luciferase expression (CALUX) system is a mechanistically based recombinant luciferase reporter gene cell bioassay used in combination with chemical extraction and clean-up methods for the detection and relative quantitation of 2,3,7,8-tetrachlorodibenzo-p-dioxin and related dioxin-like halogenated aromatic hydrocarbons in a wide variety of sample matrices. While sample extracts containing complex mixtures of chemicals can produce a variety of distinct concentration-dependent luciferase induction responses in CALUX cells, these effects are produced through a common mechanism of action (i.e. the Ah receptor (AhR)) allowing normalization of results and sample potency determination. Here we describe the diversity in CALUX response to PCDD/Fs from sediment and soil extracts and not only report the occurrence of superinduction of the CALUX bioassay, but we describe a mechanistically based approach for normalization of superinduction data that results in a more accurate estimation of the relative potency of such sample extracts. PMID:21238730

High throughput image cytometry for detection of suspicious lesions in the oral cavity

NASA Astrophysics Data System (ADS)

MacAulay, Calum; Poh, Catherine F.; Guillaud, Martial; Michele Williams, Pamela; Laronde, Denise M.; Zhang, Lewei; Rosin, Miriam P.

2012-08-01

The successful management of oral cancer depends upon early detection, which relies heavily on the clinician's ability to discriminate sometimes subtle alterations of the infrequent premalignant lesions from the more common reactive and inflammatory conditions in the oral mucosa. Even among experienced oral specialists this can be challenging, particularly when using new wide field-of-view direct fluorescence visualization devices clinically introduced for the recognition of at-risk tissue. The objective of this study is to examine if quantitative cytometric analysis of oral brushing samples could facilitate the assessment of the risk of visually ambiguous lesions. About 369 cytological samples were collected and analyzed: (1) 148 samples from pathology-proven sites of SCC, carcinoma in situ or severe dysplasia; (2) 77 samples from sites with inflammation, infection, or trauma, and (3) 144 samples from normal sites. These were randomly separated into training and test sets. The best algorithm correctly recognized 92.5% of the normal samples, 89.4% of the abnormal samples, 86.2% of the confounders in the training set as well as 100% of the normal samples, and 94.4% of the abnormal samples in the test set. These data suggest that quantitative cytology could reduce by more than 85% the number of visually suspect lesions requiring further assessment by biopsy.

Evaluation of Interleukin-17 and Interleukin-23 in Pterygium: Immunohistochemistry Study.

PubMed

Tiong, Kiew Ing; Mohd Zahidin, Aida Zairani; Sumugam, S Kala A/P; Uchang, Joseph; Mohd Isa, Hazlita Dato'

2017-01-01

To compare the interleukin-17 (IL-17) and interleukin-23 (IL-23) positive cell counts between pterygium and normal conjunctiva. A case-control study. This study received ethical approval (NMRR Research ID 23957) and informed consent was obtained from all participants. It involved 20 participants with 20 samples of pterygium and 20 samples of normal conjunctiva that were obtained from the same eye of each participant. All the participants underwent history taking, slit lamp examination, and pterygium excision surgery. Both samples underwent immunohistochemistry procedure. Pretreatment procedure was conducted using heat-induced epitope retrieval with PT link, subsequently followed by EnVision FLEX staining procedure and incubation with anti‒IL-17 antibody and anti‒IL-23 antibody. Slides were examined in high-power fields (400x) for both samples in 3 different fields. Total positive stained cell counts in all 3 fields with IL-17 and IL-23 between pterygium and normal conjunctiva were analyzed by using Wilcoxon signed rank test. IL-17 positive cell counts for normal conjunctiva showed mean 196.10 ± 80.487 but for pterygium was 331.10 ± 108.416. As for IL-23, the mean for positive cell counts for normal conjunctiva was 62.10 ± 33.462 and IL-23 positive cell counts for pterygium showed mean 102.95 ± 41.378. Both IL-17 and IL-23 were significantly increased in pterygium compared with normal conjunctiva (P < 0.001). Both IL-17 and IL-23 were found to be significantly higher in the pterygium group than in the normal conjunctiva group with P < 0.001 by Wilcoxon signed rank test. Copyright 2017 Asia-Pacific Academy of Ophthalmology.

Comparative metabolites profiles of osthole in normal and osteoporosis rats using liquid chromatography quadrupole time-of-flight mass spectrometry.

PubMed

Wang, Nani; Wang, Xuping; Zhang, Yang; Zhang, Qiaoyan; Xu, Pingcui; Xin, Hailiang; Wu, Renjie; Shou, Dan; Qin, Luping

2018-05-30

Osthole is a derivative of coumnarin, which has been used to treat several diseases, including osteoporosis. To investigate the metabolite profile of osthole in osteoporosis rats was utilized to understand its underlying mechanisms of its anti-osteoporosis effect. In this study, plasma samples were collected from normal and osteoporosis rats after oral administration of osthole and analyzed to identify the metabolites of osthole by high performance liquid chromatography quadrupole time-of-flight mass spectrometry. By comparing the molecular weight and MS fragmentation of the metabolites with those of parent drug and reference standards, a total of 36 metabolites in plasma were identified. Demethylation, hydroxylation, hydroxymethylene loss and reduction, and subsequent glucuronidation, methylation and sulfation were the major metabolic pathways of osthole in both normal and osteoporosis rats. A specific hydration metabolic pathway was found in osteoporosis rats. These results provided a meaningful basis for studying the underlying mechanism of the anti-osteoporosis effect of osthole. Copyright © 2018 Elsevier B.V. All rights reserved.

Personality correlates of criminals: A comparative study between normal controls and criminals.

PubMed

Sinha, Sudhinta

2016-01-01

Personality is a major factor in many kinds of behavior, one of which is criminal behavior. To determine what makes a criminal "a criminal," we must understand his/her personality. This study tries to identify different personality traits which link criminals to their personality. In the present study, 37 male criminals of district jail of Dhanbad (Jharkhand) and 36 normal controls were included on a purposive sampling basis. Each criminal was given a personal datasheet and Cattel's 16 personality factors (PFs) scale for assessing their sociodemographic variables and different personality traits. The objective of this study was to examine the relation between personality traits and criminal behavior, and to determine whether such factors are predictive of future recidivism. Results indicated high scores on intelligence, impulsiveness, suspicion, self-sufficient, spontaneity, self-concept control factors, and very low scores on emotionally less stable on Cattel's 16 PFs scale in criminals as compared with normal. Criminals differ from general population or non criminals in terms of personality traits.

Nonequilibrium transport of charge carriers and transient electroluminescence in organic light-emitting diodes

NASA Astrophysics Data System (ADS)

Nikitenko, V. R.; von Seggern, H.

2007-11-01

An analytic theory of nonequilibrium hopping charge transport in disordered organic materials includes quasiequilibrium (normal) and extremely nonequilibrium (dispersive) regimes as limiting cases at long and short times, respectively. In the intermediate interval of time quasiequilibrium value of mobility is nearly established while the coefficient of field-assisted diffusion continues to increase (quasidispersive regime). Therefore, normalized time dependencies of transient current in time-of-flight (TOF) conditions are practically independent of field strength and sample thickness, in good agreement both with data of TOF experiments for molecularly doped polymers and results of numerical simulations of Gaussian disorder model. An analytic model of transient electroluminescence (TEL) is developed on the base of the mentioned theory. Strong asymmetry of mobilities is presumed. In analogy with TOF transients, dispersion parameter of normalized TEL intensity is anomalously large and almost field independent in the quasidispersive regime of transport. The method for determination of mobility from TEL data is proposed.

The diagnostic capability of laser induced fluorescence in the characterization of excised breast tissues

NASA Astrophysics Data System (ADS)

Galmed, A. H.; Elshemey, Wael M.

2017-08-01

Differentiating between normal, benign and malignant excised breast tissues is one of the major worldwide challenges that need a quantitative, fast and reliable technique in order to avoid personal errors in diagnosis. Laser induced fluorescence (LIF) is a promising technique that has been applied for the characterization of biological tissues including breast tissue. Unfortunately, only few studies have adopted a quantitative approach that can be directly applied for breast tissue characterization. This work provides a quantitative means for such characterization via introduction of several LIF characterization parameters and determining the diagnostic accuracy of each parameter in the differentiation between normal, benign and malignant excised breast tissues. Extensive analysis on 41 lyophilized breast samples using scatter diagrams, cut-off values, diagnostic indices and receiver operating characteristic (ROC) curves, shows that some spectral parameters (peak height and area under the peak) are superior for characterization of normal, benign and malignant breast tissues with high sensitivity (up to 0.91), specificity (up to 0.91) and accuracy ranking (highly accurate).

Genome-wide identification of RNA editing in hepatocellular carcinoma.

PubMed

Kang, Lin; Liu, Xiaoqiao; Gong, Zhoulin; Zheng, Hancheng; Wang, Jun; Li, Yingrui; Yang, Huanming; Hardwick, James; Dai, Hongyue; Poon, Ronnie T P; Lee, Nikki P; Mao, Mao; Peng, Zhiyu; Chen, Ronghua

2015-02-01

We did whole-transcriptome sequencing and whole-genome sequencing on nine pairs of Hepatocellular carcinoma (HCC) tumors and matched adjacent tissues to identify RNA editing events. We identified mean 26,982 editing sites with mean 89.5% canonical A→G edits in each sample using an improved bioinformatics pipeline. The editing rate was significantly higher in tumors than adjacent normal tissues. Comparing the difference between tumor and normal tissues of each patient, we found 7 non-synonymous tissue specific editing events including 4 tumor-specific edits and 3 normal-specific edits in the coding region, as well as 292 edits varying in editing degree. The significant expression changes of 150 genes associated with RNA editing were found in tumors, with 3 of the 4 most significant genes being cancer related. Our results show that editing might be related to higher gene expression. These findings indicate that RNA editing modification may play an important role in the development of HCC. Copyright © 2014 Elsevier Inc. All rights reserved.

Evaluation of Chemical Warfare Agent Wipe Sampling ...

EPA Pesticide Factsheets

Report This investigation tested specific (CWAs), including sarin (GB), soman (GD), cyclosarin (GF), sulfur mustard (HD), and O-ethyl-S-(2-diisopropylaminoethyl) methylphosphonothioate (VX) on the non-ideal (e.g., porous and permeable) surfaces of drywall, vinyl tile, wood, laminate, and coated glass. Pesticides (diazinon and malathion) were used so that a comparison is possible with existing literature data (1). Experiments included testing with coupons having surface areas of 10 cm2 and 100 cm2. The 10-cm2 coupons were of a size that could easily be extracted in a 2 oz jar (to provide comparative data for CWA recoveries generated by direct extraction) and the 100-cm2 coupons better represented the area of a surface that might typically be sampled by wipe extraction. In addition, CWA, at a normalized surface concentration of 0.1 µg per cm2 surface area, were spiked on coupons of the tested surfaces. Wipes were wetted with either dichloromethane (DCM) or isopropanol (IPA) before sampling for CWA. Experimental parameters include multiple wipe types, porous/permeable surfaces, coupon surface area, solvent used to wet the wipe (i.e., wetting solvent), and the utility of VX-d14 as an extracted internal standard.

Perceived interpersonal mistreatment among obese Americans: do race, class, and gender matter?

PubMed

Carr, Deborah; Jaffe, Karen J; Friedman, Michael A

2008-11-01

We examine the extent to which body weight affects three types of perceived interpersonal mistreatment, and evaluate whether these patterns vary by race, social class, and gender in a large sample of American men and women. We use data from the first wave (1995) of the Midlife Development in the United States (N = 3,511), a survey of persons aged 25-74, to contrast underweight, normal weight, overweight, obese I, and obese II/III persons' reports of three types of perceived interpersonal mistreatment: disrespectful treatment; harassment/teasing; and being treated as if one has a character flaw. We assess whether these relationships are contingent upon one's gender, race, and occupational status. We control for possible confounding influences, including physical and mental health. In the total sample, obese I and obese II/III persons report significantly higher levels of all three types of perceived mistreatment (compared to normal weight persons), even when demographic, socioeconomic status, and health characteristics are controlled. Among black men, however, obese II/III persons report significantly lower levels of all three types of perceived mistreatment, compared to their normal weight peers. Among both men and women, obese professional workers report significantly more perceived interpersonal mistreatment, compared to obese persons of lower socioeconomic status. These findings reveal the ways that intersecting social identities may shape obese Americans' perceptions of stigmatizing interpersonal encounters.

LDOC1 mRNA is differentially expressed in chronic lymphocytic leukemia and predicts overall survival in untreated patients

PubMed Central

Duzkale, Hatice; Schweighofer, Carmen D.; Coombes, Kevin R.; Barron, Lynn L.; Ferrajoli, Alessandra; O'Brien, Susan; Wierda, William G.; Pfeifer, John; Majewski, Tadeusz; Czerniak, Bogdan A.; Jorgensen, Jeffrey L.; Medeiros, L. Jeffrey; Freireich, Emil J; Keating, Michael J.

2011-01-01

We previously identified LDOC1 as one of the most significantly differentially expressed genes in untreated chronic lymphocytic leukemia (CLL) patients with respect to the somatic mutation status of the immunoglobulin heavy-chain variable region genes. However, little is known about the normal function of LDOC1, its contribution to the pathophysiology of CLL, or its prognostic significance. In this study, we have investigated LDOC1 mRNA expression in a large cohort of untreated CLL patients, as well as in normal peripheral blood B-cell (NBC) subsets and primary B-cell lymphoma samples. We have confirmed that LDOC1 is dramatically down-regulated in mutated CLL cases compared with unmutated cases, and have identified a new splice variant, LDOC1S. We show that LDOC1 is expressed in NBC subsets (naive > memory), suggesting that it may play a role in normal B-cell development. It is also expressed in primary B-cell lymphoma samples, in which its expression is associated with somatic mutation status. In CLL, we show that high levels of LDOC1 correlate with biomarkers of poor prognosis, including cytogenetic markers, unmutated somatic mutation status, and ZAP70 expression. Finally, we demonstrate that LDOC1 mRNA expression is an excellent predictor of overall survival in untreated CLL patients. PMID:21310924

Pilot Study: The Role of the Hemispheric Lateralization in Mental Disorders by Use of the Limb (Eye, Hand, Foot) Dominance

PubMed Central

Goodarzi, Naser; Dabbaghi, Parviz; Valipour, Habib; Vafadari, Behnam

2015-01-01

Introduction: Based on the previous studies, we know that the hemispheric lateralization defects, increase the probability of psychological disorders. We also know that dominant limb is controlled by dominant hemisphere and limb preference is used as an indicator for hemisphere dominance. In this study we attempted to explore the hemispheric dominance by the use of three limbs (hand, foot and eye). Methods: We performed this survey on two samples, psychiatric patients compared with normal population. For this purpose, knowing that the organ dominance is stabilized in adolescence, and age has no effect on the people above 15, we used 48 high school girls and 65 boys as the final samples of normal population. The patient group included 57 male and 26 female who were chronic psychiatric patients. Results: The result shows that left-eye dominance is more in patients than the normal group (P=0.000) but the handedness and footedness differences are not significance. In psychotic, bipolar and depressive disorders, eye dominance had significant difference (P=0.018). But this is not true about hand and foot dominance. Discussion: Our findings proved that generally in psychiatric patients, left-eye dominance is more common, left-eye dominance is also more in psychotic and depressive disorders. It is less common in bipolar disorders. PMID:27307954

Perceived Interpersonal Mistreatment Among Obese Americans: Do Race, Class, and Gender Matter?

PubMed Central

Carr, Deborah; Jaffe, Karen J.; Friedman, Michael A.

2010-01-01

Objective: We examine the extent to which body weight affects three types of perceived interpersonal mistreatment, and evaluate whether these patterns vary by race, social class, and gender in a large sample of American men and women. Methods and Procedures: We use data from the first wave (1995) of the Midlife Development in the United States (N = 3,511), a survey of persons aged 25–74, to contrast underweight, normal weight, overweight, obese I, and obese II/III persons' reports of three types of perceived interpersonal mistreatment: disrespectful treatment; harassment/teasing; and being treated as if one has a character flaw. We assess whether these relationships are contingent upon one's gender, race, and occupational status. We control for possible confounding influences, including physical and mental health. Results: In the total sample, obese I and obese II/III persons report significantly higher levels of all three types of perceived mistreatment (compared to normal weight persons), even when demographic, socioeconomic status, and health characteristics are controlled. Among black men, however, obese II/III persons report significantly lower levels of all three types of perceived mistreatment, compared to their normal weight peers. Among both men and women, obese professional workers report significantly more perceived interpersonal mistreatment, compared to obese persons of lower socioeconomic status. Discussion: These findings reveal the ways that intersecting social identities may shape obese Americans' perceptions of stigmatizing interpersonal encounters. PMID:18978765

Role of Dicer1 in thyroid cell proliferation and differentiation.

PubMed

Penha, Ricardo Cortez Cardoso; Sepe, Romina; De Martino, Marco; Esposito, Francesco; Pellecchia, Simona; Raia, Maddalena; Del Vecchio, Luigi; Decaussin-Petrucci, Myriam; De Vita, Gabriella; Pinto, Luis Felipe Ribeiro; Fusco, Alfredo

2017-01-01

DICER1 plays a central role in the biogenesis of microRNAs and it is important for normal development. Altered microRNA expression and DICER1 dysregulation have been described in several types of tumors, including thyroid carcinomas. Recently, our group identified a new somatic mutation (c.5438A>G; E1813G) within DICER1 gene of an unknown function. Herein, we show that DICER1 is overexpressed, at mRNA level, in a significant-relative number of papillary (70%) and anaplastic (42%) thyroid carcinoma samples, whereas is drastically downregulated in all the analyzed human thyroid carcinoma cell lines (TPC-1, BCPAP, FRO and 8505c) in comparison with normal thyroid tissue samples. Conversely, DICER1 is downregulated, at protein level, in PTC in comparison with normal thyroid tissues. Our data also reveals that DICER1 overexpression positively regulates thyroid cell proliferation, whereas its silencing impairs thyroid cell differentiation. The expression of DICER1 gene mutation (c.5438A>G; E1813G) negatively affects the microRNA machinery and cell proliferation as well as upregulates DICER1 protein levels of thyroid cells but has no impact on thyroid differentiation. In conclusion, DICER1 protein is downregulated in papillary thyroid carcinomas and affects thyroid proliferation and differentiation, while DICER1 gene mutation (c.5438A>G; E1813G) compromises the DICER1 wild-type-mediated microRNA processing and cell proliferation.

A systematic evaluation of normalization methods in quantitative label-free proteomics.

PubMed

Välikangas, Tommi; Suomi, Tomi; Elo, Laura L

2018-01-01

To date, mass spectrometry (MS) data remain inherently biased as a result of reasons ranging from sample handling to differences caused by the instrumentation. Normalization is the process that aims to account for the bias and make samples more comparable. The selection of a proper normalization method is a pivotal task for the reliability of the downstream analysis and results. Many normalization methods commonly used in proteomics have been adapted from the DNA microarray techniques. Previous studies comparing normalization methods in proteomics have focused mainly on intragroup variation. In this study, several popular and widely used normalization methods representing different strategies in normalization are evaluated using three spike-in and one experimental mouse label-free proteomic data sets. The normalization methods are evaluated in terms of their ability to reduce variation between technical replicates, their effect on differential expression analysis and their effect on the estimation of logarithmic fold changes. Additionally, we examined whether normalizing the whole data globally or in segments for the differential expression analysis has an effect on the performance of the normalization methods. We found that variance stabilization normalization (Vsn) reduced variation the most between technical replicates in all examined data sets. Vsn also performed consistently well in the differential expression analysis. Linear regression normalization and local regression normalization performed also systematically well. Finally, we discuss the choice of a normalization method and some qualities of a suitable normalization method in the light of the results of our evaluation. © The Author 2016. Published by Oxford University Press.

Body Dissatisfaction in Individuals with Obesity Compared to Normal-Weight Individuals: A Systematic Review and Meta-Analysis

PubMed Central

Weinberger, Natascha-Alexandra; Kersting, Anette; Riedel-Heller, Steffi G.; Luck-Sikorski, Claudia

2017-01-01

Background Body dissatisfaction has been identified as a psychological correlate of obesity that is related to disordered eating, poor self-esteem, and depression. However, not all individuals with obesity are equally vulnerable to these correlates, and ‘normative discontent’ is present in individuals with normal weight, too. In this light, the complex relationship of body image and individual weight status seems like a worthwhile direction of research inquiry. As such, this review aims to systematically explore the degree of body dissatisfaction in individuals with obesity compared to normal-weight individuals. Methods A systematic literature search was conducted. All quantitative studies of adult samples reporting results regarding differences in body dissatisfaction between individuals with normal weight and obesity were included. Results 17 articles were found. Across studies, individuals with obesity reported higher body dissatisfaction than normal-weight individuals (questionnaires: d = 0.89, 95% CI = 0.63-1.16, p ℋ 0.001; silhouette scales: d = 1.41, 95% CI = 0.57-2.25, p ℋ 0.001). Meta-regression revealed a significant association of female gender and higher body dissatisfaction (b = 0.60, p = 0.007). Conclusion The findings underline the severity of body dissatisfaction among individuals with obesity and especially among women. Future research recommendations are discussed. PMID:28013298

Biomonitoring of 33 Elements in Blood and Urine Samples from Coastal Populations in Sanmen County of Zhejiang Province.

PubMed

Zhang, Su-jing; Luo, Ru-xin; Ma, Dong; Zhuo, Xian-yi

2016-04-01

To determine the normal reference values of 33 elements, Ag, Al, As, Au, B, Ba, Be, Ca, Cd, Co, Cr, Cs, Cu, Fe, Ga, Hg, Li, Mg, Mn, Mo, Ni, Pb, Rb, Sb, Se, Sr, Th, Ti, Tl, U, V, Zn and Zr, in the blood and urine samples from the general population in Sanmen County of Zhejiang province, a typical coastal area of eastern China. The 33 elements in 272 blood and 300 urine samples were determined by inductively coupled plasma-mass spectrometry (ICP-MS). The normality test of data was conducted using SPSS 17.0 Statistics. The data was compared with other reports. The normal reference values of the 33 elements in the blood and urine samples from the general population in Sanmen County were obtained, which of some elements were found to be similar with other reports, such as Co, Cu, Mn and Sr, while As, Cd, Hg and Pb were generally found to be higher than those previously reported. There was a wide variation between the reports from different countries in blood Ba. The normal reference values of the 33 elements in the blood and urine samples from the general population in Sanmen County are established, and successfully applied to two poisoning cases.

Reproductive Health Assessment of Female Elephants in North American Zoos and Association of Husbandry Practices with Reproductive Dysfunction in African Elephants (Loxodonta africana)

PubMed Central

Meehan, Cheryl L.; Hogan, Jennifer N.; Morfeld, Kari A.; Carlstead, Kathy

2016-01-01

As part of a multi-institutional study of zoo elephant welfare, we evaluated female elephants managed by zoos accredited by the Association of Zoos and Aquariums and applied epidemiological methods to determine what factors in the zoo environment are associated with reproductive problems, including ovarian acyclicity and hyperprolactinemia. Bi-weekly blood samples were collected from 95 African (Loxodonta africana) and 75 Asian (Elephas maximus) (8–55 years of age) elephants over a 12-month period for analysis of serum progestogens and prolactin. Females were categorized as normal cycling (regular 13- to 17-week cycles), irregular cycling (cycles longer or shorter than normal) or acyclic (baseline progestogens, <0.1 ng/ml throughout), and having Low/Normal (<14 or 18 ng/ml) or High (≥14 or 18 ng/ml) prolactin for Asian and African elephants, respectively. Rates of normal cycling, acyclicity and irregular cycling were 73.2, 22.5 and 4.2% for Asian, and 48.4, 37.9 and 13.7% for African elephants, respectively, all of which differed between species (P < 0.05). For African elephants, univariate assessment found that social isolation decreased and higher enrichment diversity increased the chance a female would cycle normally. The strongest multi-variable models included Age (positive) and Enrichment Diversity (negative) as important factors of acyclicity among African elephants. The Asian elephant data set was not robust enough to support multi-variable analyses of cyclicity status. Additionally, only 3% of Asian elephants were found to be hyperprolactinemic as compared to 28% of Africans, so predictive analyses of prolactin status were conducted on African elephants only. The strongest multi-variable model included Age (positive), Enrichment Diversity (negative), Alternate Feeding Methods (negative) and Social Group Contact (positive) as predictors of hyperprolactinemia. In summary, the incidence of ovarian cycle problems and hyperprolactinemia predominantly affects African elephants, and increases in social stability and feeding and enrichment diversity may have positive influences on hormone status. PMID:27416141

Reproductive Health Assessment of Female Elephants in North American Zoos and Association of Husbandry Practices with Reproductive Dysfunction in African Elephants (Loxodonta africana).

PubMed

Brown, Janine L; Paris, Stephen; Prado-Oviedo, Natalia A; Meehan, Cheryl L; Hogan, Jennifer N; Morfeld, Kari A; Carlstead, Kathy

2016-01-01

As part of a multi-institutional study of zoo elephant welfare, we evaluated female elephants managed by zoos accredited by the Association of Zoos and Aquariums and applied epidemiological methods to determine what factors in the zoo environment are associated with reproductive problems, including ovarian acyclicity and hyperprolactinemia. Bi-weekly blood samples were collected from 95 African (Loxodonta africana) and 75 Asian (Elephas maximus) (8-55 years of age) elephants over a 12-month period for analysis of serum progestogens and prolactin. Females were categorized as normal cycling (regular 13- to 17-week cycles), irregular cycling (cycles longer or shorter than normal) or acyclic (baseline progestogens, <0.1 ng/ml throughout), and having Low/Normal (<14 or 18 ng/ml) or High (≥14 or 18 ng/ml) prolactin for Asian and African elephants, respectively. Rates of normal cycling, acyclicity and irregular cycling were 73.2, 22.5 and 4.2% for Asian, and 48.4, 37.9 and 13.7% for African elephants, respectively, all of which differed between species (P < 0.05). For African elephants, univariate assessment found that social isolation decreased and higher enrichment diversity increased the chance a female would cycle normally. The strongest multi-variable models included Age (positive) and Enrichment Diversity (negative) as important factors of acyclicity among African elephants. The Asian elephant data set was not robust enough to support multi-variable analyses of cyclicity status. Additionally, only 3% of Asian elephants were found to be hyperprolactinemic as compared to 28% of Africans, so predictive analyses of prolactin status were conducted on African elephants only. The strongest multi-variable model included Age (positive), Enrichment Diversity (negative), Alternate Feeding Methods (negative) and Social Group Contact (positive) as predictors of hyperprolactinemia. In summary, the incidence of ovarian cycle problems and hyperprolactinemia predominantly affects African elephants, and increases in social stability and feeding and enrichment diversity may have positive influences on hormone status.

Obesity, regional body fat distribution, and the metabolic syndrome in older men and women.

PubMed

Goodpaster, Bret H; Krishnaswami, Shanthi; Harris, Tamara B; Katsiaras, Andreas; Kritchevsky, Steven B; Simonsick, Eleanor M; Nevitt, Michael; Holvoet, Paul; Newman, Anne B

2005-04-11

The metabolic syndrome is a disorder that includes dyslipidemia, insulin resistance, and hypertension and is associated with an increased risk of diabetes and cardiovascular disease. We determined whether patterns of regional fat deposition are associated with metabolic syndrome in older adults. A cross-sectional study was performed that included a random, population-based, volunteer sample of Medicare-eligible adults within the general communities of Pittsburgh, Pa, and Memphis, Tenn. The subjects consisted of 3035 men and women aged 70 to 79 years, of whom 41.7% were black. Metabolic syndrome was defined by Adult Treatment Panel III criteria, including serum triglyceride level, high-density lipoprotein cholesterol level, glucose level, blood pressure, and waist circumference. Visceral, subcutaneous abdominal, intermuscular, and subcutaneous thigh adipose tissue was measured by computed tomography. Visceral adipose tissue was associated with the metabolic syndrome in men who were of normal weight (odds ratio, 95% confidence interval: 2.1, 1.6-2.9), overweight (1.8, 1.5-2.1), and obese (1.2, 1.0-1.5), and in women who were of normal weight (3.3, 2.4-4.6), overweight (2.4, 2.0-3.0), and obese (1.7, 1.4-2.1), adjusting for race. Subcutaneous abdominal adipose tissue was associated with the metabolic syndrome only in normal-weight men (1.3, 1.1-1.7). Intermuscular adipose tissue was associated with the metabolic syndrome in normal-weight (2.3, 1.6-3.5) and overweight (1.2, 1.1-1.4) men. In contrast, subcutaneous thigh adipose tissue was inversely associated with the metabolic syndrome in obese men (0.9, 0.8-1.0) and women (0.9, 0.9-1.0). In addition to general obesity, the distribution of body fat is independently associated with the metabolic syndrome in older men and women, particularly among those of normal body weight.

Normally Expected Aberrations in the 8-hour Dynamic EKG

NASA Technical Reports Server (NTRS)

Fleck, R. L.; Arnoldi, L. B.; Townsend, J. C.; Tonesk, X.

1970-01-01

The establishment of norms for interpreting long term dynamic electrocardiograms is attempted by correlating a completely disease symptom and cardiac risk factor free sample with a non-pure sample in the direction of normality on various variables. Out of a population of 362 subjects exposed to dynamic electrocardiogram testing, a discrimination between normals and abnormals in terms of traditional risk factors was observed. The two groups differed significantly on the following variables: cholesterol, smoking, systolic blood pressure, white blood count, fasting blood sugar, uric acid, resting EKG, year of birth, and coronary insufficiency.

Improvement of High-throughput Genotype Analysis After Implementation of a Dual-curve Sybr Green I-based Quantification and Normalization Procedure

USDA-ARS?s Scientific Manuscript database

The ability to rapidly screen a large number of individuals is the key to any successful plant breeding program. One of the primary bottlenecks in high throughput screening is the preparation of DNA samples, particularly the quantification and normalization of samples for downstream processing. A ...

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

PubMed

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

2011-08-01

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

Resonance region measurements of dysprosium and rhenium

NASA Astrophysics Data System (ADS)

Leinweber, Gregory; Block, Robert C.; Epping, Brian E.; Barry, Devin P.; Rapp, Michael J.; Danon, Yaron; Donovan, Timothy J.; Landsberger, Sheldon; Burke, John A.; Bishop, Mary C.; Youmans, Amanda; Kim, Guinyun N.; Kang, yeong-rok; Lee, Man Woo; Drindak, Noel J.

2017-09-01

Neutron capture and transmission measurements have been performed, and resonance parameter analysis has been completed for dysprosium, Dy, and rhenium, Re. The 60 MeV electron accelerator at RPI Gaerttner LINAC Center produced neutrons in the thermal and epithermal energy regions for these measurements. Transmission measurements were made using 6Li glass scintillation detectors. The neutron capture measurements were made with a 16-segment NaI multiplicity detector. The detectors for all experiments were located at ≈25 m except for thermal transmission, which was done at ≈15 m. The dysprosium samples included one highly enriched 164Dy metal, 6 liquid solutions of enriched 164Dy, two natural Dy metals. The Re samples were natural metals. Their capture yield normalizations were corrected for their high gamma attenuation. The multi-level R-matrix Bayesian computer code SAMMY was used to extract the resonance parameters from the data. 164Dy resonance data were analyzed up to 550 eV, other Dy isotopes up to 17 eV, and Re resonance data up to 1 keV. Uncertainties due to resolution function, flight path, burst width, sample thickness, normalization, background, and zero time were estimated and propagated using SAMMY. An additional check of sample-to-sample consistency is presented as an estimate of uncertainty. The thermal total cross sections and neutron capture resonance integrals of 164Dy and Re were determined from the resonance parameters. The NJOY and INTER codes were used to process and integrate the cross sections. Plots of the data, fits, and calculations using ENDF/B-VII.1 resonance parameters are presented.

The Lithium Abundances of a Large Sample of Red Giants

NASA Astrophysics Data System (ADS)

Liu, Y. J.; Tan, K. F.; Wang, L.; Zhao, G.; Sato, Bun'ei; Takeda, Y.; Li, H. N.

2014-04-01

The lithium abundances for 378 G/K giants are derived with non-local thermodynamic equilibrium correction considered. Among these are 23 stars that host planetary systems. The lithium abundance is investigated, as a function of metallicity, effective temperature, and rotational velocity, as well as the impact of a giant planet on G/K giants. The results show that the lithium abundance is a function of metallicity and effective temperature. The lithium abundance has no correlation with rotational velocity at v sin i < 10 km s-1. Giants with planets present lower lithium abundance and slow rotational velocity (v sin i < 4 km s-1). Our sample includes three Li-rich G/K giants, 36 Li-normal stars, and 339 Li-depleted stars. The fraction of Li-rich stars in this sample agrees with the general rate of less than 1% in the literature, and the stars that show normal amounts of Li are supposed to possess the same abundance at the current interstellar medium. For the Li-depleted giants, Li-deficiency may have already taken place at the main sequence stage for many intermediate mass (1.5-5 M ⊙) G/K giants. Finally, we present the lithium abundance and kinematic parameters for an enlarged sample of 565 giants using a compilation of the literature, and confirm that the lithium abundance is a function of metallicity and effective temperature. With the enlarged sample, we investigate the differences between the lithium abundance in thin-/thick-disk giants, which indicate that the lithium abundance in thick-disk giants is more depleted than that in thin-disk giants.

Effect of Longitudinal Oscillations on Downward Flame Spread over Thin Solid Fuels

NASA Technical Reports Server (NTRS)

Nayagam, Vedha; Sacksteder, Kurt

2013-01-01

Downward flame spread rates over vertically vibrated thin fuel samples are measured in air at one atmospheric pressure under normal gravity. Unlike flame spread against forced-convective flows, the present results show that with increasing vibration acceleration the flame spread rate increases before being blown off at high acceleration levels causing flame extinction. A simple scaling analysis seems to explain this phenomenon, which may have important implications to flammability studies including in microgravity environments.

Ultraviolet to optical spectral distributions of northern star-forming galaxies

NASA Technical Reports Server (NTRS)

Mcquade, Kerry; Calzetti, Daniela; Kinney, Anne L.

1995-01-01

We report spectral energy distribution from the UV to the optical for a sample of 31 northern star-forming galaxies. We also present measurements for emission-line fluxes, continuum levels, and equivalent widths of absorption features for each individual spectrum as well as averages for the eight galactic activity classes, including normal, starburst, Seyfert 2, blue compact dwarf, blue compact, Low-Inonization Nuclear Emission Regions (LINER), H II, and combination LINER-H II galaxies.

Tissue spray ionization mass spectrometry for rapid recognition of human lung squamous cell carcinoma

NASA Astrophysics Data System (ADS)

Wei, Yiping; Chen, Liru; Zhou, Wei; Chingin, Konstantin; Ouyang, Yongzhong; Zhu, Tenggao; Wen, Hua; Ding, Jianhua; Xu, Jianjun; Chen, Huanwen

2015-05-01

Tissue spray ionization mass spectrometry (TSI-MS) directly on small tissue samples has been shown to provide highly specific molecular information. In this study, we apply this method to the analysis of 38 pairs of human lung squamous cell carcinoma tissue (cancer) and adjacent normal lung tissue (normal). The main components of pulmonary surfactants, dipalmitoyl phosphatidylcholine (DPPC, m/z 757.47), phosphatidylcholine (POPC, m/z 782.52), oleoyl phosphatidylcholine (DOPC, m/z 808.49), and arachidonic acid stearoyl phosphatidylcholine (SAPC, m/z 832.43), were identified using high-resolution tandem mass spectrometry. Monte Carlo sampling partial least squares linear discriminant analysis (PLS-LDA) was used to distinguish full-mass-range mass spectra of cancer samples from the mass spectra of normal tissues. With 5 principal components and 30 - 40 Monte Carlo samplings, the accuracy of cancer identification in matched tissue samples reached 94.42%. Classification of a tissue sample required less than 1 min, which is much faster than the analysis of frozen sections. The rapid, in situ diagnosis with minimal sample consumption provided by TSI-MS is advantageous for surgeons. TSI-MS allows them to make more informed decisions during surgery.

Cy5 total protein normalization in Western blot analysis.

PubMed

Hagner-McWhirter, Åsa; Laurin, Ylva; Larsson, Anita; Bjerneld, Erik J; Rönn, Ola

2015-10-01

Western blotting is a widely used method for analyzing specific target proteins in complex protein samples. Housekeeping proteins are often used for normalization to correct for uneven sample loads, but these require careful validation since expression levels may vary with cell type and treatment. We present a new, more reliable method for normalization using Cy5-prelabeled total protein as a loading control. We used a prelabeling protocol based on Cy5 N-hydroxysuccinimide ester labeling that produces a linear signal response. We obtained a low coefficient of variation (CV) of 7% between the ratio of extracellular signal-regulated kinase (ERK1/2) target to Cy5 total protein control signals over the whole loading range from 2.5 to 20.0μg of Chinese hamster ovary cell lysate protein. Corresponding experiments using actin or tubulin as controls for normalization resulted in CVs of 13 and 18%, respectively. Glyceraldehyde-3-phosphate dehydrogenase did not produce a proportional signal and was not suitable for normalization in these cells. A comparison of ERK1/2 signals from labeled and unlabeled samples showed that Cy5 prelabeling did not affect antibody binding. By using total protein normalization we analyzed PP2A and Smad2/3 levels with high confidence. Copyright © 2015 Elsevier Inc. All rights reserved.

Advanced Techniques in Pulmonary Function Test Analysis Interpretation and Diagnosis

PubMed Central

Gildea, T.J.; Bell, C. William

1980-01-01

The Pulmonary Functions Analysis and Diagnostic System is an advanced clinical processing system developed for use at the Pulmonary Division, Department of Medicine at the University of Nebraska Medical Center. The system generates comparative results and diagnostic impressions for a variety of routine and specialized pulmonary functions test data. Routine evaluation deals with static lung volumes, breathing mechanics, diffusing capacity, and blood gases while specialized tests include lung compliance studies, small airways dysfunction studies and dead space to tidal volume ratios. Output includes tabular results of normal vs. observed values, clinical impressions and commentary and, where indicated, a diagnostic impression. A number of pulmonary physiological and state variables are entered or sampled (A to D) with periodic status reports generated for the test supervisor. Among the various physiological variables sampled are respiratory frequency, minute ventilation, oxygen consumption, carbon dioxide production, and arterial oxygen saturation.

On the precision of automated activation time estimation

NASA Technical Reports Server (NTRS)

Kaplan, D. T.; Smith, J. M.; Rosenbaum, D. S.; Cohen, R. J.

1988-01-01

We examined how the assignment of local activation times in epicardial and endocardial electrograms is affected by sampling rate, ambient signal-to-noise ratio, and sinx/x waveform interpolation. Algorithms used for the estimation of fiducial point locations included dV/dtmax, and a matched filter detection algorithm. Test signals included epicardial and endocardial electrograms overlying both normal and infarcted regions of dog myocardium. Signal-to-noise levels were adjusted by combining known data sets with white noise "colored" to match the spectral characteristics of experimentally recorded noise. For typical signal-to-noise ratios and sampling rates, the template-matching algorithm provided the greatest precision in reproducibly estimating fiducial point location, and sinx/x interpolation allowed for an additional significant improvement. With few restrictions, combining these two techniques may allow for use of digitization rates below the Nyquist rate without significant loss of precision.

Audiovisual sentence repetition as a clinical criterion for auditory development in Persian-language children with hearing loss.

PubMed

Oryadi-Zanjani, Mohammad Majid; Vahab, Maryam; Rahimi, Zahra; Mayahi, Anis

2017-02-01

It is important for clinician such as speech-language pathologists and audiologists to develop more efficient procedures to assess the development of auditory, speech and language skills in children using hearing aid and/or cochlear implant compared to their peers with normal hearing. So, the aim of study was the comparison of the performance of 5-to-7-year-old Persian-language children with and without hearing loss in visual-only, auditory-only, and audiovisual presentation of sentence repetition task. The research was administered as a cross-sectional study. The sample size was 92 Persian 5-7 year old children including: 60 with normal hearing and 32 with hearing loss. The children with hearing loss were recruited from Soroush rehabilitation center for Persian-language children with hearing loss in Shiraz, Iran, through consecutive sampling method. All the children had unilateral cochlear implant or bilateral hearing aid. The assessment tool was the Sentence Repetition Test. The study included three computer-based experiments including visual-only, auditory-only, and audiovisual. The scores were compared within and among the three groups through statistical tests in α = 0.05. The score of sentence repetition task between V-only, A-only, and AV presentation was significantly different in the three groups; in other words, the highest to lowest scores belonged respectively to audiovisual, auditory-only, and visual-only format in the children with normal hearing (P < 0.01), cochlear implant (P < 0.01), and hearing aid (P < 0.01). In addition, there was no significant correlationship between the visual-only and audiovisual sentence repetition scores in all the 5-to-7-year-old children (r = 0.179, n = 92, P = 0.088), but audiovisual sentence repetition scores were found to be strongly correlated with auditory-only scores in all the 5-to-7-year-old children (r = 0.943, n = 92, P = 0.000). According to the study's findings, audiovisual integration occurs in the 5-to-7-year-old Persian children using hearing aid or cochlear implant during sentence repetition similar to their peers with normal hearing. Therefore, it is recommended that audiovisual sentence repetition should be used as a clinical criterion for auditory development in Persian-language children with hearing loss. Copyright © 2016. Published by Elsevier B.V.

Thermophysical properties of lunar materials. I - Thermal radiation properties of lunar materials from the Apollo missions

NASA Technical Reports Server (NTRS)

Birkebak, R. C.

1974-01-01

The successful landings on the moon of the Apollo flights and the return of samples of lunar surface material has permitted the measurement of the thermophysical properties necessary for heat transfer calculations. The characteristics of the Apollo samples are discussed along with remote sensing results which made it possible to deduce many of the thermophysical properties of the lunar surface. Definitions considered in connection with thermal radiation measurements include the bond albedo, the geometric albedo, the normal albedo, the directional reflectance, the bidirectional reflectance, and the directional emittance. The measurement techniques make use of a directional reflectance apparatus, a bidirectional reflectance apparatus, and a spectral emittance apparatus.

Optical diagnosis of dengue virus infected human blood using Mueller matrix polarimetry

NASA Astrophysics Data System (ADS)

Anwar, Shahzad; Firdous, Shamaraz

2016-08-01

Currently dengue fever diagnosis methods include capture ELISAs, immunofluorescence tests, and hemagglutination assays. In this study optical diagnosis of dengue virus infection in the whole blood is presented utilizing Mueller matrix polarimetry. Mueller matrices of about 50 dengue viral infected and 25 non-dengue healthy blood samples were recorded utilizing light source from 500 to 700 nm with scanning step of 10 nm. Polar decomposition of the Mueller matrices for all the blood samples was performed that yielded polarization properties including depolarization, diattenuation, degree of polarization, retardance and optical activity, out of which, depolarization index clusters up the diseased and healthy in to different separate groups. The average depolarized light in the case of dengue infection in the whole blood at 500 nm is 18%, whereas for the healthy blood samples it is 13.5%. This suggests that depolarization index of polarized light at the wavelengths of 500, 510, 520, 530 and 540 nm, we find that in case of depolarization index values are higher for dengue viral infection as compared to normal samples. This technique can effectively be used for the characterization of the dengue virus infected at an early stage of disease.

Influence of field penetration ratios and filamentation on end-effect related hysteretic loss reductions for superconducting strips

NASA Astrophysics Data System (ADS)

Dong, K.; Sumption, M.; Collings, E. W.; Majoros, M.; Yu, H.; Hu, M.

2017-12-01

There are a few key conductor-specific factors which influence the power loss of superconductors; these include critical current, geometry, and normal metal resistivity. This paper focuses on the influence of sample geometry on the power loss of superconducting strips and the effect of filamentation and sample length as a function of the field penetration state of the superconductor. We start with the analytical equations for infinite slabs and strips and then consider the influence of end effects for both unstriated and striated conductor. The loss is then calculated and compared as a function of applied field for striated and unstriated conductors. These results are much more general than they might seem at first glance, since they will be important building blocks for analytic loss calculations for twisted geometries for coated conductors, including helical (Conductor on Round Core, CORC), and twisted (e.g., twist stack cables) geometries. We show that for relatively low field penetration, end effects and reduced field penetration both reduce loss. In addition, for filamentary samples the relevant ratio of length scales becomes the filament width to sample length, thus modifying the loss ratios.

Evaluating the 'Focus on Normal Birth and Reducing Caesarean section Rates Rapid Improvement Programme': A mixed method study in England.

PubMed

Marshall, Joyce L; Spiby, Helen; McCormick, Felicia

2015-02-01

caesarean section plays an important role in ensuring safety of mother and infant but rising rates are not accompanied by measurable improvements in maternal or neonatal mortality or morbidity. The 'Focus on Normal Birth and Reducing Caesarean section Rates Rapid Improvement Programme' was a facilitative initiative developed to promote opportunities for normal birth and reduce caesarean section rates in England. to evaluate the 'Focus on Normal Birth and Reducing Caesarean section Rates' programme, by assessment of: impact on caesarean section rates, use of service improvements tools and participants׳ perceptions of factors that sustain or hinder work within participating maternity units. a mixed methods approach included analysis of mode of birth data, web-based questionnaires and in-depth semi-structured telephone interviews. twenty Hospital Trusts in England (selected from 68 who applied) took part in the 'Focus on Normal Birth and Reducing Caesarean section Rates Rapid Improvement Programme' initiative. In each hospital Trust, the head of midwifery, an obstetrician, the relevant lead for organisational development, a supervisor of midwives, or a clinical midwife and a service user representative were invited to participate in the independent evaluation. collection and analysis of mode of birth data from 20 participating hospital Trusts, web-based questionnaires administered to key individuals in all 20 Trusts and in-depth semi-structured telephone interviews conducted with key individuals in a sample of six Trusts. there was a marginal decline of 0.5% (25.9% from 26.4%) in mean total caesarean section rate in the period 1 January 2009 to 31 January 2010 compared to the baseline period (1 July-31 December 2008). Reduced total caesarean section rates were achieved in eight trusts, all with higher rates at the beginning of the initiative. Features associated with lower caesarean section rates included a shared philosophy prioritising normal birth, clear communication across disciplines and strong leadership at a range of levels, including executive support and clinical leaders within each discipline. it is important that the philosophy and organisational context of care are examined to identify potential barriers and facilitative factors. Copyright © 2014 Elsevier Ltd. All rights reserved.

On designing a new cumulative sum Wilcoxon signed rank chart for monitoring process location

PubMed Central

Nazir, Hafiz Zafar; Tahir, Muhammad; Riaz, Muhammad

2018-01-01

In this paper, ranked set sampling is used for developing a non-parametric location chart which is developed on the basis of Wilcoxon signed rank statistic. The average run length and some other characteristics of run length are used as the measures to assess the performance of the proposed scheme. Some selective distributions including Laplace (or double exponential), logistic, normal, contaminated normal and student’s t-distributions are considered to examine the performance of the proposed Wilcoxon signed rank control chart. It has been observed that the proposed scheme shows superior shift detection ability than some of the competing counterpart schemes covered in this study. Moreover, the proposed control chart is also implemented and illustrated with a real data set. PMID:29664919

Seven novel mutations in the long isoform of the USH2A gene in Chinese families with nonsyndromic retinitis pigmentosa and Usher syndrome Type II.

PubMed

Xu, Wenjun; Dai, Hanjun; Lu, Tingting; Zhang, Xiaohui; Dong, Bing; Li, Yang

2011-01-01

To describe the clinical and genetic findings in one Chinese family with autosomal recessive retinitis pigmentosa (arRP) and in three unrelated Chinese families with Usher syndrome type II (USH2). One family (FR1) with arRP and three unrelated families (F6, F7, and F8) with Usher syndrome (USH), including eight affected members and seven unaffected family individuals were examined clinically. The study included 100 normal Chinese individuals as normal controls. After obtaining informed consent, peripheral blood samples from all participants were collected and genomic DNA was extracted. Genotyping and haplotyping analyses were performed on the known genetic loci for arRP with a panel of polymorphic markers in family FR1. In all four families, the coding region (exons 2-72), including the intron-exon boundary of the USH2A (Usher syndrome type -2A protein) gene, was screened by PCR and direct DNA sequencing. Whenever substitutions were identified in a patient, a restriction fragment length polymorphism (RFLP) analysis, single strand conformation polymorphism (SSCP) analysis, or high resolution melt curve analysis (HRM) was performed on all available family members and on the 100 normal controls. The affected individuals presented with typical fundus features of retinitis pigmentosa (RP), including narrowing of the vessels, bone-spicule pigmentation, and waxy optic discs. The electroretinogram (ERG) wave amplitudes of the available probands were undetectable. Audiometric tests in the affected individuals in family FR1 were normal, while indicating moderate to severe sensorineural hearing impairment in the affected individuals in families F6, F7, and F8. Vestibular function was normal in all patients from all four families. The disease-causing gene in family FR1 was mapped to the USH2A locus on chromosome 1q41. Seven novel mutations (two missenses, one 7-bp deletion, two small deletions, and two nonsenses) were detected in the four families after sequencing analysis of USH2A. The results further support that mutations of USH2A are also responsible for non-syndromic RP. The mutation spectrum among Chinese patients might differ from that among European Caucasians.

Automated labelling of cancer textures in colorectal histopathology slides using quasi-supervised learning.

PubMed

Onder, Devrim; Sarioglu, Sulen; Karacali, Bilge

2013-04-01

Quasi-supervised learning is a statistical learning algorithm that contrasts two datasets by computing estimate for the posterior probability of each sample in either dataset. This method has not been applied to histopathological images before. The purpose of this study is to evaluate the performance of the method to identify colorectal tissues with or without adenocarcinoma. Light microscopic digital images from histopathological sections were obtained from 30 colorectal radical surgery materials including adenocarcinoma and non-neoplastic regions. The texture features were extracted by using local histograms and co-occurrence matrices. The quasi-supervised learning algorithm operates on two datasets, one containing samples of normal tissues labelled only indirectly, and the other containing an unlabeled collection of samples of both normal and cancer tissues. As such, the algorithm eliminates the need for manually labelled samples of normal and cancer tissues for conventional supervised learning and significantly reduces the expert intervention. Several texture feature vector datasets corresponding to different extraction parameters were tested within the proposed framework. The Independent Component Analysis dimensionality reduction approach was also identified as the one improving the labelling performance evaluated in this series. In this series, the proposed method was applied to the dataset of 22,080 vectors with reduced dimensionality 119 from 132. Regions containing cancer tissue could be identified accurately having false and true positive rates up to 19% and 88% respectively without using manually labelled ground-truth datasets in a quasi-supervised strategy. The resulting labelling performances were compared to that of a conventional powerful supervised classifier using manually labelled ground-truth data. The supervised classifier results were calculated as 3.5% and 95% for the same case. The results in this series in comparison with the benchmark classifier, suggest that quasi-supervised image texture labelling may be a useful method in the analysis and classification of pathological slides but further study is required to improve the results. Copyright © 2013 Elsevier Ltd. All rights reserved.

Hypermethylated APC in serous carcinoma based on a meta-analysis of ovarian cancer.

PubMed

Shen, Chunyan; Sheng, Qifang; Zhang, Xiaojie; Fu, Yuling; Zhu, Kemiao

2016-09-26

The reduced expression of the Adenomatous polyposis coli (APC) gene, a tumor suppressor gene, through promoter hypermethylation has been reported to play a key role in the carcinogenesis. However, the correlation between APC promoter hypermethylation and ovarian cancer (OC) remains to be clarified. A comprehensive literature search was carried out in related research databases. The overall odds ratio (OR) and corresponding 95 % confidence interval (CI) were used to evaluate the effects of APC promoter hypermethylation on OC and clinicopathological characteristics. Ultimately, 12 eligible studies were used in our study, including 806 OC samples, 429 normal controls, 109 benign lesions and 75 LMP samples. The pooled OR showed that APC promoter hypermethylation was significantly higher in OC than in normal and benign controls (OR = 6.18 and OR = 3.26, respectively). No significant correlation was observed between OC and low malignant potential (LMP) tumors (P = 0.436). In the comparison of OC and normal controls, subgroup analysis based on race showed that the overall OR of APC promoter hypermethylation was significant and similar in Asians and Caucasians (OR = 8.34 and OR = 5.39, respectively). A subgroup analysis based on sample type found that the pooled OR was significantly higher in blood than in tissue (OR = 18.71 and OR = 5.74, respectively). A significant association was not observed between APC promoter hypermethylation and tumor grade or tumor stage. The pooled OR indicated that APC promoter hypermethylation was significantly lower in serous carcinoma than in non-serous carcinoma (OR = 0.56, P = 0.02). No obvious publication bias was detected by Egger's test (all P > 0.05). APC promoter hypermethylation may be linked to the increased risk of OC. It was associated with histological type, but not with tumor grade or tumor stage. Moreover, hypermethylated APC may be a noninvasive biomarker using blood samples. Future studies are required to validate these results.

Application of Monte Carlo cross-validation to identify pathway cross-talk in neonatal sepsis.

PubMed

Zhang, Yuxia; Liu, Cui; Wang, Jingna; Li, Xingxia

2018-03-01

To explore genetic pathway cross-talk in neonates with sepsis, an integrated approach was used in this paper. To explore the potential relationships between differently expressed genes between normal uninfected neonates and neonates with sepsis and pathways, genetic profiling and biologic signaling pathway were first integrated. For different pathways, the score was obtained based upon the genetic expression by quantitatively analyzing the pathway cross-talk. The paired pathways with high cross-talk were identified by random forest classification. The purpose of the work was to find the best pairs of pathways able to discriminate sepsis samples versus normal samples. The results found 10 pairs of pathways, which were probably able to discriminate neonates with sepsis versus normal uninfected neonates. Among them, the best two paired pathways were identified according to analysis of extensive literature. Impact statement To find the best pairs of pathways able to discriminate sepsis samples versus normal samples, an RF classifier, the DS obtained by DEGs of paired pathways significantly associated, and Monte Carlo cross-validation were applied in this paper. Ten pairs of pathways were probably able to discriminate neonates with sepsis versus normal uninfected neonates. Among them, the best two paired pathways ((7) IL-6 Signaling and Phospholipase C Signaling (PLC); (8) Glucocorticoid Receptor (GR) Signaling and Dendritic Cell Maturation) were identified according to analysis of extensive literature.

Biochemical and molecular characterization of thyroid tissue by micro-Raman spectroscopy and gene expression analysis

NASA Astrophysics Data System (ADS)

Neto, Lázaro P. M.; Martin, Aírton A.; Soto, Claudio A. T.; Santos, André B. O.; Mello, Evandro S.; Pereira, Marina A.; Cernea, Cláudio R.; Brandão, Lenine G.; Canevari, Renata A.

2016-02-01

Thyroid carcinomas represent the main endocrine malignancy and their diagnosis may produce inconclusive results. Raman spectroscopy and gene expression analysis have shown excellent results on the differentiation of carcinomas. This study aimed to improve the discrimination between different thyroid pathologies combining of both analyses. A total of 35 thyroid tissues samples including normal tissue (n=10), goiter (n=10), papillary (n=10) and follicular carcinomas (n=5) were analyzed. Confocal Raman spectra was obtain by using a Rivers Diagnostic System, 785 nm laser excitation and CCD detector. The data was processed by the software Labspec5 and Origin 8.5 and analyzed by Minitab® program. The gene expression analysis was performed by qRT-PCR technique for TG, TPO, PDGFB, SERPINA1, LGALS3 and TFF3 genes and statistically analyzed by Mann-Whitney test. The confocal Raman spectroscopy allowed a maximum discrimination of 91.1% between normal and tumor tissues, 84.8% between benign and malignant pathologies and 84.6% among carcinomas analyzed. Significant differences was observed for TG, LGALS3, SERPINA1 and TFF3 genes between benign lesions and carcinomas, and SERPINA1 and TFF3 genes between papillary and follicular carcinomas. Principal component analysis was performed using PC1 and PC2 in the papillary carcinoma samples that showed over gene expression when compared with normal sample, where 90% of discrimination was observed at the Amide 1 (1655 cm-1), and at the tyrosine spectra region (856 cm-1). The discrimination of tissues thyroid carried out by confocal Raman spectroscopy and gene expression analysis indicate that these techniques are promising tools to be used in the diagnosis of thyroid lesions.

Human papillomavirus cervical infection and associated risk factors in a region of Argentina with a high incidence of cervical carcinoma.

PubMed Central

Tonon, S A; Picconi, M A; Zinovich, J B; Liotta, D J; Bos, P D; Galuppo, J A; Alonio, L V; Ferreras, J A; Teyssié, A R

1999-01-01

OBJECTIVE: To assess the prevalence and potential risk factors associated with human papillomavirus (HPV) cervical infection among women residing in a region of northeastern Argentina with a high incidence of cervical cancer. METHODS: A case-control study of 330 women participating in a cervical cytological screening program conducted in Posadas city, Misiones, Argentina, from February 1997 to November 1998 was carried out. Standardized questionnaires were administered, and clinical examination including colposcopy was performed. Fresh endocervical specimens for HPV DNA detection by generic polymerase chain reaction were collected and the products typed by dot-blot hybridization. RESULTS: Human papillomavirus DNA was found in 61% of samples analyzed (185/301). Samples with normal cytology had a 43% infection rate (85/199), while those classified as low-grade squamous intraepithelial lesion, high-grade squamous intraepithelial lesion, and invasive cervical carcinoma had an infection rate of 96% (53/55), 100% (29/29), and 100% (18/18), respectively. Human papillomavirus typing showed a 64% (118/185) prevalence of type 16 among all the infected population analyzed; type 16 was detected among 49% (42/85) of infected samples with normal cytology and in an average of 74% (74/100) with abnormal cytology. Sexual behavior, residence in southern Paraguay, and history of a previous sexually transmitted diseases were the main risk factors associated with high-grade cervical lesions. CONCLUSIONS: An elevated prevalence of HPV infection was detected in this population, which also has a high incidence of cervical cancer. The broad distribution of high-risk HPV type 16 in women with normal cytology and colposcopy suggests that viral infection is an important determinant of regional cancer incidence. PMID:10524669

Reducing Individual Variation for fMRI Studies in Children by Minimizing Template Related Errors

PubMed Central

Weng, Jian; Dong, Shanshan; He, Hongjian; Chen, Feiyan; Peng, Xiaogang

2015-01-01

Spatial normalization is an essential process for group comparisons in functional MRI studies. In practice, there is a risk of normalization errors particularly in studies involving children, seniors or diseased populations and in regions with high individual variation. One way to minimize normalization errors is to create a study-specific template based on a large sample size. However, studies with a large sample size are not always feasible, particularly for children studies. The performance of templates with a small sample size has not been evaluated in fMRI studies in children. In the current study, this issue was encountered in a working memory task with 29 children in two groups. We compared the performance of different templates: a study-specific template created by the experimental population, a Chinese children template and the widely used adult MNI template. We observed distinct differences in the right orbitofrontal region among the three templates in between-group comparisons. The study-specific template and the Chinese children template were more sensitive for the detection of between-group differences in the orbitofrontal cortex than the MNI template. Proper templates could effectively reduce individual variation. Further analysis revealed a correlation between the BOLD contrast size and the norm index of the affine transformation matrix, i.e., the SFN, which characterizes the difference between a template and a native image and differs significantly across subjects. Thereby, we proposed and tested another method to reduce individual variation that included the SFN as a covariate in group-wise statistics. This correction exhibits outstanding performance in enhancing detection power in group-level tests. A training effect of abacus-based mental calculation was also demonstrated, with significantly elevated activation in the right orbitofrontal region that correlated with behavioral response time across subjects in the trained group. PMID:26207985

Evaluation of toxicity to the amphipod, Hyalella azteca, and to the midge, Chironomus dilutus; and bioaccumulation by the oligochaete, Lumbriculus variegatus, with exposure to PCB-contaminated sediments from Anniston, Alabama

USGS Publications Warehouse

Ingersoll, Christopher G.; Steevens, Jeffery A.; MacDonald, Donald D.; Brumbaugh, William G.; Coady, Matthew R.; Farrar, J. Daniel; Lotufo, Guilherme R.; Kemble, Nile E.; Kunz, James L.; Stanley, Jacob K.; Sinclair, Jesse A.; Ingersoll, Christopher G.; Steevens, Jeffery A.; MacDonald, Donald D.

2014-01-01

The U.S. Environmental Protection Agency (USEPA) requested that as part of the remedial investigation for the Anniston, Alabama Polychlorinated Biphenyl (PCB) Site (Anniston PCB Site), that Pharmacia Corporation and Solutia Inc. (P/S) perform long-term reproduction toxicity tests with the amphipod, Hyalella azteca, and the midge, Chironomus dilutus, and bioaccumulation tests with the oligochaete, Lumbriculus variegatus, using sediment samples collected from reference locations and from Operable Unit 4 of the Anniston PCB Site. The sediment toxicity testing and sediment bioaccumulation results will be used by ARCADIS U.S., Inc. (ARCADIS) as part of a weight-of-evidence assessment to evaluate risks and establish sediment remediation goals for contaminants to sediment-dwelling organisms inhabiting the Anniston PCB Site. The goal of this study was to characterize relations between sediment chemistry and sediment toxicity and relations between sediment chemistry and sediment bioaccumulation in samples of sediments collected from the Anniston PCB Site. A total of 32 samples were evaluated from six test sites and one reference site to provide a wide range in concentrations of chemicals of potential concern (COPCs) including PCBs in samples of whole sediment. The goal of this study was not to determine the extent of sediment contamination across the Anniston PCB Site. Hence, the test sites or samples collected from within a test site were not selected to represent the spatial extent of sediment contamination across the Anniston PCB Site. Sediment chemistry, pore-water chemistry, and sediment toxicity data were generated for 26 sediment samples from the Anniston PCB Site. All of the samples were evaluated to determine if they qualified as reference sediment samples. Those samples that met the chemical selection criteria and biological selection criteria were identified as reference samples and used to develop the reference envelope for each toxicity test endpoint. Physical characterization of samples of whole sediment included analyses of grain size, TOC, and nutrients. Organic chemical characterization of samples of whole sediment included PCB homologs and select (13) PCB congeners, parent and alkylated polycyclic aromatic hydrocarbons (PAHs), organochlorine pesticides, and polychlorinated dibenzo-p-dioxins; and dibenzofurans. The PCB aroclors analyzed included 1016, 1221, 1232, 1242, 1248, 1254, 1260, 1262 and 1268. Analyses of whole sediment also included total metals, simultaneously extracted metals, and acid volatile sulfide. Chemical characterization of samples of pore water isolated from samples of whole sediment at the start of the sediment toxicity exposures or at the start of the sediment bioaccumulation exposures included metals, major cations, major anions, dissolved organic carbon, and additional water-quality characteristics. Concentrations of metals or PCBs in pore water during the sediment toxicity exposures or during sediment bioaccumulation exposures also were determined using peeper samples (for metals) or solid-phase microextraction (SPME) samplers (for PCBs). The bioavailability and bioaccumulation of PCBs in 14 sediment samples were investigated using SPME passive samplers and the 28-d L. variegatus whole-sediment bioaccumulation exposures In general the accumulation of PCBs consistently was predicted through the use of organic carbon normalization and equilibrium partitioning. In these sediments, PCB homologs were accumulated differently based on bioavailability and potential to accumulate in oligochaetes. As part of this assessment homolog specific biota sediment accumulation factor values were developed that could be applied across the larger site to predict tissue levels of PCBs. The whole-sediment toxicity tests done with H. azteca and C. dilutus met the established ASTM and USEPA test acceptability criteria. The most responsive H. azteca endpoints were day 42 survival normalized young per female and day 28 biomass and that the most responsive C. dilutus endpoints were adult biomass and percent adult emergence. Overall, between the two species, the most responsive endpoint assessed for these two species was H. azteca survival-normalized young per female (67 percent of the samples classified as toxic). Concentration-response models (CRMs) and site-specific sediment toxicity thresholds (TTs) were generated with matching sediment chemistry and sediment toxicity data. Sediment chemistry, pore-water chemistry, and sediment toxicity data were evaluated for as many as 26 sediment samples from the Anniston PCB Site. The reference-envelope approach was used to identify the sediment samples that were toxic to benthic invertebrates. This procedure involved identification of reference sediment samples, normalizing the toxicity data to reflect control responses, developing a reference envelope for each toxicity test endpoint, and designating each sediment sample as toxic or not toxic for each toxicity test endpoint, for each species, and for all species combined. These results demonstrated percent emergence of adult C. dilutus, biomass of adult C. dilutus, and reproduction of H. azteca normalized to percent survival were among the most responsive endpoints that were evaluated. Therefore, these endpoints were selected for CRM development. The site-specific TTs for whole sediment provide a reliable basis for identifying toxic and not toxic sediment samples in the Anniston PCB Site (that is, for correctly classifying the sediment samples used to derive the TTs as toxic or not toxic, for the endpoint used to derive the TTs). Among the 69 TTs for sediment, the TTLRs for total PCB homologs [499 to 1,870 micrograms per kilogram dry weight (μg/kg DW)] and for lead [(9.48 to 10.3 milligrams per kilogram (mg/kg) DW] based on reproduction of H. azteca or based on emergence or biomass of adult C. dilutus, were the most reliable. Such TTs had low rates of false negative errors (that is, only 0 to 11 percent of the samples below the TT were toxic to benthic invertebrates), low rates of false positive errors (only 0 to 6 percent of the samples greater than the TT were not toxic to benthic invertebrates), and high rates of correct classification (that is, 92 to 96 percent). The site-specific TTs for PCBs and other COPCs derived in this study also were compared to empirically based sediment quality guidelines (SQGs), to equilibrium-partitioning based SQGs, and to the results of spiked-sediment toxicity tests. The results of this evaluation indicated that the site-specific sediment TTs for PCBs were comparable to the consensus-based SQGs that were derived for PCBs. In addition, the site-specific sediment TTs for PCBs are well within the range of SQGs derived using the equilibrium partitioning approach. The site-specific sediment TTs for PCBs also are consistent with the results of chronic TTs that have been estimated for benthic invertebrates using the results of spiked-sediment toxicity tests. As the site-specific sediment TTs for PCBs are consistent with empirically based SQGs, equilibrium-partitioning based SQGs, and results of sediment-spiking studies, these site- specific sediment TTs likely represent the concentrations of PCBs that are sufficient to cause toxicity to benthic invertebrates (as opposed to simply being correlated with adverse effects on the survival, weight, or reproduction of benthic invertebrates). Importantly, such site-specific sediment TTs have been demonstrated to accurately classify sediment samples as toxic or not toxic to benthic invertebrates at the Anniston PCB Site. In contrast, the TTs for metals, PAHs, and organochlorine pesticides were generally lower than consensus-based SQGs (that is, probable effect concentrations), and LC50s (median lethal effect concentrations) generated in spiked-sediment toxicity tests, indicating that these COPCs are likely not the main contributors to the observed toxicity of the site sediments evaluated in this study. The reproduction endpoint for H. azteca provided lower TTs compared to the day 28 biomass endpoint for H. azteca and the emergence or biomass endpoints for adult C. dilutus provided lower TTs compared to the day 13 biomass endpoint for C. dilutus.

[Prevalence of metabolic syndrome in children with and without obesity].

PubMed

Guzmán-Guzmán, Iris Paola; Salgado-Bernabé, Aralia Berenice; Muñoz Valle, José Francisco; Vences-Velázquez, Amalia; Parra-Rojas, Isela

2015-03-09

Childhood obesity is considered the main risk factor for the development of metabolic syndrome (MetS) during childhood, adolescence and adulthood. This study aimed to determine the prevalence of MetS components and its main defining combinations in a sample of school children with and without obesity. A total of 225 children aged 6-12 years, 106 obese and 119 with normal weight were included. MetS was defined by the presence of 3 or more of the following: obesity as a body mass index ≥ 95th percentile, fasting glucose ≥ 100 mg/dL, triglycerides ≥ 150 mg/dL, high density lipoproteins cholesterol (HDL-c)<40 mg/dL and systolic and diastolic blood pressure ≥ 95th percentile. We found MetS components in both groups. Most frequent abnormalities in the obese group included increased levels of HDL-c, triglycerides, fasting glucose and total cholesterol, while increased levels of glucose and total cholesterol, and lower HDL-c levels predominated in the normal weight group. The prevalence of MetS in the obese group was 44.3% and, in normal weight children, it was 0.84%. The 3 main components that defined the MetS in the obese group were obesity/triglycerides/HDL-c (34.0%), obesity/glucose/triglycerides/HDL-c (29.8%) and obesity/glucose/HDL-c (14.9%), while the only combination observed in the normal weight group was glucose/HDL-c/triglycerides. A percentage of 44.3 of obese school children had MetS, and dyslipidemia showed to be strong determinants of MetS. Although the prevalence of MetS was low in children with normal weight, one third of them showed one of the components of MetS. Copyright © 2013 Elsevier España, S.L.U. All rights reserved.

Use of the Keele injector for sample introduction for gas chromatographic analysis of vinclozolin in lettuces.

PubMed

Shim, J H; Lee, Y S; Kim, M R; Lee, C J; Kim, I S

2003-10-10

We examined a Keele injector for sample introduction for gas chromatographic analysis of vinclozolin treated in lettuces. Samples in milligram quantity were introduced into a glass tube in a Keele injector at a gas chromatograph injection port. The glass tube was then crushed to allow the sample to carry onto a capillary column in a normal manner. The standard calibration curve for quantitative detection of vinclozolin was obtained by determining vinclozolin spiked in samples at variable concentrations. The calibration curve showed a linear response to vinclozolin ranging from 0.05 to 1.0 microg/g, giving a slope value of 174.8, the y-intercept value of -2.8146 and the mean r2-value of 0.9994. Limit of quantification for vinclozolin was 0.05 microg/g by this method, comparable to 0.01 microg/g by a normal injector. When samples treated previously with vinclozolin were determined by the Keele injector, vinclozolin was found to be about 30% lower as compared to a normal method, suggesting about 70% recovery of the spiked vinclozolin by the Keele injector. From these results, the Keele injector was suggested to be potential for sample introduction in gas chromatographic analysis of vinclozolin in lettuce samples.

The Diversity of Anomalous HEDs: Isotopic Constraints on the Connection of EET 92023, GRA 98098, and Dhofar 700 With Vesta

NASA Technical Reports Server (NTRS)

Sanborn, M. E.; Yin, Q.-Z.; Mittlefehldt, D. W.

2016-01-01

The possibility for multiple parent bodies, instead of a common parent body of Vesta, for eucrites has been suggested based on the variable oxygen isotopic composition observed in some eucrites.. Recently, we added an extra dimension to the discussion based on the (epsilon)54Cr composition of the same eucrites with known (delta)17O to compare with the normal eucrites. The combined (delta)17O and (epsilon)54Cr isotope systematics for Pasamonte, PCA 91007, A-881394, and Ibitira indicate their likely origin from multiple different parent bodies than the normal eucrites. Often the qualifier anomalous is used to identify HEDs with (delta)17O values that deviate significantly (>3(sigma)) from the mean HED (delta)17O. However, variations in eucrites and diogenites also include unique geochemical characteristics such as bulk composition, trace element abundances, or volatile concentrations, in addition to (delta)17O. Here, we investigate three such geochemically anomalous HEDs: Elephant Moraine (EET) 92023, Graves Nunataks (GRA) 98098, and Dhofar 700. In addition, to verify the homogeneity of (epsilon)54Cr observed for normal HEDs thus far, a set of seven eucrites and diogenites considered normal samples were also investigated.

Design and simulation of optoelectronic complementary dual neural elements for realizing a family of normalized vector 'equivalence-nonequivalence' operations

NASA Astrophysics Data System (ADS)

Krasilenko, Vladimir G.; Nikolsky, Aleksandr I.; Lazarev, Alexander A.; Magas, Taras E.

2010-04-01

Equivalence models (EM) advantages of neural networks (NN) are shown in paper. EMs are based on vectormatrix procedures with basic operations of continuous neurologic: normalized vector operations "equivalence", "nonequivalence", "autoequivalence", "autononequivalence". The capacity of NN on the basis of EM and of its modifications, including auto-and heteroassociative memories for 2D images, exceeds in several times quantity of neurons. Such neuroparadigms are very perspective for processing, recognition, storing large size and strongly correlated images. A family of "normalized equivalence-nonequivalence" neuro-fuzzy logic operations on the based of generalized operations fuzzy-negation, t-norm and s-norm is elaborated. A biologically motivated concept and time pulse encoding principles of continuous logic photocurrent reflexions and sample-storage devices with pulse-width photoconverters have allowed us to design generalized structures for realization of the family of normalized linear vector operations "equivalence"-"nonequivalence". Simulation results show, that processing time in such circuits does not exceed units of micro seconds. Circuits are simple, have low supply voltage (1-3 V), low power consumption (milliwatts), low levels of input signals (microwatts), integrated construction, satisfy the problem of interconnections and cascading.

Constraints on the sum of neutrino masses using cosmological data including the latest extended Baryon Oscillation Spectroscopic Survey DR14 quasar sample

NASA Astrophysics Data System (ADS)

Wang, Sai; Wang, Yi-Fan; Xia, Dong-Mei

2018-05-01

We investigate the constraints on the sum of neutrino masses ({{Σ }}{m}ν ) using the most recent cosmological data, which combines the distance measurement from baryonic acoustic oscillation in the extended Baryon Oscillation Spectroscopic Survey DR14 quasar sample with the power spectra of temperature and polarization anisotropies in the cosmic microwave background from the Planck 2015 data release. We also use other low-redshift observations, including the baryonic acoustic oscillation at relatively low redshifts, Type Ia supernovae, and the local measurement of the Hubble constant. In the standard cosmological constant Λ cold dark matter plus massive neutrino model, we obtain the 95% upper limit to be {{Σ }}{m}ν < 0.129{eV} for the degenerate mass hierarchy, {{Σ }}{m}ν < 0.159{eV} for the normal mass hierarchy, and {{Σ }}{m}ν < 0.189{eV} for the inverted mass hierarchy. Based on Bayesian evidence, we find that the degenerate hierarchy is positively supported, and the current data combination cannot distinguish between normal and inverted hierarchies. Assuming the degenerate mass hierarchy, we extend our study to non-standard cosmological models including generic dark energy, spatial curvature, and extra relativistic degrees of freedom, but find these models are not favored by the data. SW is Supported by a grant from the Research Grant Council of the Hong Kong Special Administrative Region, China (14301214), DMX is Supported by the National Natural Science Foundation of China (11505018) and the Chongqing Science and Technology Plan Project (Cstc2015jvyj40031)

Normalized stiffness ratios for mechanical characterization of isotropic acoustic foams.

PubMed

Sahraoui, Sohbi; Brouard, Bruno; Benyahia, Lazhar; Parmentier, Damien; Geslain, Alan

2013-12-01

This paper presents a method for the mechanical characterization of isotropic foams at low frequency. The objective of this study is to determine the Young's modulus, the Poisson's ratio, and the loss factor of commercially available foam plates. The method is applied on porous samples having square and circular sections. The main idea of this work is to perform quasi-static compression tests of a single foam sample followed by two juxtaposed samples having the same dimensions. The load and displacement measurements lead to a direct extraction of the elastic constants by means of normalized stiffness and normalized stiffness ratio which depend on Poisson's ratio and shape factor. The normalized stiffness is calculated by the finite element method for different Poisson ratios. The no-slip boundary conditions imposed by the loading rigid plates create interfaces with a complex strain distribution. Beforehand, compression tests were performed by means of a standard tensile machine in order to determine the appropriate pre-compression rate for quasi-static tests.

Colloidal-facilitated transport of inorganic contaminants in ground water: part 1, sampling considerations

USGS Publications Warehouse

Puls, Robert W.; Eychaner, James H.; Powell, Robert M.

1996-01-01

Investigations at Pinal Creek, Arizona, evaluated routine sampling procedures for determination of aqueous inorganic geochemistry and assessment of contaminant transport by colloidal mobility. Sampling variables included pump type and flow rate, collection under air or nitrogen, and filter pore diameter. During well purging and sample collection, suspended particle size and number as well as dissolved oxygen, temperature, specific conductance, pH, and redox potential were monitored. Laboratory analyses of both unfiltered samples and the filtrates were performed by inductively coupled argon plasma, atomic absorption with graphite furnace, and ion chromatography. Scanning electron microscopy with Energy Dispersive X-ray was also used for analysis of filter particulates. Suspended particle counts consistently required approximately twice as long as the other field-monitored indicators to stabilize. High-flow-rate pumps entrained normally nonmobile particles. Difference in elemental concentrations using different filter-pore sizes were generally not large with only two wells having differences greater than 10 percent in most wells. Similar differences (>10%) were observed for some wells when samples were collected under nitrogen rather than in air. Fe2+/Fe3+ ratios for air-collected samples were smaller than for samples collected under a nitrogen atmosphere, reflecting sampling-induced oxidation.

Normal Approximations to the Distributions of the Wilcoxon Statistics: Accurate to What "N"? Graphical Insights

ERIC Educational Resources Information Center

Bellera, Carine A.; Julien, Marilyse; Hanley, James A.

2010-01-01

The Wilcoxon statistics are usually taught as nonparametric alternatives for the 1- and 2-sample Student-"t" statistics in situations where the data appear to arise from non-normal distributions, or where sample sizes are so small that we cannot check whether they do. In the past, critical values, based on exact tail areas, were…

Sensory Motor Inhibition as a Prerequisite for Theory-of-Mind: A Comparison of Clinical and Normal Preschoolers Differing in Sensory Motor Abilities

ERIC Educational Resources Information Center

Chasiotis, Athanasios; Kiessling, Florian; Winter, Vera; Hofer, Jan

2006-01-01

After distinguishing between neocortical abilities for executive control and subcortical sensory motor skills for proprioceptive and vestibular integration, we compare a sample of 116 normal preschoolers with a sample of 31 preschoolers receiving occupational therapeutical treatment. This is done in an experimental design controlled for age (mean:…

Laboratory-based ROTEM(®) analysis: implementing pneumatic tube transport and real-time graphic transmission.

PubMed

Colucci, G; Giabbani, E; Barizzi, G; Urwyler, N; Alberio, L

2011-08-01

ROTEM(®) is considered a helpful point-of-care device to monitor blood coagulation. Centrally performed analysis is desirable but rapid transport of blood samples and real-time transmission of graphic results are an important prerequisite. The effect of sample transport through a pneumatic tube system on ROTEM(®) results is unknown. The aims of the present work were (i) to determine the influence of blood sample transport through a pneumatic tube system on ROTEM(®) parameters compared to manual transportation, and (ii) to verify whether graphic results can be transmitted on line via virtual network computing using local area network to the physician in charge of the patient. Single centre study with 30 normal volunteers. Two whole blood samples were transferred to the central haematology laboratory by either normal transport or pneumatic delivery. EXTEM, INTEM, FIBTEM and APTEM were analysed in parallel with two ROTEM(®) devices and compared. Connection between central laboratory, emergency and operating rooms was established using local area network. All collected ROTEM(®) parameters were within normal limits. No statistically significant differences between normal transport and pneumatic delivery were observed. Real-time transmission of the original ROTEM(®) curves using local area network is feasible and easy to establish. At our institution, transport of blood samples by pneumatic delivery does not influence ROTEM(®) parameters. Blood samples can be analysed centrally, and results transmitted live via virtual network computing to emergency or operating rooms. Prior to analyse blood samples centrally, the type of sample transport should be tested to exclude in vitro blood activation by local pneumatic transport system. © 2011 Blackwell Publishing Ltd.

Evaluation of a new tear osmometer for repeatability and accuracy, using 0.5-microL (500-Nanoliter) samples.

PubMed

Yildiz, Elvin H; Fan, Vincent C; Banday, Hina; Ramanathan, Lakshmi V; Bitra, Ratna K; Garry, Eileen; Asbell, Penny A

2009-07-01

To evaluate the repeatability and accuracy of a new tear osmometer that measures the osmolality of 0.5-microL (500-nanoliter) samples. Four standardized solutions were tested with 0.5-microL (500-nanoliter) samples for repeatability of measurements and comparability to standardized technique. Two known standard salt solutions (290 mOsm/kg H2O, 304 mOsm/kg H2O), a normal artificial tear matrix sample (306 mOsm/kg H2O), and an abnormal artificial tear matrix sample (336 mOsm/kg H2O) were repeatedly tested (n = 20 each) for osmolality with use of the Advanced Instruments Model 3100 Tear Osmometer (0.5-microL [500-nanoliter] sample size) and the FDA-approved Advanced Instruments Model 3D2 Clinical Osmometer (250-microL sample size). Four standard solutions were used, with osmolality values of 290, 304, 306, and 336 mOsm/kg H2O. The respective precision data, including the mean and standard deviation, were: 291.8 +/- 4.4, 305.6 +/- 2.4, 305.1 +/- 2.3, and 336.4 +/- 2.2 mOsm/kg H2O. The percent recoveries for the 290 mOsm/kg H2O standard solution, the 304 mOsm/kg H2O reference solution, the normal value-assigned 306 mOsm/kg H2O sample, and the abnormal value-assigned 336 mOsm/kg H2O sample were 100.3, 100.2, 99.8, and 100.3 mOsm/kg H2O, respectively. The repeatability data are in accordance with data obtained on clinical osmometers with use of larger sample sizes. All 4 samples tested on the tear osmometer have osmolality values that correlate well to the clinical instrument method. The tear osmometer is a suitable instrument for testing the osmolality of microliter-sized samples, such as tears, and therefore may be useful in diagnosing, monitoring, and classifying tear abnormalities such as the severity of dry eye disease.

COX-2 expression in canine anal sac adenocarcinomas and in non-neoplastic canine anal sacs.

PubMed

Knudsen, C S; Williams, A; Brearley, M J; Demetriou, J L

2013-09-01

Anal sac adenocarcinoma (ASAC) is a clinically significant canine neoplasm characterized by early lymphatic invasion. Up-regulation of cyclooxygenase isoform 2 (COX-2) has been confirmed in several animal and human neoplastic tissues. The aim of the current study was primarily to evaluate COX-2 expression in canine ASAC and compare it to COX-2 expression in non-neoplastic canine anal sac tissue using immunohistochemistry with scoring for percentage positivity and intensity. Twenty-five ASAC samples and 22 normal anal sacs were available for evaluation. All canine ASAC samples and the normal anal sac tissues stained positively for COX-2. However, while normal anal sac tissue showed strong staining of the ductal epithelial cells, ASAC samples showed staining of the neoplastic glandular epithelial cells, with varying percentage positivity and intensity between ASAC samples. COX-2 immunoreactivity of ASAC samples was of low intensity in 52% and high in 12% of the cases; the remaining samples were of intermediate intensity. Seventy-six per cent of the ASAC had over 50% of the neoplastic glandular cells staining positive. These results confirm that COX-2 is expressed in the neoplastic glandular epithelial cells in canine ASAC and suggest a potential role for COX-2 inhibitors in the management of ASAC. Furthermore, the results indicate that COX-2 is expressed in ductal epithelial cells of the normal anal sac. Copyright © 2013 Elsevier Ltd. All rights reserved.

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.

Evaluation of Bias-Variance Trade-Off for Commonly Used Post-Summarizing Normalization Procedures in Large-Scale Gene Expression Studies

PubMed Central

Qiu, Xing; Hu, Rui; Wu, Zhixin

2014-01-01

Normalization procedures are widely used in high-throughput genomic data analyses to remove various technological noise and variations. They are known to have profound impact to the subsequent gene differential expression analysis. Although there has been some research in evaluating different normalization procedures, few attempts have been made to systematically evaluate the gene detection performances of normalization procedures from the bias-variance trade-off point of view, especially with strong gene differentiation effects and large sample size. In this paper, we conduct a thorough study to evaluate the effects of normalization procedures combined with several commonly used statistical tests and MTPs under different configurations of effect size and sample size. We conduct theoretical evaluation based on a random effect model, as well as simulation and biological data analyses to verify the results. Based on our findings, we provide some practical guidance for selecting a suitable normalization procedure under different scenarios. PMID:24941114

An investigation into the enzyme histochemistry of adenocarcinomas of human large intestine and of the transitional epithelium immediately adjacent to them

PubMed Central

Marsden, J. R.; Dawson, I. M. P.

1974-01-01

Histochemical enzymatic studies were performed on 30 freshly resected large bowel carcinomas, 30 samples of normal colonic epithelium, and six samples of the histologically normal epithelium (so-called transitional epithelium) immediately adjacent to a carcinoma. Five enzymes were studied: nicotine adenine dinucleotide tetrazolium reductase (NADH-TR), glucose-6-phosphate dehydrogenase, succinate dehydrogenase, monoamine oxidase, and acid phosphatase. Quantitative and qualitative differences in enzyme activity were observed between normal, transitional, and carcinomatous mucosa as follows: monoamine oxidase activity was moderate in normal mucosa, high in transitional mucosa, and low in carcinoma. Succinate dehydrogenase activity was high in transitional mucosa and low or moderate in normal and carcinomatous mucosa. Glucose-6-phosphate dehydrogenase activity showed a gradation from low in normal mucosa to high in carcinoma while acid phosphatase showed the reverse of this pattern. The tetrazolium reductase activity was low or moderate in normal and transitional mucosa and high in carcinoma. These differences in enzyme activity and their possible clinical and metabolic significance are discussed. ImagesFig 2Fig 3 PMID:4154840

Development of isotope labeling LC-MS for human salivary metabolomics and application to profiling metabolome changes associated with mild cognitive impairment.

PubMed

Zheng, Jiamin; Dixon, Roger A; Li, Liang

2012-12-18

Saliva is a readily available biofluid that may contain metabolites of interest for diagnosis and prognosis of diseases. In this work, a differential (13)C/(12)C isotope dansylation labeling method, combined with liquid chromatography Fourier transform ion cyclotron resonance mass spectrometry (LC-FTICR-MS), is described for quantitative profiling of the human salivary metabolome. New strategies are presented to optimize the sample preparation and LC-MS detection processes. The strategies allow the use of as little of 5 μL of saliva sample as a starting material to determine the concentration changes of an average of 1058 ion pairs or putative metabolites in comparative saliva samples. The overall workflow consists of several steps including acetone-induced protein precipitation, (12)C-dansylation labeling of the metabolites, and LC-UV measurement of the total concentration of the labeled metabolites in individual saliva samples. A pooled sample was prepared from all the individual samples and labeled with (13)C-dansylation to serve as a reference. Using this metabolome profiling method, it was found that compatible metabolome results could be obtained after saliva samples were stored in tubes normally used for genetic material collection at room temperature, -20 °C freezer, and -80 °C freezer over a period of 1 month, suggesting that many saliva samples already collected in genomic studies could become a valuable resource for metabolomics studies, although the effect of much longer term of storage remains to be determined. Finally, the developed method was applied for analyzing the metabolome changes of two different groups: normal healthy older adults and comparable older adults with mild cognitive impairment (MCI). Top-ranked 18 metabolites successfully distinguished the two groups, among which seven metabolites were putatively identified while one metabolite, taurine, was definitively identified.

Terahertz spectroscopy for the study of paraffin-embedded gastric cancer samples

NASA Astrophysics Data System (ADS)

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

2015-01-01

Terahertz (THz) spectroscopy constitute promising technique for biomedical applications as a complementary and powerful tool for diseases screening specially for early cancer diagnostic. The THz radiation is not harmful to biological tissues. As increased blood supply in cancer-affected tissues and consequent local increase in tissue water content makes THz technology a potentially attractive. In the present work, samples of healthy and adenocarcinoma-affected gastric tissue were analyzed using transmission time-domain THz spectroscopy (THz-TDS). The work shows the capability of the technique to distinguish between normal and cancerous regions in dried and paraffin-embedded samples. Plots of absorption coefficient α and refractive index n of normal and cancer affected tissues, are presented and the conditions for discrimination between normal and affected tissues are discussed.

Equilibrium Passive Sampling of POP in Lipid-Rich and Lean Fish Tissue: Quality Control Using Performance Reference Compounds.

PubMed

Rusina, Tatsiana P; Carlsson, Pernilla; Vrana, Branislav; Smedes, Foppe

2017-10-03

Passive sampling is widely used to measure levels of contaminants in various environmental matrices, including fish tissue. Equilibrium passive sampling (EPS) of persistent organic pollutants (POP) in fish tissue has been hitherto limited to application in lipid-rich tissue. We tested several exposure methods to extend EPS applicability to lean tissue. Thin-film polydimethylsiloxane (PDMS) passive samplers were exposed statically to intact fillet and fish homogenate and dynamically by rolling with cut fillet cubes. The release of performance reference compounds (PRC) dosed to passive samplers prior to exposure was used to monitor the exchange process. The sampler-tissue exchange was isotropic, and PRC were shown to be good indicators of sampler-tissue equilibration status. The dynamic exposures demonstrated equilibrium attainment in less than 2 days for all three tested fish species, including lean fish containing 1% lipid. Lipid-based concentrations derived from EPS were in good agreement with lipid-normalized concentrations obtained using conventional solvent extraction. The developed in-tissue EPS method is robust and has potential for application in chemical monitoring of biota and bioaccumulation studies.

Expression of the G protein-coupled estrogen receptor (GPER) in endometriosis: a tissue microarray study.

PubMed

Samartzis, Nicolas; Samartzis, Eleftherios P; Noske, Aurelia; Fedier, André; Dedes, Konstantin J; Caduff, Rosmarie; Fink, Daniel; Imesch, Patrick

2012-04-20

The G protein-coupled estrogen receptor (GPER) is thought to be involved in non-genomic estrogen responses as well as processes such as cell proliferation and migration. In this study, we analyzed GPER expression patterns from endometriosis samples and normal endometrial tissue samples and compared these expression profiles to those of the classical sex hormone receptors. A tissue microarray, which included 74 samples from different types of endometriosis (27 ovarian, 19 peritoneal and 28 deep-infiltrating) and 30 samples from normal endometrial tissue, was used to compare the expression levels of the GPER, estrogen receptor (ER)-alpha, ER-beta and progesterone receptor (PR). The immunoreactive score (IRS) was calculated separately for epithelium and stroma as the product of the staining intensity and the percentage of positive cells. The expression levels of the hormonal receptors were dichotomized into low (IRS < 6) and high (IRS > = 6) expression groups. The mean epithelial IRS (+/- standard deviation, range) of cytoplasmic GPER expression was 1.2 (+/- 1.7, 0-4) in normal endometrium and 5.1 (+/- 3.5, 0-12) in endometriosis (p < 0.001), of nuclear GPER 6.4 (+/- 2.6, 0-12) and 6.8 (+/- 2.9, 2-12; p = 0.71), of ER-alpha 10.6 (+/- 2.4, 3-12) and 9.8 (+/- 3.0, 2-12; p = 0.26), of ER-beta 2.4 (+/- 2.2; 0-8) and 5.6 (+/- 2.6; 0-10; p < 0.001), and of PR 11.5 (+/- 1.7; 3-12) and 8.1 (+/- 4.5; 0-12; p < 0.001), respectively. The mean stromal IRS of nuclear GPER expression was 7.7 (+/- 3.0; 2-12) in endometrium and 10.8 (+/- 1.7; 6-12) in endometriosis (p < 0.001), of ER-alpha 8.7 (+/- 3.1; 2-12) and 10.6 (+/- 2.4; 2-12; p = 0.001), of ER-beta 1.8 (+/- 2.0; 0-8) and 5.4 (+/- 2.5; 0-10; p < 0.001), and of PR 11.7 (+/- 0.9; 8-12) and 10.9 (+/- 2.0; 3-12; p = 0.044), respectively. Cytoplasmic GPER expression was not detectable in the stroma of endometrium and endometriosis. The observed frequency of high epithelial cytoplasmic GPER expression levels was 50% (n = 30/60) in the endometriosis and none (0/30) in the normal endometrium samples (p < 0.001). High epithelial cytoplasmic GPER expression levels were more frequent in endometriomas (14/20, 70%; p = 0.01), as compared to peritoneal (9/18, 50%) or deep-infiltrating endometriotic lesions (7/22, 31.8%). The frequency of high stromal nuclear GPER expression levels was 100% (n = 74/74) in endometriosis and 76.7% (n = 23/30) in normal endometrium (p < 0.001). The frequency of high epithelial nuclear GPER expression levels did not differ between endometriosis and normal endometrium. The present data indicate a unique GPER expression pattern in endometriosis, especially in endometriomas as compared to the normal endometrium. The overexpression of GPER in endometriotic lesions suggests a potential role for GPER in the hormonal regulation of endometriosis, which should be taken into consideration for future hormonal treatment strategies.

MicroRNA array normalization: an evaluation using a randomized dataset as the benchmark.

PubMed

Qin, Li-Xuan; Zhou, Qin

2014-01-01

MicroRNA arrays possess a number of unique data features that challenge the assumption key to many normalization methods. We assessed the performance of existing normalization methods using two microRNA array datasets derived from the same set of tumor samples: one dataset was generated using a blocked randomization design when assigning arrays to samples and hence was free of confounding array effects; the second dataset was generated without blocking or randomization and exhibited array effects. The randomized dataset was assessed for differential expression between two tumor groups and treated as the benchmark. The non-randomized dataset was assessed for differential expression after normalization and compared against the benchmark. Normalization improved the true positive rate significantly in the non-randomized data but still possessed a false discovery rate as high as 50%. Adding a batch adjustment step before normalization further reduced the number of false positive markers while maintaining a similar number of true positive markers, which resulted in a false discovery rate of 32% to 48%, depending on the specific normalization method. We concluded the paper with some insights on possible causes of false discoveries to shed light on how to improve normalization for microRNA arrays.

MicroRNA Array Normalization: An Evaluation Using a Randomized Dataset as the Benchmark

PubMed Central

Qin, Li-Xuan; Zhou, Qin

2014-01-01

MicroRNA arrays possess a number of unique data features that challenge the assumption key to many normalization methods. We assessed the performance of existing normalization methods using two microRNA array datasets derived from the same set of tumor samples: one dataset was generated using a blocked randomization design when assigning arrays to samples and hence was free of confounding array effects; the second dataset was generated without blocking or randomization and exhibited array effects. The randomized dataset was assessed for differential expression between two tumor groups and treated as the benchmark. The non-randomized dataset was assessed for differential expression after normalization and compared against the benchmark. Normalization improved the true positive rate significantly in the non-randomized data but still possessed a false discovery rate as high as 50%. Adding a batch adjustment step before normalization further reduced the number of false positive markers while maintaining a similar number of true positive markers, which resulted in a false discovery rate of 32% to 48%, depending on the specific normalization method. We concluded the paper with some insights on possible causes of false discoveries to shed light on how to improve normalization for microRNA arrays. PMID:24905456

Vector wind and vector wind shear models 0 to 27 km altitude for Cape Kennedy, Florida, and Vandenberg AFB, California

NASA Technical Reports Server (NTRS)

Smith, O. E.

1976-01-01

The techniques are presented to derive several statistical wind models. The techniques are from the properties of the multivariate normal probability function. Assuming that the winds can be considered as bivariate normally distributed, then (1) the wind components and conditional wind components are univariate normally distributed, (2) the wind speed is Rayleigh distributed, (3) the conditional distribution of wind speed given a wind direction is Rayleigh distributed, and (4) the frequency of wind direction can be derived. All of these distributions are derived from the 5-sample parameter of wind for the bivariate normal distribution. By further assuming that the winds at two altitudes are quadravariate normally distributed, then the vector wind shear is bivariate normally distributed and the modulus of the vector wind shear is Rayleigh distributed. The conditional probability of wind component shears given a wind component is normally distributed. Examples of these and other properties of the multivariate normal probability distribution function as applied to Cape Kennedy, Florida, and Vandenberg AFB, California, wind data samples are given. A technique to develop a synthetic vector wind profile model of interest to aerospace vehicle applications is presented.

An integrative approach to assess X-chromosome inactivation using allele-specific expression with applications to epithelial ovarian cancer.

PubMed

Larson, Nicholas B; Fogarty, Zachary C; Larson, Melissa C; Kalli, Kimberly R; Lawrenson, Kate; Gayther, Simon; Fridley, Brooke L; Goode, Ellen L; Winham, Stacey J

2017-12-01

X-chromosome inactivation (XCI) epigenetically silences transcription of an X chromosome in females; patterns of XCI are thought to be aberrant in women's cancers, but are understudied due to statistical challenges. We develop a two-stage statistical framework to assess skewed XCI and evaluate gene-level patterns of XCI for an individual sample by integration of RNA sequence, copy number alteration, and genotype data. Our method relies on allele-specific expression (ASE) to directly measure XCI and does not rely on male samples or paired normal tissue for comparison. We model ASE using a two-component mixture of beta distributions, allowing estimation for a given sample of the degree of skewness (based on a composite likelihood ratio test) and the posterior probability that a given gene escapes XCI (using a Bayesian beta-binomial mixture model). To illustrate the utility of our approach, we applied these methods to data from tumors of ovarian cancer patients. Among 99 patients, 45 tumors were informative for analysis and showed evidence of XCI skewed toward a particular parental chromosome. For 397 X-linked genes, we observed tumor XCI patterns largely consistent with previously identified consensus states based on multiple normal tissue types. However, 37 genes differed in XCI state between ovarian tumors and the consensus state; 17 genes aberrantly escaped XCI in ovarian tumors (including many oncogenes), whereas 20 genes were unexpectedly inactivated in ovarian tumors (including many tumor suppressor genes). These results provide evidence of the importance of XCI in ovarian cancer and demonstrate the utility of our two-stage analysis. © 2017 WILEY PERIODICALS, INC.

Electrical resistivity well-logging system with solid-state electronic circuitry

USGS Publications Warehouse

Scott, James Henry; Farstad, Arnold J.

1977-01-01

An improved 4-channel electrical resistivity well-logging system for use with a passive probe with electrodes arranged in the 'normal' configuration has been designed and fabricated by Westinghouse Electric Corporation to meet technical specifications developed by the U.S. Geological Survey. Salient features of the system include solid-state switching and current regulation in the transmitter circuit to produce a constant-current source square wave, and synchronous solid-state switching and sampling of the potential waveform in the receiver circuit to provide an analog dc voltage proportions to the measured resistivity. Technical specifications and design details are included in this report.

[Intraocular and serum antibody titers to Leptospira in 150 horses with equine recurrent uveitis (ERU) subjected to vitrectomy].

PubMed

Wollanke, B; Gerhards, H; Brem, S; Kopp, H; Meyer, P

1998-04-01

Between February 1993 and July 1997, 150 horses suffering from recurrent uveitis were subjected to parsplana vitrectomy. In these horses, antibody titers to Leptospira serovars were determined in serum samples and in samples from diluted vitreous collected during vitrectomy. Although the vitreous samples were diluted with 250 ml of balanced salt solution, in 86 of the 150 vitreous samples (= 57%) the antibody titers were higher than in the serum samples. Additionally, serum samples from 77 horses suffering from ERU, but which were not subjected to vitrectomy, and serum samples from 97 horses with clinically normal eyes were analyzed for antibodies to Leptospira serovars. Among the 227 horses with ERU (150 treated surgically, 77 treated conservatively) 50 horses (50 of 227 = 22%) had serum antibody titers to Leptospira serovars of > or = 1:800. Among the 97 horses with clinically normal eyes, 24 horses (24 of 97 = 25%) had serum antibody titers to Leptospira serovars of > or = 1:800. In undiluted vitreous samples from 20 horses with clinically normal eyes, no antibody titers to Leptospira serovars could be detected. Among the 150 horses with ERU, 90 animals (90 of 150 = 60%) had antibody titers of > or = 1:100 in the diluted vitreous samples, the difference being highly significant (p < 0.001). The findings are discussed in relation to the etiology of recurrent uveitis in horses.

Differentiating cancerous from normal breast tissue by redox imaging

NASA Astrophysics Data System (ADS)

Xu, He N.; Tchou, Julia; Feng, Min; Zhao, Huaqing; Li, Lin Z.

2015-02-01

Abnormal metabolism can be a hallmark of cancer occurring early before detectable histological changes and may serve as an early detection biomarker. The current gold standard to establish breast cancer (BC) diagnosis is histological examination of biopsy. Previously we have found that pre-cancer and cancer tissues in animal models displayed abnormal mitochondrial redox state. Our technique of quantitatively measuring the mitochondrial redox state has the potential to be implemented as an early detection tool for cancer and may provide prognostic value. We therefore in this present study, investigated the feasibility of quantifying the redox state of tumor samples from 16 BC patients. Tumor tissue aliquots were collected from both normal and cancerous tissue from the affected cancer-bearing breasts of 16 female patients (5 TNBC, 9 ER+, 2 ER+/Her2+) shortly after surgical resection. All specimens were snap-frozen with liquid nitrogen on site and scanned later with the Chance redox scanner, i.e., the 3D cryogenic NADH/oxidized flavoprotein (Fp) fluorescence imager. Our preliminary results showed that both NADH and Fp (including FAD, i.e., flavin adenine dinucleotide) signals in the cancerous tissues roughly tripled to quadrupled those in the normal tissues (p<0.05) and the redox ratio Fp/(NADH+Fp) was about 27% higher in the cancerous tissues than in the normal ones (p<0.05). Our findings suggest that the redox state could differentiate between cancer and non-cancer breast tissues in human patients and this novel redox scanning procedure may assist in tissue diagnosis in freshly procured biopsy samples prior to tissue fixation. We are in the process of evaluating the prognostic value of the redox imaging indices for BC.

Prevalence of transactive response DNA-binding protein 43 (TDP-43) proteinopathy in cognitively normal older adults: systematic review and meta-analysis.

PubMed

Nascimento, C; Di Lorenzo Alho, A T; Bazan Conceição Amaral, C; Leite, R E P; Nitrini, R; Jacob-Filho, W; Pasqualucci, C A; Hokkanen, S R K; Hunter, S; Keage, H; Kovacs, G G; Grinberg, L T; Suemoto, C K

2018-04-01

To perform a systematic review and meta-analysis on the prevalence of transactive response DNA-binding protein 43 (TDP-43) proteinopathy in cognitively normal older adults. We systematically reviewed and performed a meta-analysis on the prevalence of TDP-43 proteinopathy in older adults with normal cognition, evaluated by the Mini-Mental State Examination or the Clinical Dementia Rating. We estimated the overall prevalence of TDP-43 using random-effect models, and stratified by age, sex, sample size, study quality, antibody used to assess TDP-43 aggregates, analysed brain regions, Braak stage, Consortium to Establish a Registry for Alzheimer's Disease score, hippocampal sclerosis and geographic location. A total of 505 articles were identified in the systematic review, and 7 were included in the meta-analysis with 1196 cognitively normal older adults. We found an overall prevalence of TDP-43 proteinopathy of 24%. Prevalence of TDP-43 proteinopathy varied widely across geographic location (North America: 37%, Asia: 29%, Europe: 14%, and Latin America: 11%). Estimated prevalence of TDP-43 proteinopathy also varied according to study quality (quality score >7: 22% vs. quality score <7: 42%), antibody used to assess TDP-43 proteinopathy (native: 18% vs. hyperphosphorylated: 24%) and presence of hippocampal sclerosis (without 24% vs. with hippocampal sclerosis: 48%). Other stratified analyses by age, sex, analysed brain regions, sample size and severity of AD neuropathology showed similar pooled TDP-43 prevalence. Different methodology to access TDP-43, and also differences in lifestyle and genetic factors across different populations could explain our results. Standardization of TDP-43 measurement, and future studies about the impact of genetic and lifestyle characteristics on the development of neurodegenerative diseases are needed. © 2017 British Neuropathological Society.

Expression screening of cancer/testis genes in prostate cancer identifies NR6A1 as a novel marker of disease progression and aggressiveness.

PubMed

Mathieu, Romain; Evrard, Bertrand; Fromont, Gaëlle; Rioux-Leclercq, Nathalie; Godet, Julie; Cathelineau, Xavier; Guillé, François; Primig, Michael; Chalmel, Frédéric

2013-07-01

Cancer/Testis (CT) genes are expressed in male gonads, repressed in most healthy somatic tissues and de-repressed in various somatic malignancies including prostate cancers (PCa). Because of their specific expression signature and their associations with tumor aggressiveness and poor outcomes, CT genes are considered to be useful biomarkers and they are also targets for the development of new anti-cancer immunotherapies. The aim of this study was to identify novel CT genes associated with hormone-sensitive prostate cancer (HSPC), and castration-resistant prostate cancer (CRPC). To identify novel CT genes we screened genes for which transcripts were detected by RNA profiling specifically in normal testis and in either HSPC or CRPC as compared to normal prostate and 44 other healthy tissues using GeneChips. The expression and clinicopathological significance of a promising candidate--NR6A1--was examined in HSPC, CRPC, and metastatic site samples using tissue microarrays. We report the identification of 98 genes detected in CRPC, HSPC and testicular samples but not in the normal controls. Among them, cellular levels of NR6A1 were found to be higher in HSPC compared to normal prostate and further increased in metastatic lesions and CRPC. Furthermore, increased NR6A1 immunoreactivity was significantly associated with a high Gleason score, advanced pT stage and cancer cell proliferation. Our results show that cellular levels of NR6A1 are correlated with disease progression in PCa. We suggest that this essential orphan nuclear receptor is a potential therapeutic target as well as a biomarker of PCa aggressiveness. Copyright © 2013 Wiley Periodicals, Inc.

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:22952972

Correlation of gene expression with bladder capacity in interstitial cystitis/bladder pain syndrome.

PubMed

Colaco, Marc; Koslov, David S; Keys, Tristan; Evans, Robert J; Badlani, Gopal H; Andersson, Karl-Erik; Walker, Stephen J

2014-10-01

Interstitial cystitis and bladder pain syndrome are terms used to describe a heterogeneous chronic pelvic and bladder pain disorder. Despite its significant prevalence, our understanding of disease etiology is poor. We molecularly characterized interstitial cystitis/bladder pain syndrome and determined whether there are clinical factors that correlate with gene expression. Bladder biopsies from female subjects with interstitial cystitis/bladder pain syndrome and female controls without signs of the disease were collected and divided into those with normal and low anesthetized bladder capacity, respectively. Samples then underwent RNA extraction and microarray assay. Data generated by these assays were analyzed using Omics Explorer (Qlucore, Lund, Sweden), GeneSifter® Analysis Edition 4.0 and Ingenuity® Pathway Analysis to determine similarity among samples within and between groups, and measure differentially expressed transcripts unique to each phenotype. A total of 16 subjects were included in study. Principal component analysis and unsupervised hierarchical clustering showed clear separation between gene expression in tissues from subjects with low compared to normal bladder capacity. Gene expression in tissue from patients with interstitial cystitis/bladder pain syndrome who had normal bladder capacity did not significantly differ from that in controls without interstitial cystitis/bladder pain syndrome. Pairwise analysis revealed that pathways related to inflammatory and immune response were most involved. Microarray analysis provides insight into the potential pathological condition underlying interstitial cystitis/bladder pain syndrome. This pilot study shows that patients with this disorder who have low compared to normal bladder capacity have significantly different molecular characteristics, which may reflect a difference in disease pathophysiology. Copyright © 2014 American Urological Association Education and Research, Inc. Published by Elsevier Inc. All rights reserved.

Differences in proximal (cardia) versus distal (antral) gastric carcinogenesis via retinoblastoma pathway

PubMed Central

Gulmann, Christian; Hegarty, Helen; Grace, Antoinette; Leader, Mary; Patchett, Stephen; Kay, Elaine

2004-01-01

AIM: Disruption of cell cycle regulation is a critical event in carcinogenesis, and alteration of the retinoblastoma (pRb) tumour suppressor pathway is frequent. The aim of this study was to compare alterations in this pathway in proximal and distal gastric carcinogenesis in an effort to explain the observed striking epidemiological differences. METHODS: Immunohistochemistry was performed to investigate expression of p16 and pRb in the following groups of both proximal (cardia) and distal (antral) tissue samples: (a) biopsies showing normal mucosa, (b) biopsies showing intestinal metaplasia and, (c) gastric cancer resection specimens including uninvolved mucosa and tumour. RESULTS: In the antrum there were highly significant trends for increased p16 expression with concomitant (and in the group of carcinomas inversely proportional) decreased pRb expression from normal mucosa to intestinal metaplasia to uninvolved mucosa (from cancer resections) to carcinoma. In the cardia, there were no differences in p16 expression between the various types of tissue samples whereas pRb expression was higher in normal mucosa compared with intestinal metaplasia and tissue from cancer resections. CONCLUSION: Alterations in the pRb pathway appear to play a more significant role in distal gastric carcinogenesis. It may be an early event in the former location since the trend towards p16 overexpression with concomitant pRb underexpression was seen as early as between normal mucosa and intestinal metaplasia. Importantly, the marked differences in expression of pRb and p16 between the cardia and antrum strongly support the hypothesis that tumours of the two locations are genetically different which may account for some of the observed epidemiological differences. PMID:14695761

Assessment of Bax and Bcl-2 Immunoexpression in Patients with Oral Lichen Planus and Oral Squamous Cell Carcinoma

PubMed Central

Nafarzadeh, Shima; Jafari, Sina; Bijani, Ali

2013-01-01

Lichen planus (LP) is a chronic inflammatory disease of probable immune-based etiology. The pathogenesis of LP is unclear, but apoptotic changes in epidermal (epithelial) cells have been reported. Destruction of the basal cell layer is observed and many changes in cell proliferation, cell repair and cell death occur in the injured mucosal epithelium. The aim of this study was to evaluate and compare the expression of bax and bcl-2 in oral lichen planus (OLP), well differentiated oral squamous cell carcinoma (WOSCC) and normal mucosa. Sixty one paraffin-embedded biopsy including 11 cases of WOSCC, 30 cases of OLP (n=15 erosive OLP [OLP-E], n=15 reticular OLP [OLP-R]) and 20 normal mucosa were entered in our research. We used immunohistochemistry staining method for assessing bax and bcl-2 expression in epithelial layers. The percentage of stained cells was estimated in 5 randomized microscopic fields and classified as (-): 0%, (+) :< 10%, (++): 10-25%, (+++): 26-50%, (++++): > 50% positive cells. The data were analyzed with Mann-Whitney, Chi Square, and Kruskal-Wallis tests. Significant differences in bax expression were observed among OLP, WOSCC compared to normal mucosa (P=0.008). No significant difference in bax expression between OLP-E and OLP-R compared to WOSCC was seen (P>0.05). Bcl-2 was negative for all OLP and normal mucosa samples, and weak positivity was observed in WOSCC samples. According to the findings of our study, it may be possible to correlate the difference of bax and bcl-2 expression levels among the mentioned lesions to the malignant potential of OLP. PMID:24551804

Fluorescence lifetime spectroscopy for guided therapy of brain tumors.

PubMed

Butte, Pramod V; Mamelak, Adam N; Nuno, Miriam; Bannykh, Serguei I; Black, Keith L; Marcu, Laura

2011-01-01

This study evaluates the potential of time-resolved laser induced fluorescence spectroscopy (TR-LIFS) as intra-operative tool for the delineation of brain tumor from normal brain. Forty two patients undergoing glioma (WHO grade I-IV) surgery were enrolled in this study. A TR-LIFS prototype apparatus (gated detection, fast digitizer) was used to induce in-vivo fluorescence using a pulsed N2 laser (337 nm excitation, 0.7 ns pulse width) and to record the time-resolved spectrum (360-550 nm range, 10 nm interval). The sites of TR-LIFS measurement were validated by conventional histopathology (H&E staining). Parameters derived from the TR-LIFS data including intensity values and time-resolved intensity decay features (average fluorescence lifetime and Laguerre coefficients values) were used for tissue characterization and classification. 71 areas of tumor and normal brain were analyzed. Several parameters allowed for the differentiation of distinct tissue types. For example, normal cortex (N=35) and normal white matter (N=12) exhibit a longer-lasting fluorescence emission at 390 nm (τ390=2.12±0.10 ns) when compared with 460 nm (τ460=1.16±0.08 ns). High grade glioma (grades III and IV) samples (N=17) demonstrate emission peaks at 460 nm, with large variation at 390 nm while low grade glioma (I and II) samples (N=7) demonstrated a peak fluorescence emission at 460 nm. A linear discriminant algorithm allowed for the classification of low-grade gliomas with 100% sensitivity and 98% specificity. High-grade glioma demonstrated a high degree of heterogeneity thus reducing the discrimination accuracy of these tumors to 47% sensitivity and 94% specificity. Current findings demonstrate that TR-LIFS holds the potential to diagnose brain tumors intra-operatively and to provide a valuable tool for aiding the neurosurgeon-neuropathologist team in to rapidly distinguish between tumor and normal brain during surgery. Copyright © 2010 Elsevier Inc. All rights reserved.

Perceived functional impact of abnormal facial appearance.

PubMed

Rankin, Marlene; Borah, Gregory L

2003-06-01

Functional facial deformities are usually described as those that impair respiration, eating, hearing, or speech. Yet facial scars and cutaneous deformities have a significant negative effect on social functionality that has been poorly documented in the scientific literature. Insurance companies are declining payments for reconstructive surgical procedures for facial deformities caused by congenital disabilities and after cancer or trauma operations that do not affect mechanical facial activity. The purpose of this study was to establish a large, sample-based evaluation of the perceived social functioning, interpersonal characteristics, and employability indices for a range of facial appearances (normal and abnormal). Adult volunteer evaluators (n = 210) provided their subjective perceptions based on facial physical appearance, and an analysis of the consequences of facial deformity on parameters of preferential treatment was performed. A two-group comparative research design rated the differences among 10 examples of digitally altered facial photographs of actual patients among various age and ethnic groups with "normal" and "abnormal" congenital deformities or posttrauma scars. Photographs of adult patients with observable congenital and posttraumatic deformities (abnormal) were digitally retouched to eliminate the stigmatic defects (normal). The normal and abnormal photographs of identical patients were evaluated by the large sample study group on nine parameters of social functioning, such as honesty, employability, attractiveness, and effectiveness, using a visual analogue rating scale. Patients with abnormal facial characteristics were rated as significantly less honest (p = 0.007), less employable (p = 0.001), less trustworthy (p = 0.01), less optimistic (p = 0.001), less effective (p = 0.02), less capable (p = 0.002), less intelligent (p = 0.03), less popular (p = 0.001), and less attractive (p = 0.001) than were the same patients with normal facial appearances. Facial deformity caused by trauma, congenital disabilities, and postsurgical sequelae present with significant adverse functional consequences. Facial deformities have a significant negative effect on perceptions of social functionality, including employability, honesty, and trustworthiness. Adverse perceptions of patients with facial deformities occur regardless of sex, educational level, and age of evaluator.

Correlation between chronic arthritis patients confirmed with questionnaire and serologic test of Lyme disease

NASA Astrophysics Data System (ADS)

Rotan, H.; Ginting, Y.; Loesnihari, R.; Kembaren, T.; Marpaung, B.

2018-03-01

Lyme borreliosis is the most common tick-borne disease, and frequency of arthritis complication later. The objective of this study was to determine the seroprevalence of Lyme disease and to evaluate its correlation with chronic arthritis. This epidemiologic cross sectional study included 41 healthy individuals who had chronic arthritis and bitten by ticks underwent questionnaires, and laboratory tests consisted of a routine blood sample, serum uric acid, and IgG ELISA for Lyme. There was 7.32% presence of positive IgG for Lyme. Samples with positive IgG for Lyme were further evaluated for rheumatology marker. We found three samples with a positive rheumatoid factor, two samples had positive anti-MCV, and 1 sample had slightly increased CRP. Three Lyme positive samples had normal EULAR scoring. It was the first Lyme disease case found in Indonesia, particularly in 4 villages of Sibolangit, Deli Serdang, North Sumatera. The assessment made by analysis the questionnaire, evaluation the blood test, and confirmed positive Lyme disease, and at last, we found the correlation between chronic arthritis with positive test Lyme.

Microarray R-based analysis of complex lysate experiments with MIRACLE

PubMed Central

List, Markus; Block, Ines; Pedersen, Marlene Lemvig; Christiansen, Helle; Schmidt, Steffen; Thomassen, Mads; Tan, Qihua; Baumbach, Jan; Mollenhauer, Jan

2014-01-01

Motivation: Reverse-phase protein arrays (RPPAs) allow sensitive quantification of relative protein abundance in thousands of samples in parallel. Typical challenges involved in this technology are antibody selection, sample preparation and optimization of staining conditions. The issue of combining effective sample management and data analysis, however, has been widely neglected. Results: This motivated us to develop MIRACLE, a comprehensive and user-friendly web application bridging the gap between spotting and array analysis by conveniently keeping track of sample information. Data processing includes correction of staining bias, estimation of protein concentration from response curves, normalization for total protein amount per sample and statistical evaluation. Established analysis methods have been integrated with MIRACLE, offering experimental scientists an end-to-end solution for sample management and for carrying out data analysis. In addition, experienced users have the possibility to export data to R for more complex analyses. MIRACLE thus has the potential to further spread utilization of RPPAs as an emerging technology for high-throughput protein analysis. Availability: Project URL: http://www.nanocan.org/miracle/ Contact: mlist@health.sdu.dk Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25161257

Microarray R-based analysis of complex lysate experiments with MIRACLE.

PubMed

List, Markus; Block, Ines; Pedersen, Marlene Lemvig; Christiansen, Helle; Schmidt, Steffen; Thomassen, Mads; Tan, Qihua; Baumbach, Jan; Mollenhauer, Jan

2014-09-01

Reverse-phase protein arrays (RPPAs) allow sensitive quantification of relative protein abundance in thousands of samples in parallel. Typical challenges involved in this technology are antibody selection, sample preparation and optimization of staining conditions. The issue of combining effective sample management and data analysis, however, has been widely neglected. This motivated us to develop MIRACLE, a comprehensive and user-friendly web application bridging the gap between spotting and array analysis by conveniently keeping track of sample information. Data processing includes correction of staining bias, estimation of protein concentration from response curves, normalization for total protein amount per sample and statistical evaluation. Established analysis methods have been integrated with MIRACLE, offering experimental scientists an end-to-end solution for sample management and for carrying out data analysis. In addition, experienced users have the possibility to export data to R for more complex analyses. MIRACLE thus has the potential to further spread utilization of RPPAs as an emerging technology for high-throughput protein analysis. Project URL: http://www.nanocan.org/miracle/. Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press.

Tissue and organ donation for research in forensic pathology: the MRC Sudden Death Brain and Tissue Bank.

PubMed

Millar, T; Walker, R; Arango, J-C; Ironside, J W; Harrison, D J; MacIntyre, D J; Blackwood, D; Smith, C; Bell, J E

2007-12-01

Novel methodological approaches to the investigation of brain and non-central nervous system disorders have led to increased demand for well-characterized, high quality human tissue samples, particularly from control cases. In the setting of the new Human Tissue legislation, we sought to determine whether relatives who have been suddenly bereaved are willing to grant authorization for research use of post mortem tissue samples and organs in sufficient numbers to support the establishment of a brain and tissue bank based in the forensic service. Research authorization was sought from families on the day prior to forensic post mortem examination followed up by written confirmation. We have to date selected individuals who have died suddenly (age range 1-89 years) and who were likely to have normal brains or who had displayed symptoms of a CNS disorder of interest to researchers, including psychiatric disorders. One hundred and eleven families have been approached during the first 2 years of this project. Research use of tissue samples was authorized by 96% of families and 17% agreed to whole brain donation. Audit of families' experience does not suggest that they are further distressed by being approached. Respondents expressed a clear view that the opportunity for research donation should be open to all bereaved families. Despite the sometimes long post mortem intervals, the quality of tissue samples is good, as assessed by a range of markers including Agilent BioAnalyzer quantification of RNA integrity (mean value 6.4). We conclude that the vast majority of families are willing to support research use of post mortem tissues even in the context of sudden bereavement and despite previous adverse publicity. The potential for acquisition of normal CNS and non-CNS tissues and of various hard-to-get CNS disorders suggests that efforts to access the forensic post mortem service for research material are eminently worthwhile. (c) 2007 Pathological Society of Great Britain and Ireland

Rotor component displacement measurement system

DOEpatents

Mercer, Gary D.; Li, Ming C.; Baum, Charles R.

2003-05-27

A measuring system for measuring axial displacement of a tube relative to an axially stationary component in a rotating rotor assembly includes at least one displacement sensor adapted to be located normal to a longitudinal axis of the tube; an insulated cable system adapted for passage through the rotor assembly; a rotatable proximitor module located axially beyond the rotor assembly to which the cables are connected; and a telemetry system operatively connected to the proximitor module for sampling signals from the proximitor module and forwarding data to a ground station.

Multiplex Immunoassay Profiling of Hormones Involved in Metabolic Regulation.

PubMed

Stephen, Laurie; Guest, Paul C

2018-01-01

Multiplex immunoassays are used for rapid profiling of biomarker proteins and small molecules in biological fluids. The advantages over single immunoassays include lower sample consumption, cost, and labor. This chapter details a protocol to develop a 5-plex assay for glucagon-like peptide 1, growth hormone, insulin, leptin, and thyroid-stimulating hormone on the Luminex ® platform. The results of the analysis of insulin in normal control subjects are given due to the important role of this hormone in nutritional programming diseases.

Isotopic compositions of the elements 2013 (IUPAC Technical Report)

USGS Publications Warehouse

Meija, Juris; Coplen, Tyler B.; Berglund, Michael; Brand, Willi A.; De Bièvre, Paul; Gröning, Manfred; Holden, Norman E.; Irrgeher, Johanna; Loss, Robert D.; Walczyk, Thomas; Prohaska, Thomas

2016-01-01

The Commission on Isotopic Abundances and Atomic Weights (ciaaw.org) of the International Union of Pure and Applied Chemistry (iupac.org) has revised the Table of Isotopic Compositions of the Elements (TICE). The update involved a critical evaluation of the recent published literature. The new TICE 2013 includes evaluated data from the “best measurement” of the isotopic abundances in a single sample, along with a set of representative isotopic abundances and uncertainties that accommodate known variations in normal terrestrial materials.

On simple aerodynamic sensitivity derivatives for use in interdisciplinary optimization

NASA Technical Reports Server (NTRS)

Doggett, Robert V., Jr.

1991-01-01

Low-aspect-ratio and piston aerodynamic theories are reviewed as to their use in developing aerodynamic sensitivity derivatives for use in multidisciplinary optimization applications. The basic equations relating surface pressure (or lift and moment) to normal wash are given and discussed briefly for each theory. The general means for determining selected sensitivity derivatives are pointed out. In addition, some suggestions in very general terms are included as to sample problems for use in studying the process of using aerodynamic sensitivity derivatives in optimization studies.

Intrinsic fluorescence based in-vivo detection of cervical precancer with hand held prototype device

NASA Astrophysics Data System (ADS)

Meena, Bharat Lal; Raikwar, Akanksha; Pandey, Kiran; Agarwal, Asha; Pantola, Chayanika; Pradhan, Asima

2018-02-01

A prototype device (hand held probe) designed and fabricated in the lab has been tested for cervical precancer detection using intrinsic fluorescence. The intrinsic fluorescence gets strongly modulated by the interplay of scattering and absorption. This masks valuable biochemical information which is present in the intrinsic fluorescence. These distortion effects can be minimized by normalizing the polarized fluorescence spectra by the polarized elastic scattering spectra. The measurements have been made with a in-house fabricated device using a 405 nm diode laser and white light source respectively. 166 sites of different grades of cervical pre-cancer biopsy samples (CIN I and CIN II) (CIN: cervical intraepithelial neoplastic) have been discriminated from 29 sites of normal biopsy samples using principal component analysis (PCA) based linear discriminant analysis (LDA). The sensitivity and specificity for discrimination of normal samples from CIN I are found to be 99% and 96% respectively. Further the normal samples can be discriminated from CIN II samples with 96% sensitivity and 96% specificity. Based on these promising ex-vivo results an in-vivo study on patients has been initiated in the hospital. The hand held device built in-house shows promise as a useful tool for in vivo cervical precancer detection by polarized fluorescence. Preliminary in-vivo results on 10 patients indicate the efficacy of the hand held device for screening cervical precancers using intrinsic fluorescence.

The behaviour of cross-helicity and residual energy at different heliolatitudes - Ulysses data

NASA Astrophysics Data System (ADS)

Popescu, Emil; Popescu, Nedelia Antonia

In this paper we analyze the variations of the normalized cross-helicity (?C ) and normalized residual energy (σR), that characterize the Alfvenic fluctuations in the solar wind. For this purpose we consider data from SWOOPS and VHM instruments on board of Ulysses mission, for solar wind plasma parameters and magnetic field data, for the year 2001. In order to analyze the behaviour of the normalized cross-helicity, σC, and normalized residual energy, σR, at different heliolatitudes, as well as the relation between σR and σC, we determine their distributions for three periods of time: DOY 240 - DOY 348 (for a data sample at high heliolatitudes, between 69°N - 82.2°N), DOY 154 - DOY 181.5 (for a data sample at middle heliolatitudes, between 15°N - 35°N), and DOY 88 - DOY 118 (for a data sample at middle heliolatitudes, between 15°S - 35°S). The results on the residual energy σR versus cross-helicity σC distribution reveal a middle heliolatitude data sample that presents a more dispersed distribution than the high heliolatitude data sample. A different behaviour of the σC distributions was observed for the periods covering the middle heliolatitudes for the southern and northern hemispheres. This is because during the third period of time, transient events as ICMEs with strong magnetic field strength and high velocity are encountered.

Glucose transporter-1 (GLUT-1) immunoreactivity in benign, premalignant and malignant lesions of the gallbladder.

PubMed

Legan, Mateja; Tevžič, Spela; Tolar, Ana; Luzar, Boštjan; Marolt, Vera Ferlan

2011-03-01

GLUT-1 is a transmembrane glucose transport protein that allows the facilitated transport of glucose into cells, normally expressed in tissues which depend mainly on glucose metabolism. Enhanced expression of GLUT-1 can also be found in a large spectrum of carcinomas. This study aimed to investigate GLUT-1 expression in gallbladder tissue: from normal tissue samples, hyperplasias, low-grade and high-grade dysplasias to gallbladder carcinomas. In all, 115 archived samples of gallbladder tissue from 68 patients, presented after cholecystectomy, were immunohistochemically stained for GLUT-1. According to the intensity of GLUT-1 immunoreactivity, samples were divided into negative (stained 0-10% of cells stained), positive with weak to moderate (10-50%) and positive with strong (>50%) GLUT-1 expression. The GLUT-1 immunoreactivity of the samples showed a characteristic increase from premalignant lesions to carcinomas. Normal gallbladder tissue samples did not express GLUT-1 (100%). Weak expression was shown only focally in hyperplasias, but to a greater extent with low-grade dysplasias (20%), high-grade dysplasias (40%) and carcinomas (51.8%). Normal gallbladder tissue is GLUT-1 negative. GLUT-1 expression in carcinoma tissue is significantly higher than in dysplastic lesions. Strong GLUT-1 expression indicates 100% specificity for detecting gallbladder carcinomas. Therefore, GLUT-1 is a candidate as a diagnostic as well as a tissue prognostic marker in gallbladder carcinoma patients.

Considerations for potency equivalent calculations in the Ah receptor-based CALUX bioassay: normalization of superinduction results for improved sample potency estimation.

PubMed

Baston, David S; Denison, Michael S

2011-02-15

The chemically activated luciferase expression (CALUX) system is a mechanistically based recombinant luciferase reporter gene cell bioassay used in combination with chemical extraction and clean-up methods for the detection and relative quantitation of 2,3,7,8-tetrachlorodibenzo-p-dioxin and related dioxin-like halogenated aromatic hydrocarbons in a wide variety of sample matrices. While sample extracts containing complex mixtures of chemicals can produce a variety of distinct concentration-dependent luciferase induction responses in CALUX cells, these effects are produced through a common mechanism of action (i.e. the Ah receptor (AhR)) allowing normalization of results and sample potency determination. Here we describe the diversity in CALUX response to PCDD/Fs from sediment and soil extracts and not only report the occurrence of superinduction of the CALUX bioassay, but we describe a mechanistically based approach for normalization of superinduction data that results in a more accurate estimation of the relative potency of such sample extracts. Copyright © 2010 Elsevier B.V. All rights reserved.

A feasibility study in adapting Shamos Bickel and Hodges Lehman estimator into T-Method for normalization

NASA Astrophysics Data System (ADS)

Harudin, N.; Jamaludin, K. R.; Muhtazaruddin, M. Nabil; Ramlie, F.; Muhamad, Wan Zuki Azman Wan

2018-03-01

T-Method is one of the techniques governed under Mahalanobis Taguchi System that developed specifically for multivariate data predictions. Prediction using T-Method is always possible even with very limited sample size. The user of T-Method required to clearly understanding the population data trend since this method is not considering the effect of outliers within it. Outliers may cause apparent non-normality and the entire classical methods breakdown. There exist robust parameter estimate that provide satisfactory results when the data contain outliers, as well as when the data are free of them. The robust parameter estimates of location and scale measure called Shamos Bickel (SB) and Hodges Lehman (HL) which are used as a comparable method to calculate the mean and standard deviation of classical statistic is part of it. Embedding these into T-Method normalize stage feasibly help in enhancing the accuracy of the T-Method as well as analysing the robustness of T-method itself. However, the result of higher sample size case study shows that T-method is having lowest average error percentages (3.09%) on data with extreme outliers. HL and SB is having lowest error percentages (4.67%) for data without extreme outliers with minimum error differences compared to T-Method. The error percentages prediction trend is vice versa for lower sample size case study. The result shows that with minimum sample size, which outliers always be at low risk, T-Method is much better on that, while higher sample size with extreme outliers, T-Method as well show better prediction compared to others. For the case studies conducted in this research, it shows that normalization of T-Method is showing satisfactory results and it is not feasible to adapt HL and SB or normal mean and standard deviation into it since it’s only provide minimum effect of percentages errors. Normalization using T-method is still considered having lower risk towards outlier’s effect.

Quantitative proteomics analysis by iTRAQ in human nuclear cataracts of different ages and normal lens nuclei.

PubMed

Zhou, Hai Yan; Yan, Hong; Wang, Li Li; Yan, Wei Jia; Shui, Ying Bo; Beebe, David C

2015-08-01

The goal of this study was to quantitatively identify the differentially expressed proteins in nuclear cataracts of different ages and normal lens nuclei in humans. Forty-eight human lens nucleus samples with hardness grades III, IV were obtained during cataract surgery by extracapsular cataract extraction. Seven normal transparent human lens nuclei were obtained from fresh normal cadaver eyes during corneal transplantation surgery. Lens nuclei were divided into seven groups according to age and optic axis: Group A (average age 80.8 ± 1.2 years), Group B (average age 57.0 ± 4.0 years), Group C average age 80.3 ± 4.5 years), Group D (average age 56.9 ± 4.2 years), Group E (average age 78.1 ± 2.5 years), Group F (average age 57.6 ± 3.3 years) and Group G (seven normal transparent human lenses from normal cadaver eyes, average age 34.7 ± 4.2 years). Water-soluble, water-insoluble, and water-insoluble-urea-soluble protein fractions were extracted from samples. The three-part protein fractions from the individual lenses were combined to form the total proteins of each sample. The proteomic profiles of each group were further analyzed using 8-plex iTRAQ labeling combined with 2D-LC-MS/MS. The data were analyzed with the ProteinPilot software for peptide matching, protein identification, and quantification. Differentially expressed proteins were validated by Western blotting. We employed biological and technical replicates and selected the intersection of the two results, which included 80 proteins. Nine proteins were differentially expressed among the 80 proteins identified using proteomic techniques. In age-related nuclear cataracts (ARNC), the expression levels of fatty acid-binding protein and pterin-4-alpha-carbinolamine dehydratase were upregulated, whereas the levels of alpha-crystallin B chain (CRYAB), GSH synthetase, phakinin, gamma-crystallin C, phosphoglycerate kinase 1, betaine-homocysteine S-methyltransferase 1 (BHMT1), and spectrin beta chain were downregulated. These proteins may be associated with abnormal protein aggregation and oxidative stress. GSH synthetase and CRYAB expression levels in the nuclear cataract decreased with age. The mass spectrometric analysis results were consistent with the Western blot validation. The results indicate that CRYAB and GSH synthetase may be involved in ARNC pathogenesis. iTRAQ combined with 2D-LC-MS/MS provides new methods for future studies of pathological mechanisms and protective drug development for ARNC. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

ASSOCIATION BETWEEN VISUAL FUNCTION AND SUBRETINAL DRUSENOID DEPOSITS IN NORMAL AND EARLY AGE-RELATED MACULAR DEGENERATION EYES.

PubMed

Neely, David; Zarubina, Anna V; Clark, Mark E; Huisingh, Carrie E; Jackson, Gregory R; Zhang, Yuhua; McGwin, Gerald; Curcio, Christine A; Owsley, Cynthia

2017-07-01

To examine the association between subretinal drusenoid deposits (SDDs) identified by multimodal retinal imaging and visual function in older eyes with normal macular health or in the earliest phases of age-related macular degeneration (AMD). Age-related macular degeneration status for each eye was defined according to the Age-Related Eye Disease Study (AREDS) 9-step classification system (normal = Step 1, early AMD = Steps 2-4) based on color fundus photographs. Visual functions measured were best-corrected photopic visual acuity, contrast and light sensitivity, mesopic visual acuity, low-luminance deficit, and rod-mediated dark adaptation. Subretinal drusenoid deposits were identified through multimodal imaging (color fundus photographs, infrared reflectance and fundus autofluorescence images, and spectral domain optical coherence tomography). The sample included 1,202 eyes (958 eyes with normal health and 244 eyes with early AMD). In normal eyes, SDDs were not associated with any visual function evaluated. In eyes with early AMD, dark adaptation was markedly delayed in eyes with SDDs versus no SDD (a 4-minute delay on average), P = 0.0213. However, this association diminished after age adjustment, P = 0.2645. Other visual functions in early AMD eyes were not associated with SDDs. In a study specifically focused on eyes in normal macular health and in the earliest phases of AMD, early AMD eyes with SDDs have slower dark adaptation, largely attributable to the older ages of eyes with SDD; they did not exhibit deficits in other visual functions. Subretinal drusenoid deposits in older eyes in normal macular health are not associated with any visual functions evaluated.

The Relations between Children's Reading Comprehension, Working Memory, Language Skills and Components of Reading Decoding in a Normal Sample

ERIC Educational Resources Information Center

Goff, Deborah A.; Pratt, Chris; Ong, Ben

2005-01-01

The primary aim of the current study was to identify the strongest independent predictors of reading comprehension using word reading, language and memory variables in a normal sample of 180 children in grades 3-5, with a range of word reading skills. It was hypothesized that orthographic processing, receptive vocabulary and verbal working memory…

The Effect of Multicollinearity and the Violation of the Assumption of Normality on the Testing of Hypotheses in Regression Analysis.

ERIC Educational Resources Information Center

Vasu, Ellen S.; Elmore, Patricia B.

The effects of the violation of the assumption of normality coupled with the condition of multicollinearity upon the outcome of testing the hypothesis Beta equals zero in the two-predictor regression equation is investigated. A monte carlo approach was utilized in which three differenct distributions were sampled for two sample sizes over…

BODY MASS INDEX AND SELF-EMPLOYMENT IN SOUTH KOREA.

PubMed

Han, Euna; Kim, Tae Hyun

2017-07-01

This study assesses differential labour performance by body mass index (BMI), focusing on heterogeneity across three distinct employment statuses: unemployed, self-employed and salaried. Data were drawn from the Korean Labor and Income Panel Study. The final sample included 15,180 person-year observations (9645 men and 5535 women) between 20 and 65 years of age. The findings show that (i) overweight/obese women are less likely to have salaried jobs than underweight/normal weight women, whereas overweight/obese men are more likely to be employed in both the salaried and self-employed sectors than underweight/normal men, (ii) overweight/obese women have lower wages only in permanent salaried jobs than underweight/normal weight women, whereas overweight/obese men earn higher wages only in salaried temporary jobs than underweight/normal weight women, (iii) overweight/obese women earn lower wages only in service, sales, semi-professional and blue-collar jobs in the salaried sector than underweight/normal weight women, whereas overweight/obese men have lower wages only in sales jobs in the self-employed sector than underweight/normal weight women. The statistically significant BMI penalty in labour market outcomes, which occurs only in the salaried sector for women, implies that there is an employers' distaste for workers with a high BMI status and that it is a plausible mechanism for job market penalty related to BMI status. Thus, heterogeneous job characteristics across and within salaried versus self-employed sectors need to be accounted for when assessing the impact of BMI status on labour market outcomes.

Investigation of phosphoserine and cytidine 5'-phosphate by heteronuclear two-dimensional spectroscopy: samples with strong proton coupling

NASA Astrophysics Data System (ADS)

Bolton, Philip H.

Heteronuclear two-dimensional magnetic resonance is a novel method for investigating the conformations of cellular phosphates. The two-dimensional proton spectra are detected indirectly via the phosphorus-31 nucleus and thus allow determination of proton chemical shifts and coupling constants in situations in which the normal proton spectrum is obscured. Previous investigations of cellular phosphates with relatively simple spin systems have shown that the two-dimensional proton spectrum can be readily related to the normal proton spectrum by subspectral analysis. The normal proton spectrum can be decomposed into two subspectra, one for each polarization of the phosphorus-31 nucleus. The two-dimensional spectrum arises from the difference between the subspectra, and the normal proton spectrum is the sum. This allows simulation of the two-dimensional spectra and hence determination of the proton chemical shifts and coupling constants. Many cellular phosphates of interest, such as 5'-nucleotides and phosphoserine, contain three protons coupled to the phosphorus which are strongly coupled to one another. These samples are amenable to the two-dimensional method and the straightforward subspectral analysis is preserved when a 90° pulse is applied to the protons in the magnetization transfer step. The two-dimensional proton spectra of the samples investigated here have higher resolution than the normal proton spectra, revealing spectral features not readily apparent in the normal proton spectra.

Assessment of 1H NMR-based metabolomics analysis for normalization of urinary metals against creatinine.

PubMed

Cassiède, Marc; Nair, Sindhu; Dueck, Meghan; Mino, James; McKay, Ryan; Mercier, Pascal; Quémerais, Bernadette; Lacy, Paige

2017-01-01

Proton nuclear magnetic resonance ( 1 H NMR, or NMR) spectroscopy and inductively coupled plasma-mass spectrometry (ICP-MS) are commonly used for metabolomics and metal analysis in urine samples. However, creatinine quantification by NMR for the purpose of normalization of urinary metals has not been validated. We assessed the validity of using NMR analysis for creatinine quantification in human urine samples in order to allow normalization of urinary metal concentrations. NMR and ICP-MS techniques were used to measure metabolite and metal concentrations in urine samples from 10 healthy subjects. For metabolite analysis, two magnetic field strengths (600 and 700MHz) were utilized. In addition, creatinine concentrations were determined by using the Jaffe method. Creatinine levels were strongly correlated (R 2 =0.99) between NMR and Jaffe methods. The NMR spectra were deconvoluted with a target database containing 151 metabolites that are present in urine. A total of 50 metabolites showed good correlation (R 2 =0.7-1.0) at 600 and 700MHz. Metal concentrations determined after NMR-measured creatinine normalization were comparable to previous reports. NMR analysis provided robust urinary creatinine quantification, and was sufficient for normalization of urinary metal concentrations. We found that NMR-measured creatinine-normalized urinary metal concentrations in our control subjects were similar to general population levels in Canada and the United Kingdom. Copyright © 2016 Elsevier B.V. All rights reserved.

Impact of microRNAs on regulatory networks and pathways in human colorectal carcinogenesis and development of metastasis

PubMed Central

2013-01-01

Background Qualitative alterations or abnormal expression of microRNAs (miRNAs) in colon cancer have mainly been demonstrated in primary tumors. Poorly overlapping sets of oncomiRs, tumor suppressor miRNAs and metastamiRs have been linked with distinct stages in the progression of colorectal cancer. To identify changes in both miRNA and gene expression levels among normal colon mucosa, primary tumor and liver metastasis samples, and to classify miRNAs into functional networks, in this work miRNA and gene expression profiles in 158 samples from 46 patients were analysed. Results Most changes in miRNA and gene expression levels had already manifested in the primary tumors while these levels were almost stably maintained in the subsequent primary tumor-to-metastasis transition. In addition, comparing normal tissue, tumor and metastasis, we did not observe general impairment or any rise in miRNA biogenesis. While only few mRNAs were found to be differentially expressed between primary colorectal carcinoma and liver metastases, miRNA expression profiles can classify primary tumors and metastases well, including differential expression of miR-10b, miR-210 and miR-708. Of 82 miRNAs that were modulated during tumor progression, 22 were involved in EMT. qRT-PCR confirmed the down-regulation of miR-150 and miR-10b in both primary tumor and metastasis compared to normal mucosa and of miR-146a in metastases compared to primary tumor. The upregulation of miR-201 in metastasis compared both with normal and primary tumour was also confirmed. A preliminary survival analysis considering differentially expressed miRNAs suggested a possible link between miR-10b expression in metastasis and patient survival. By integrating miRNA and target gene expression data, we identified a combination of interconnected miRNAs, which are organized into sub-networks, including several regulatory relationships with differentially expressed genes. Key regulatory interactions were validated experimentally. Specific mixed circuits involving miRNAs and transcription factors were identified and deserve further investigation. The suppressor activity of miR-182 on ENTPD5 gene was identified for the first time and confirmed in an independent set of samples. Conclusions Using a large dataset of CRC miRNA and gene expression profiles, we describe the interplay of miRNA groups in regulating gene expression, which in turn affects modulated pathways that are important for tumor development. PMID:23987127

Differential expression of colon cancer associated transcript1 (CCAT1) along the colonic adenoma-carcinoma sequence.

PubMed

Alaiyan, Bilal; Ilyayev, Nadia; Stojadinovic, Alexander; Izadjoo, Mina; Roistacher, Marina; Pavlov, Vera; Tzivin, Victoria; Halle, David; Pan, Honguang; Trink, Barry; Gure, Ali O; Nissan, Aviram

2013-04-17

The transition from normal epithelium to adenoma and, to invasive carcinoma in the human colon is associated with acquired molecular events taking 5-10 years for malignant transformation. We discovered CCAT1, a non-coding RNA over-expressed in colon cancer (CC), but not in normal tissues, thereby making it a potential disease-specific biomarker. We aimed to define and validate CCAT1 as a CC-specific biomarker, and to study CCAT1 expression across the adenoma-carcinoma sequence of CC tumorigenesis. Tissue samples were obtained from patients undergoing resection for colonic adenoma(s) or carcinoma. Normal colonic tissue (n = 10), adenomatous polyps (n = 18), primary tumor tissue (n = 22), normal mucosa adjacent to primary tumor (n = 16), and lymph node(s) (n = 20), liver (n = 8), and peritoneal metastases (n = 19) were studied. RNA was extracted from all tissue samples, and CCAT1 expression was analyzed using quantitative real time-PCR (qRT-PCR) with confirmatory in-situ hybridization (ISH). Borderline expression of CCAT1 was identified in normal tissue obtained from patients with benign conditions [mean Relative Quantity (RQ) = 5.9]. Significant relative CCAT1 up-regulation was observed in adenomatous polyps (RQ = 178.6 ± 157.0; p = 0.0012); primary tumor tissue (RQ = 64.9 ± 56.9; p = 0.0048); normal mucosa adjacent to primary tumor (RQ = 17.7 ± 21.5; p = 0.09); lymph node, liver and peritoneal metastases (RQ = 11,414.5 ± 12,672.9; 119.2 ± 138.9; 816.3 ± 2,736.1; p = 0.0001, respectively). qRT-PCR results were confirmed by ISH, demonstrating significant correlation between CCAT1 up-regulation measured using these two methods. CCAT1 is up-regulated across the colon adenoma-carcinoma sequence. This up-regulation is evident in pre-malignant conditions and through all disease stages, including advanced metastatic disease suggesting a role in both tumorigenesis and the metastatic process.

Statistical analysis tables for truncated or censored samples

NASA Technical Reports Server (NTRS)

Cohen, A. C.; Cooley, C. G.

1971-01-01

Compilation describes characteristics of truncated and censored samples, and presents six illustrations of practical use of tables in computing mean and variance estimates for normal distribution using selected samples.

Adenoviral receptor expression of normal bladder and transitional cell carcinoma of the bladder.

PubMed

Buscarini, Maurizio; Quek, Marcus L; Gilliam-Hegarich, Susan; Kasahara, Nori; Bochner, Bernard

2007-01-01

The insertion of absent or underexpressed genes into cancer cells to alter their malignant phenotype is an important potential application of available gene therapy technology. One of the more common viral vector systems that has been extensively studied for this purpose are the replication-deficient adenoviruses (Ad). Adenoviral infection of cells is mediated through a complex pathway, initiated following viral-cell attachment. Adenoviral-cell attachment occurs following interactions with a 46-kDa transmembrane protein with high affinity for both the Coxsackie and adenovirus, designated the CAR (Coxsackie and adenoviral receptor). Additional important cell-viral interactions that occur involve the alpha(v)-based integrins, specifically alpha(v)beta3 and alpha(v)beta5. The purpose of the present study was to determine the extent of expression and localization of the known Ad receptor proteins (CAR, alpha(v)beta3, and alpha(v)beta5) in normal and cancerous human bladders. Frozen tissue samples of normal bladder and invasive transitional cell cancers of the bladder were evaluated. Tissue blocks containing muscle-invasive transitional cell carcinoma (TCC) were obtained following radical cystectomy, which were performed at our institution. Thirty-two invasive transitional cell bladder tumors were evaluated, each with a matched sample of histologically normal-appearing bladder used as a control. Four additional samples of normal bladder were obtained from patients with no evidence of disease of the bladder and served as further controls. Three additional cases of invasive bladder cancer with no matching normal tissue were also evaluated. Identification of the CAR receptor was performed using the anti-CAR mouse monoclonal antibody designated RmBC. The integrins alpha(v)beta3 and alpha(v)beta5 were identified using the mouse monoclonal antibodies designated LM609 and P1F6 respectively. All slides were evaluated by two of the authors (M.B., B.B.) without knowledge of the clinical and pathological data. Normal bladder: Normal bladder mucosa demonstrated a marked positivity for CAR in 29/35 (82.8%) cases. In contrast, normal transitional epithelial cells were uniformly negative when tested for the integrins alpha(v)beta3 and alpha(v)beta5. Subepithelial tissues, specifically the connective tissue components of the lamina propria and deep muscle wall of the bladder, were positive for alpha(v)beta3 and for alpha(v)beta5 in 61 and 75% of samples, respectively. Endothelial cells associated with the various layers throughout the bladder uniformly expressed both integrins and served as a consistent internal control for both antibodies. An almost identical staining pattern of the endothelium was observed using LM609 and P1F6 in all samples tested. Bladder transitional cell carcinoma: CAR immunoreactivity against TCC cells was uniformly decreased compared to normal transitional cells. Nine tumors exhibited a weak positivity for CAR while the remaining samples were negative. In some cases, the absence of CAR positivity was associated with histological evidence of carcinoma in situ. In 6 cases, it led to the identification of small regions of carcinoma in situ that were not noted on primary pathological evaluation. Peritumoral connective tissue expressed both integrins in the majority of cases, similar to the pattern described above for normal bladder. Transitional cell cancers demonstrated a similar pattern of expression of alpha(v)beta5, in which all tumor cells exhibited minimal or no staining. The success of all viral-mediated gene therapy strategies relies on the ability of the vector to efficiently deliver its genetic material to a target cell population. In the current study, we demonstrate that the bladder epithelial layer consistently expresses high levels of CAR. Deeper layers of the epithelium also express CAR, including the basal layer cells. A decrease in the expression of CAR appears as an early event in bladder carcinogenesis. We observed that both alpha(v)beta3 and alpha(v)beta5 are strongly expressed in muscle cells surrounding the neoplastic cells, as well as within the peritumoral connective tissue. In cases of invasive bladder cancer that have lost CAR expression, an adenoviral vector may still be utilized through the less efficient interactions with the integrins. Bladder tumor tissue may be less susceptible to an adenoviral-mediated gene therapy approach in which a significant percentage of tumor cells require transduction. Adenoviral uptake by tumor or peritumoral cells with subsequent gene transfer could be predicted by the level of CAR and alpha(v)-based integrin expression. This would enhance our ability to identify those patients whose tumors would be more susceptible to Ad-mediated gene delivery as part of an antitumor treatment. 2007 S. Karger AG, Basel

The association between content of the elements S, Cl, K, Fe, Cu, Zn and Br in normal and cirrhotic liver tissue from Danes and Greenlandic Inuit examined by dual hierarchical clustering analysis.

PubMed

Laursen, Jens; Milman, Nils; Pind, Niels; Pedersen, Henrik; Mulvad, Gert

2014-01-01

Meta-analysis of previous studies evaluating associations between content of elements sulphur (S), chlorine (Cl), potassium (K), iron (Fe), copper (Cu), zinc (Zn) and bromine (Br) in normal and cirrhotic autopsy liver tissue samples. Normal liver samples from 45 Greenlandic Inuit, median age 60 years and from 71 Danes, median age 61 years. Cirrhotic liver samples from 27 Danes, median age 71 years. Element content was measured using X-ray fluorescence spectrometry. Dual hierarchical clustering analysis, creating a dual dendrogram, one clustering element contents according to calculated similarities, one clustering elements according to correlation coefficients between the element contents, both using Euclidian distance and Ward Procedure. One dendrogram separated subjects in 7 clusters showing no differences in ethnicity, gender or age. The analysis discriminated between elements in normal and cirrhotic livers. The other dendrogram clustered elements in four clusters: sulphur and chlorine; copper and bromine; potassium and zinc; iron. There were significant correlations between the elements in normal liver samples: S was associated with Cl, K, Br and Zn; Cl with S and Br; K with S, Br and Zn; Cu with Br. Zn with S and K. Br with S, Cl, K and Cu. Fe did not show significant associations with any other element. In contrast to simple statistical methods, which analyses content of elements separately one by one, dual hierarchical clustering analysis incorporates all elements at the same time and can be used to examine the linkage and interplay between multiple elements in tissue samples. Copyright © 2013 Elsevier GmbH. All rights reserved.

EEG based topography analysis in string recognition task

NASA Astrophysics Data System (ADS)

Ma, Xiaofei; Huang, Xiaolin; Shen, Yuxiaotong; Qin, Zike; Ge, Yun; Chen, Ying; Ning, Xinbao

2017-03-01

Vision perception and recognition is a complex process, during which different parts of brain are involved depending on the specific modality of the vision target, e.g. face, character, or word. In this study, brain activities in string recognition task compared with idle control state are analyzed through topographies based on multiple measurements, i.e. sample entropy, symbolic sample entropy and normalized rhythm power, extracted from simultaneously collected scalp EEG. Our analyses show that, for most subjects, both symbolic sample entropy and normalized gamma power in string recognition task are significantly higher than those in idle state, especially at locations of P4, O2, T6 and C4. It implies that these regions are highly involved in string recognition task. Since symbolic sample entropy measures complexity, from the perspective of new information generation, and normalized rhythm power reveals the power distributions in frequency domain, complementary information about the underlying dynamics can be provided through the two types of indices.

Electron localization mechanism in the normal state of high- T c superconductors

NASA Astrophysics Data System (ADS)

Yamani, Z.; Akhavan, M.

The ceramic compounds Gd 1- xPr xCu 3O 7- y (GdPr-123) with 0.0 ≤ x≤1.0, were synthesized by standard solid state reaction technique. XRD analysis shows a predominantly single phase perovskite structure with the orthorhombic Pmmm symmetry. The samples have been examined for superconductivity by measuring electrical resistivity within the temperature range 10-300 K. These measurements show a suppression of superconductivity with increasing x. It is observed that the critical Pr concentration ( x cr) required to suppress superconductivity is about 0.45, the samples with x < 0.45 become superconducting and are metallic in their normal state, the samples with x ≥ 0.45 do not become superconducting and show a semiconducting behavior above 10 K. To interpret the normal state properties of the samples, the quantum percolation theory based on localized states is applied. A cross-over between variable-range hopping (VRH) and Coulomb gap (CG) mechanisms is observed as a result of decreasing the Pr content.

Detection of survivin 2α gene expression in thyroid nodules.

PubMed

Kyani, Keyhaneh; Babaei, Esmaeil; Feizi, Mohammad Ali Hosseinpour; Vandghanooni, Somayeh; Montazeri, Vahid; Halimi, Monireh

2014-01-01

Functional studies of the survivin splice variants have been performed almost exclusively in various types of cancer and produced remarkable advances in our understanding of cancer biology and cancer genetics. To observation the expression of survivin 2α in thyroid nodules and estimate its potential as a new molecular marker in thyroid nodules screening and malignant thyroid, as well. We detected the expression of a splice variant of survivin, survivin 2α, in thyroid nodules. Expression of survivin 2α mRNA was evaluated with specific primers by Hemi-Nested RT-PCR in 77 thyroid nodules including malignant and benign tumors, non-tumoral (goiter and thyroiditis) as well as surgical margin, non-neoplastic normal tissues adjacent to the malignant lesions. Our data revealed for the first time the expression of survivin 2α in thyroid nodules. It was detected in 85.7% of non-neoplastic surgical margin tissues, 71.4% of non tumoral, 63.2% of tumoral samples. Also, the expression of survivin 2α in benign tumor samples (64.2%) is more than malignant groups (62.8%). Survivin 2α expression is the highest in non-neoplastic surgical margin rather than other samples and the lowest expression was that of malignancy. According to the results, it can be concluded that survivin 2α protein may be has a vital protective effect throw survivin quenching due to the high expression in normal tissue compared with lesions.

DEVELOPMENT OF MOTIVATION SCALE - CLINICAL VALIDATION WITH ALCOHOL DEPENDENTS

PubMed Central

Neeliyara, Teresa; Nagalakshmi, S.V.

1994-01-01

This study focusses on the development of a comprehensive multi-dimensional scale for assessing motivation for change in the alcohol dependent population. After establishing face validity, the items evolved were administered to a normal sample of 600 male subjects in whom psychiatric illness was ruled out. The data thus obtained was subjected to factor analysis. Six factors were obtained which accounted for 55.2% of variance. These together formed a 80 item five point scale and norms were established on a sample of 600 normal subjects. Further clinical validation was established on 30 alcohol dependent subjects and 30 normals. The status of motivation was found to be inadequate in alcohol dependent individuals as compared to the normals. Split-half reliability was carried out and the tool was found to be highly reliable. PMID:21743674

[Identification and management of intra-operative suspicious tissues in 20 transsphenoidal surgery cases].

PubMed

Liu, Jun-Feng; Ke, Chang-Shu; Chen, Xi; Xu, Yu; Zhang, Hua-Qiu; Chen, Juan; Gan, Chao; Li, Chao-Xi; Lei, Ting

2013-05-01

To determine appropriate protocols for the identification and management of intra operative suspicious tissues during transsphenoidal surgery. Clinical data and pathological reports of 20 patients with intra-operative suspicious tissues during transsphenoidal surgeries were analyzed retrospectively. The methods for discriminating between adenoma and normal pituitary tissues were reviewed. The postoperative pathological reports revealed that adenoma and normal pituitary tissues coexisted in 9 samples, while 5 samples were identified as normal pituitary tissues, 2 as adenoma tissues, and 4 as other tissues. Adenomas were distinguished from normal pituitary tissues on the basis of intra-operative appearance, texture, blood supply and possible existence of boundary. If decisions are difficult to made during surgeries from the appearance of the suspicious tissues, pathological examinations are advised as a guidance for the next steps.

Interpreting the concordance statistic of a logistic regression model: relation to the variance and odds ratio of a continuous explanatory variable.

PubMed

Austin, Peter C; Steyerberg, Ewout W

2012-06-20

When outcomes are binary, the c-statistic (equivalent to the area under the Receiver Operating Characteristic curve) is a standard measure of the predictive accuracy of a logistic regression model. An analytical expression was derived under the assumption that a continuous explanatory variable follows a normal distribution in those with and without the condition. We then conducted an extensive set of Monte Carlo simulations to examine whether the expressions derived under the assumption of binormality allowed for accurate prediction of the empirical c-statistic when the explanatory variable followed a normal distribution in the combined sample of those with and without the condition. We also examine the accuracy of the predicted c-statistic when the explanatory variable followed a gamma, log-normal or uniform distribution in combined sample of those with and without the condition. Under the assumption of binormality with equality of variances, the c-statistic follows a standard normal cumulative distribution function with dependence on the product of the standard deviation of the normal components (reflecting more heterogeneity) and the log-odds ratio (reflecting larger effects). Under the assumption of binormality with unequal variances, the c-statistic follows a standard normal cumulative distribution function with dependence on the standardized difference of the explanatory variable in those with and without the condition. In our Monte Carlo simulations, we found that these expressions allowed for reasonably accurate prediction of the empirical c-statistic when the distribution of the explanatory variable was normal, gamma, log-normal, and uniform in the entire sample of those with and without the condition. The discriminative ability of a continuous explanatory variable cannot be judged by its odds ratio alone, but always needs to be considered in relation to the heterogeneity of the population.

Cytogenetic study is not essential in patients with aplastic anemia

PubMed Central

Dutta, Atreyee; De, Rajib; Dolai, Tuphan K; Mitra, Pradip K; Halder, Ajanta

2017-01-01

Depending on contemporary treatment approach of aggressive immunosuppression, Aplastic Anemia (AA) is caused by immunological destruction of otherwise normal hematopoietic stem cells. The aim was to summarize the cytogenetic abnormalities in AA patients and the frequency of Fanconi Anemia (FA) in morphologically normal AA patients in eastern India. Ethical clearances were obtained from both institutions involved in this study. Out of 72800 patients attending the outpatient department, 520 pancytopenia patients were screened for AA after Bone marrow (BM) aspiration and biopsy. Samples were collected from 117 cases in 3 phases. 51 peripheral venous blood (PVB) samples in the first phase, 19 BM & PVB paired samples in the second phase and 47 BM samples in third phase were collected followed by leukocyte and/or BM stem cell culture. Next GTG banding and karyotyping were performed. PVB was collected from 63 (< 50 years) AA patients and stress cytogenetics was done to diagnose FA. In the first phase of the study, out of 51 PVB samples, 1 (1.96%) showed a unique chromosomal abnormality, i.e. 45,XY,rob(14:21)(p10:q10)[20]. In the second phase of study, among 19 BM & PVB paired samples, 1 (5.26%) showed abnormal karyotype i.e. 45,X,-Y[3]/46,XY[47]. In the third phase of the study, 47 BM samples showed normal karyotype. Only 6 (9.52%) cases were found positive for stress cytogenetics. A negligible percentage showing cytogenetic abnormality in such a considerable number of AA cases indicates that routine cytogenetic analysis of AA patient is not essential. A significant percentage was positive for stress cytogenetics; suggestive for FA, even the patients were morphologically normal. PMID:29181263