Molecular mechanics of Staphylococcus aureus adhesin, CNA, and the inhibition of bacterial adhesion by stretching collagen

PubMed Central

Madani, Ali; Garakani, Kiavash

2017-01-01

Bacterial adhesion to collagen, the most abundant protein in humans, is a critical step in the initiation and persistence of numerous bacterial infections. In this study, we explore the collagen binding mechanism of the multi-modular cell wall anchored collagen adhesin (CNA) in Staphylococcus aureus and examine how applied mechanical forces can modulate adhesion ability. The common structural-functional elements and domain organization of CNA are present across over 50 genera of bacteria. Through the use of molecular dynamics models and normal mode analysis, we shed light on the CNA’s structural and conformational dynamics and its interactions with collagen that lead to collagen binding. Our results suggest that the linker region, CNA165-173, acts as a hinge exhibiting bending, extensional, and torsional modes of structural flexibility and its residues are key in the interaction of the CNA-collagen complex. Steered molecular dynamics simulations were conducted with umbrella sampling. During the course of these simulations, the ‘locking’ latch from the CNA N2 domain was dissociated from its groove in the CNA N1 domain, implying the importance of the latch for effective ligand binding. Finally, we observed that the binding efficiency of the CNA N1-N2 domains to collagen decreases greatly with increasing tensile force application to the collagen peptides. Thus, CNA and similar adhesins might preferentially bind to sites in which collagen fibers are cleaved, such as in wounded, injured, or inflamed tissues, or in which the collagenous tissue is less mature. As alternative techniques for control of bacterial infection are in-demand due to the rise of bacterial antibiotic resistance, results from our computational studies with respect to the mechanoregulation of the collagen binding site may inspire new therapeutics and engineering solutions by mechanically preventing colonization and/or further pathogenesis. PMID:28665944

A Role for Community Colleges in Navy Training.

ERIC Educational Resources Information Center

Golfin, Peggy A.; White, John D.; Curtin, Lisa A.

This document from the Center for Naval Analysis (CNA) discusses the role of community colleges in Navy training. CNA conducted a study to discover whether outsourcing courses such as air conditioning and refrigeration and information systems administration to community colleges was feasible and cost effective. Analyses focused on two community…

Structure identification methods for atomistic simulations of crystalline materials

DOE PAGES

Stukowski, Alexander

2012-05-28

Here, we discuss existing and new computational analysis techniques to classify local atomic arrangements in large-scale atomistic computer simulations of crystalline solids. This article includes a performance comparison of typical analysis algorithms such as common neighbor analysis (CNA), centrosymmetry analysis, bond angle analysis, bond order analysis and Voronoi analysis. In addition we propose a simple extension to the CNA method that makes it suitable for multi-phase systems. Finally, we introduce a new structure identification algorithm, the neighbor distance analysis, which is designed to identify atomic structure units in grain boundaries.

An Analysis of Female Representation and Marines Performance in Aviation and Logistics Occupations

DTIC Science & Technology

2016-02-01

Parcell, Ann D., Apriel K. Hodari, and Robert W. Shuford. 2003. Predictors of Officer Success. CNA Corporation. CRM D0007437.A2/Final. [18] Kraus...Shuford. 2007. Black and Hispanic Marines: Their Accessions, Representation, Success, and Retention in the Corps. CNA Corporation. CRM D0016910.A1/Final

iGC-an integrated analysis package of gene expression and copy number alteration.

PubMed

Lai, Yi-Pin; Wang, Liang-Bo; Wang, Wei-An; Lai, Liang-Chuan; Tsai, Mong-Hsun; Lu, Tzu-Pin; Chuang, Eric Y

2017-01-14

With the advancement in high-throughput technologies, researchers can simultaneously investigate gene expression and copy number alteration (CNA) data from individual patients at a lower cost. Traditional analysis methods analyze each type of data individually and integrate their results using Venn diagrams. Challenges arise, however, when the results are irreproducible and inconsistent across multiple platforms. To address these issues, one possible approach is to concurrently analyze both gene expression profiling and CNAs in the same individual. We have developed an open-source R/Bioconductor package (iGC). Multiple input formats are supported and users can define their own criteria for identifying differentially expressed genes driven by CNAs. The analysis of two real microarray datasets demonstrated that the CNA-driven genes identified by the iGC package showed significantly higher Pearson correlation coefficients with their gene expression levels and copy numbers than those genes located in a genomic region with CNA. Compared with the Venn diagram approach, the iGC package showed better performance. The iGC package is effective and useful for identifying CNA-driven genes. By simultaneously considering both comparative genomic and transcriptomic data, it can provide better understanding of biological and medical questions. The iGC package's source code and manual are freely available at https://www.bioconductor.org/packages/release/bioc/html/iGC.html .

Integrated analysis of copy number alteration and RNA expression profiles of cancer using a high-resolution whole-genome oligonucleotide array.

PubMed

Jung, Seung-Hyun; Shin, Seung-Hun; Yim, Seon-Hee; Choi, Hye-Sun; Lee, Sug-Hyung; Chung, Yeun-Jun

2009-07-31

Recently, microarray-based comparative genomic hybridization (array-CGH) has emerged as a very efficient technology with higher resolution for the genome-wide identification of copy number alterations (CNA). Although CNAs are thought to affect gene expression, there is no platform currently available for the integrated CNA-expression analysis. To achieve high-resolution copy number analysis integrated with expression profiles, we established human 30k oligoarray-based genome-wide copy number analysis system and explored the applicability of this system for integrated genome and transcriptome analysis using MDA-MB-231 cell line. We compared the CNAs detected by the oligoarray with those detected by the 3k BAC array for validation. The oligoarray identified the single copy difference more accurately and sensitively than the BAC array. Seventeen CNAs detected by both platforms in MDA-MB-231 such as gains of 5p15.33-13.1, 8q11.22-8q21.13, 17p11.2, and losses of 1p32.3, 8p23.3-8p11.21, and 9p21 were consistently identified in previous studies on breast cancer. There were 122 other small CNAs (mean size 1.79 mb) that were detected by oligoarray only, not by BAC-array. We performed genomic qPCR targeting 7 CNA regions, detected by oligoarray only, and one non-CNA region to validate the oligoarray CNA detection. All qPCR results were consistent with the oligoarray-CGH results. When we explored the possibility of combined interpretation of both DNA copy number and RNA expression profiles, mean DNA copy number and RNA expression levels showed a significant correlation. In conclusion, this 30k oligoarray-CGH system can be a reasonable choice for analyzing whole genome CNAs and RNA expression profiles at a lower cost.

Stratification of clear cell renal cell carcinoma (ccRCC) genomes by gene-directed copy number alteration (CNA) analysis

PubMed Central

Thiesen, H.-J.; Steinbeck, F.; Maruschke, M.; Koczan, D.; Ziems, B.; Hakenberg, O. W.

2017-01-01

Tumorigenic processes are understood to be driven by epi-/genetic and genomic alterations from single point mutations to chromosomal alterations such as insertions and deletions of nucleotides up to gains and losses of large chromosomal fragments including products of chromosomal rearrangements e.g. fusion genes and proteins. Overall comparisons of copy number alterations (CNAs) presented in 48 clear cell renal cell carcinoma (ccRCC) genomes resulted in ratios of gene losses versus gene gains between 26 ccRCC Fuhrman malignancy grades G1 (ratio 1.25) and 20 G3 (ratio 0.58). Gene losses and gains of 15762 CNA genes were mapped to 795 chromosomal cytoband loci including 280 KEGG pathways. CNAs were classified according to their contribution to Fuhrman tumour gradings G1 and G3. Gene gains and losses turned out to be highly structured processes in ccRCC genomes enabling the subclassification and stratification of ccRCC tumours in a genome-wide manner. CNAs of ccRCC seem to start with common tumour related gene losses flanked by CNAs specifying Fuhrman grade G1 losses and CNA gains favouring grade G3 tumours. The appearance of recurrent CNA signatures implies the presence of causal mechanisms most likely implicated in the pathogenesis and disease-outcome of ccRCC tumours distinguishing lower from higher malignant tumours. The diagnostic quality of initial 201 genes (108 genes supporting G1 and 93 genes G3 phenotypes) has been successfully validated on published Swiss data (GSE19949) leading to a restricted CNA gene set of 171 CNA genes of which 85 genes favour Fuhrman grade G1 and 86 genes Fuhrman grade G3. Regarding these gene sets overall survival decreased with the number of G3 related gene losses plus G3 related gene gains. CNA gene sets presented define an entry to a gene-directed and pathway-related functional understanding of ongoing copy number alterations within and between individual ccRCC tumours leading to CNA genes of prognostic and predictive value. PMID:28486536

Stratification of clear cell renal cell carcinoma (ccRCC) genomes by gene-directed copy number alteration (CNA) analysis.

PubMed

Thiesen, H-J; Steinbeck, F; Maruschke, M; Koczan, D; Ziems, B; Hakenberg, O W

2017-01-01

Tumorigenic processes are understood to be driven by epi-/genetic and genomic alterations from single point mutations to chromosomal alterations such as insertions and deletions of nucleotides up to gains and losses of large chromosomal fragments including products of chromosomal rearrangements e.g. fusion genes and proteins. Overall comparisons of copy number alterations (CNAs) presented in 48 clear cell renal cell carcinoma (ccRCC) genomes resulted in ratios of gene losses versus gene gains between 26 ccRCC Fuhrman malignancy grades G1 (ratio 1.25) and 20 G3 (ratio 0.58). Gene losses and gains of 15762 CNA genes were mapped to 795 chromosomal cytoband loci including 280 KEGG pathways. CNAs were classified according to their contribution to Fuhrman tumour gradings G1 and G3. Gene gains and losses turned out to be highly structured processes in ccRCC genomes enabling the subclassification and stratification of ccRCC tumours in a genome-wide manner. CNAs of ccRCC seem to start with common tumour related gene losses flanked by CNAs specifying Fuhrman grade G1 losses and CNA gains favouring grade G3 tumours. The appearance of recurrent CNA signatures implies the presence of causal mechanisms most likely implicated in the pathogenesis and disease-outcome of ccRCC tumours distinguishing lower from higher malignant tumours. The diagnostic quality of initial 201 genes (108 genes supporting G1 and 93 genes G3 phenotypes) has been successfully validated on published Swiss data (GSE19949) leading to a restricted CNA gene set of 171 CNA genes of which 85 genes favour Fuhrman grade G1 and 86 genes Fuhrman grade G3. Regarding these gene sets overall survival decreased with the number of G3 related gene losses plus G3 related gene gains. CNA gene sets presented define an entry to a gene-directed and pathway-related functional understanding of ongoing copy number alterations within and between individual ccRCC tumours leading to CNA genes of prognostic and predictive value.

Characterization of calcineurin from Cryptococcus humicola and the application of calcineurin in aluminum tolerance.

PubMed

Zhang, Lei; Zhang, Jing-Jing; Liu, Shuai; Nian, Hong-Juan; Chen, Li-Mei

2017-03-29

Calcineurin (CaN) is a Ca 2+ - and calmodulin (CaM)-dependent serine/threonine phosphatase. Previous studies have found that CaN is involved in the regulation of the stress responses. In this study, the growth of Cryptococcus humicola was inhibited by the CaN inhibitor tacrolimus (FK506) under aluminum (Al) stress. The expression of CNA encoding a catalytic subunit A (CNA) and its interaction with CaM were upregulated when the concentration of Al was increased. A CaM-binding domain and key amino acids responsible for interaction with CaM were identified. ∆CNAb with a deletion from S454 to A639 was detected to bind to CaM, while ∆CNAa with a deletion from R436 to A639 showed no binding to CaM. The binding affinities of CNA1 and CNA2, in which I439 or I443 were replaced by Ala, were decreased relative to wild-type CNA. The phosphatase activities of ∆CNAa, CNA1 and CNA2 were lower than the wild-type protein. These results suggest that the region between R436 and S454 is essential for the interaction with CaM and I439, I443 are key amino acids in this region. The ability of the CNA transgenic yeast to develop resistance to Al was significantly higher than that of control yeast. Residual Al in the CNA transgenic yeast culture media was significantly lower than the amount of Al originally added to the media or the residual Al remaining in the control yeast culture media. These findings suggest that CNA confers Al tolerance, and the mechanism of Al tolerance may involve absorption of active Al. Al stress up-regulated the expression of CNA. CaM-binding domain and key amino acids responsible for interaction with CaM were identified and both are required for phosphatase activities. CNA conferred yeast Al resistance indicating that the gene has a potential to improve Al-tolerance through gene engineering.

Significance of genomic instability in breast cancer in atomic bomb survivors: analysis of microarray-comparative genomic hybridization.

PubMed

Oikawa, Masahiro; Yoshiura, Koh-ichiro; Kondo, Hisayoshi; Miura, Shiro; Nagayasu, Takeshi; Nakashima, Masahiro

2011-12-07

It has been postulated that ionizing radiation induces breast cancers among atomic bomb (A-bomb) survivors. We have reported a higher incidence of HER2 and C-MYC oncogene amplification in breast cancers from A-bomb survivors. The purpose of this study was to clarify the effect of A-bomb radiation exposure on genomic instability (GIN), which is an important hallmark of carcinogenesis, in archival formalin-fixed paraffin-embedded (FFPE) tissues of breast cancer by using microarray-comparative genomic hybridization (aCGH). Tumor DNA was extracted from FFPE tissues of invasive ductal cancers from 15 survivors who were exposed at 1.5 km or less from the hypocenter and 13 calendar year-matched non-exposed patients followed by aCGH analysis using a high-density oligonucleotide microarray. The total length of copy number aberrations (CNA) was used as an indicator of GIN, and correlation with clinicopathological factors were statistically tested. The mean of the derivative log ratio spread (DLRSpread), which estimates the noise by calculating the spread of log ratio differences between consecutive probes for all chromosomes, was 0.54 (range, 0.26 to 1.05). The concordance of results between aCGH and fluorescence in situ hybridization (FISH) for HER2 gene amplification was 88%. The incidence of HER2 amplification and histological grade was significantly higher in the A-bomb survivors than control group (P = 0.04, respectively). The total length of CNA tended to be larger in the A-bomb survivors (P = 0.15). Correlation analysis of CNA and clinicopathological factors revealed that DLRSpread was negatively correlated with that significantly (P = 0.034, r = -0.40). Multivariate analysis with covariance revealed that the exposure to A-bomb was a significant (P = 0.005) independent factor which was associated with larger total length of CNA of breast cancers. Thus, archival FFPE tissues from A-bomb survivors are useful for genome-wide aCGH analysis. Our results suggested that A-bomb radiation may affect the increased amount of CNA as a hallmark of GIN and, subsequently, be associated with a higher histologic grade in breast cancer found in A-bomb survivors.

Significance of genomic instability in breast cancer in atomic bomb survivors: analysis of microarray-comparative genomic hybridization

PubMed Central

2011-01-01

Background It has been postulated that ionizing radiation induces breast cancers among atomic bomb (A-bomb) survivors. We have reported a higher incidence of HER2 and C-MYC oncogene amplification in breast cancers from A-bomb survivors. The purpose of this study was to clarify the effect of A-bomb radiation exposure on genomic instability (GIN), which is an important hallmark of carcinogenesis, in archival formalin-fixed paraffin-embedded (FFPE) tissues of breast cancer by using microarray-comparative genomic hybridization (aCGH). Methods Tumor DNA was extracted from FFPE tissues of invasive ductal cancers from 15 survivors who were exposed at 1.5 km or less from the hypocenter and 13 calendar year-matched non-exposed patients followed by aCGH analysis using a high-density oligonucleotide microarray. The total length of copy number aberrations (CNA) was used as an indicator of GIN, and correlation with clinicopathological factors were statistically tested. Results The mean of the derivative log ratio spread (DLRSpread), which estimates the noise by calculating the spread of log ratio differences between consecutive probes for all chromosomes, was 0.54 (range, 0.26 to 1.05). The concordance of results between aCGH and fluorescence in situ hybridization (FISH) for HER2 gene amplification was 88%. The incidence of HER2 amplification and histological grade was significantly higher in the A-bomb survivors than control group (P = 0.04, respectively). The total length of CNA tended to be larger in the A-bomb survivors (P = 0.15). Correlation analysis of CNA and clinicopathological factors revealed that DLRSpread was negatively correlated with that significantly (P = 0.034, r = -0.40). Multivariate analysis with covariance revealed that the exposure to A-bomb was a significant (P = 0.005) independent factor which was associated with larger total length of CNA of breast cancers. Conclusions Thus, archival FFPE tissues from A-bomb survivors are useful for genome-wide aCGH analysis. Our results suggested that A-bomb radiation may affect the increased amount of CNA as a hallmark of GIN and, subsequently, be associated with a higher histologic grade in breast cancer found in A-bomb survivors. PMID:22152285

Tracking Sodium-Antimonide Phase Transformations in Sodium-Ion Anodes: Insights from Operando Pair Distribution Function Analysis and Solid-State NMR Spectroscopy

DOE PAGES

Allan, Phoebe K.; Griffin, John M.; Darwiche, Ali; ...

2016-01-29

We use operando pair distribution function (PDF) analysis and ex situ 23Na magic-angle spinning solid-state nuclear magnetic resonance (MAS ssNMR) spectroscopy to gain insight into the alloying mechanism of high-capacity antimony anodes for sodium-ion batteries. Subtraction of the PDF of crystalline Na xSb phases from the total PDF, an approach constrained by chemical phase information gained from 23Na ssNMR in reference to relevant model compounds, identifies two previously uncharacterized intermediate species formed electrochemically; a-Na 3–xSb (x ≈ 0.4–0.5), a structure locally similar to crystalline Na 3Sb (c-Na 3Sb) but with significant numbers of sodium vacancies and a limited correlation length,more » and a-Na1.7Sb, a highly amorphous structure featuring some Sb–Sb bonding. The first sodiation breaks down the crystalline antimony to form first a-Na 3–xSb and, finally, crystalline Na 3Sb. Desodiation results in the formation of an electrode formed of a composite of crystalline and amorphous antimony networks. We link the different reactivity of these networks to a series of sequential sodiation reactions manifesting as a cascade of processes observed in the electrochemical profile of subsequent cycles. The amorphous network reacts at higher voltages reforming a-Na 1.7Sb, then a-Na 3–xSb, whereas lower potentials are required for the sodiation of crystalline antimony, which reacts to form a-Na 3–xSb without the formation of a-Na 1.7Sb. a-Na 3–xSb is converted to crystalline Na 3Sb at the end of the second discharge. In the end, we find no evidence of formation of NaSb. Variable temperature 23Na NMR experiments reveal significant sodium mobility within c-Na 3Sb; this is a possible contributing factor to the excellent rate performance of Sb anodes.« less

Tracking Sodium-Antimonide Phase Transformations in Sodium-Ion Anodes: Insights from Operando Pair Distribution Function Analysis and Solid-State NMR Spectroscopy

PubMed Central

2016-01-01

Operando pair distribution function (PDF) analysis and ex situ 23Na magic-angle spinning solid-state nuclear magnetic resonance (MAS ssNMR) spectroscopy are used to gain insight into the alloying mechanism of high-capacity antimony anodes for sodium-ion batteries. Subtraction of the PDF of crystalline NaxSb phases from the total PDF, an approach constrained by chemical phase information gained from 23Na ssNMR in reference to relevant model compounds, identifies two previously uncharacterized intermediate species formed electrochemically; a-Na3–xSb (x ≈ 0.4–0.5), a structure locally similar to crystalline Na3Sb (c-Na3Sb) but with significant numbers of sodium vacancies and a limited correlation length, and a-Na1.7Sb, a highly amorphous structure featuring some Sb–Sb bonding. The first sodiation breaks down the crystalline antimony to form first a-Na3–xSb and, finally, crystalline Na3Sb. Desodiation results in the formation of an electrode formed of a composite of crystalline and amorphous antimony networks. We link the different reactivity of these networks to a series of sequential sodiation reactions manifesting as a cascade of processes observed in the electrochemical profile of subsequent cycles. The amorphous network reacts at higher voltages reforming a-Na1.7Sb, then a-Na3–xSb, whereas lower potentials are required for the sodiation of crystalline antimony, which reacts to form a-Na3–xSb without the formation of a-Na1.7Sb. a-Na3–xSb is converted to crystalline Na3Sb at the end of the second discharge. We find no evidence of formation of NaSb. Variable temperature 23Na NMR experiments reveal significant sodium mobility within c-Na3Sb; this is a possible contributing factor to the excellent rate performance of Sb anodes. PMID:26824406

CNA-loaded PLGA nanoparticles improve humoral response againstS. aureus-mediated infections in a mouse model: subcutaneous vs. nasal administration strategy.

PubMed

Genta, Ida; Colonna, Claudia; Conti, Bice; Caliceti, Paolo; Salmaso, Stefano; Speziale, Pietro; Pietrocola, Giampiero; Chiesa, Enrica; Modena, Tiziana; Dorati, Rossella

2016-12-01

The aim of this work was the assessment of the "in vivo" immune response of a poly(lactide-co-glycolide)-based nanoparticulate adjuvant for a sub-unit vaccine, namely, a purified recombinant collagen-binding bacterial adhesion fragment (CNA19), against Staphylococcus aureus-mediated infections. "In vivo" immunogenicity studies were performed on mice: immunisation protocols encompassed subcutaneous and intranasal administration of CNA19 formulated as nanoparticles (NPs) and furthermore, CNA19-loaded NPs formulated in a set-up thermosetting chitosan-β-glycerolphosphate (chitosan-β-GP) solution for intranasal route in order to extend antigen exposure to nasal mucosa. CNA19 loaded NPs (mean size of about 195 nm, 9.04 ± 0.37μg/mg as CNA19 loading capacity) confirmed as suitable vaccine for subcutaneous administration with a more pronounced adjuvant effect (about 3-fold higher) with respect to aluminium, recognised as "reference" adjuvant. CNA19 loaded NPs formulated in an optimised thermogelling chitosan-β-GP solution showed promising results for eliciting an effective humoral response and a good chance as intranasal boosting dose.

Rules of performance in the nursing home: A grounded theory of nurse-CNA communication.

PubMed

Madden, Connie; Clayton, Margaret; Canary, Heather E; Towsley, Gail; Cloyes, Kristin; Lund, Dale

This study offers an initial theoretical understanding of nurse-CNA communication processes from the perspectives of nurses and CNAs who are providing direct care to residents in nursing homes. A grounded theory approach provided an understanding of nurse-CNA communication process within the complexities of the nursing home setting. Four themes (maintaining information flow, following procedure, fostering collegiality, and showing respect) describe the "rules of performance" that intertwine in nuanced relationships to guide nurse-CNA communication processes. Understanding how these rules of performance guide nurse-CNA communication processes, and how they are positively and negatively influenced, suggests that nurse-CNA communication during direct care of nursing home residents could be improved through policy and education that is specifically designed to be relevant and applicable to direct care providers in the nursing home environment. Copyright © 2016 Elsevier Inc. All rights reserved.

Clinical omics analysis of colorectal cancer incorporating copy number aberrations and gene expression data.

PubMed

Yoshida, Tsuyoshi; Kobayashi, Takumi; Itoda, Masaya; Muto, Taika; Miyaguchi, Ken; Mogushi, Kaoru; Shoji, Satoshi; Shimokawa, Kazuro; Iida, Satoru; Uetake, Hiroyuki; Ishikawa, Toshiaki; Sugihara, Kenichi; Mizushima, Hiroshi; Tanaka, Hiroshi

2010-07-29

Colorectal cancer (CRC) is one of the most frequently occurring cancers in Japan, and thus a wide range of methods have been deployed to study the molecular mechanisms of CRC. In this study, we performed a comprehensive analysis of CRC, incorporating copy number aberration (CRC) and gene expression data. For the last four years, we have been collecting data from CRC cases and organizing the information as an "omics" study by integrating many kinds of analysis into a single comprehensive investigation. In our previous studies, we had experienced difficulty in finding genes related to CRC, as we observed higher noise levels in the expression data than in the data for other cancers. Because chromosomal aberrations are often observed in CRC, here, we have performed a combination of CNA analysis and expression analysis in order to identify some new genes responsible for CRC. This study was performed as part of the Clinical Omics Database Project at Tokyo Medical and Dental University. The purpose of this study was to investigate the mechanism of genetic instability in CRC by this combination of expression analysis and CNA, and to establish a new method for the diagnosis and treatment of CRC. Comprehensive gene expression analysis was performed on 79 CRC cases using an Affymetrix Gene Chip, and comprehensive CNA analysis was performed using an Affymetrix DNA Sty array. To avoid the contamination of cancer tissue with normal cells, laser micro-dissection was performed before DNA/RNA extraction. Data analysis was performed using original software written in the R language. We observed a high percentage of CNA in colorectal cancer, including copy number gains at 7, 8q, 13 and 20q, and copy number losses at 8p, 17p and 18. Gene expression analysis provided many candidates for CRC-related genes, but their association with CRC did not reach the level of statistical significance. The combination of CNA and gene expression analysis, together with the clinical information, suggested UGT2B28, LOC440995, CXCL6, SULT1B1, RALBP1, TYMS, RAB12, RNMT, ARHGDIB, S1000A2, ABHD2, OIT3 and ABHD12 as genes that are possibly associated with CRC. Some of these genes have already been reported as being related to CRC. TYMS has been reported as being associated with resistance to the anti-cancer drug 5-fluorouracil, and we observed a copy number increase for this gene. RALBP1, ARHGDIB and S100A2 have been reported as oncogenes, and we observed copy number increases in each. ARHGDIB has been reported as a metastasis-related gene, and our data also showed copy number increases of this gene in cases with metastasis. The combination of CNA analysis and gene expression analysis was a more effective method for finding genes associated with the clinicopathological classification of CRC than either analysis alone. Using this combination of methods, we were able to detect genes that have already been associated with CRC. We also identified additional candidate genes that may be new markers or targets for this form of cancer.

A network of epigenetic modifiers and DNA repair genes controls tissue-specific copy number alteration preference.

PubMed

Cramer, Dina; Serrano, Luis; Schaefer, Martin H

2016-11-10

Copy number alterations (CNAs) in cancer patients show a large variability in their number, length and position, but the sources of this variability are not known. CNA number and length are linked to patient survival, suggesting clinical relevance. We have identified genes that tend to be mutated in samples that have few or many CNAs, which we term CONIM genes (COpy Number Instability Modulators). CONIM proteins cluster into a densely connected subnetwork of physical interactions and many of them are epigenetic modifiers. Therefore, we investigated how the epigenome of the tissue-of-origin influences the position of CNA breakpoints and the properties of the resulting CNAs. We found that the presence of heterochromatin in the tissue-of-origin contributes to the recurrence and length of CNAs in the respective cancer type.

Are nursing home survey deficiencies higher in facilities with greater staff turnover.

PubMed

Lerner, Nancy B; Johantgen, Meg; Trinkoff, Alison M; Storr, Carla L; Han, Kihye

2014-02-01

To examine CNA and licensed nurse (RN+LPN/LVN) turnover in relation to numbers of deficiencies in nursing homes. A secondary data analysis of information from the National Nursing Home Survey (NNHS) and contemporaneous data from the Online Survey, Certification and Reporting (OSCAR) database. Data were linked by facility as the unit of analysis to determine the relationship of CNA and licensed nurse turnover on nursing home deficiencies. The 2004 NNHS used a multistage sampling strategy to generate a final sample of 1174 nursing homes, which represent 16,100 NHs in the United States. This study focused on the 1151 NNHS facilities with complete deficiency data. Turnover was defined as the total CNAs/licensed nurse full-time equivalents (FTEs) who left during the preceding 3 months (full- and part-time) divided by the total FTE. NHs with high turnover were defined as those with rates above the 75th percentile (25.3% for CNA turnover and 17.9% for licensed nurse turnover) versus all other facilities. This study used selected OSCAR deficiencies from the Quality of Care, Quality of Life, and Resident Behavior categories, which are considered to be more closely related to nursing care. We defined NHs with high deficiencies as those with numbers of deficiencies above the 75th percentile versus all others. Using SUDAAN PROC RLOGIST, we included NNHS sampling design effects and examined associations of CNA/licensed nurse turnover with NH deficiencies, adjusting for staffing, skill mix, bed size, and ownership in binomial logistic regression models. High CNA turnover was associated with high numbers of Quality of Care (OR 1.53, 95% CI 1.10-2.13), Resident Behavior (OR 1.42, 95% CI 1.03-1.97) and total selected deficiencies (OR 1.54, 95% CI 1.12-2.12). Licensed nurse turnover was significantly related to Quality of Care deficiencies (OR 2.06, 95% CI 1.50-2.82) and total selected deficiencies (OR 1.71, 95% CI 1.25-2.33). When both CNA turnover and licensed nurse turnover were included in the same model, high licensed nurse turnover was significantly associated with Quality of Care and total deficiencies, whereas CNA turnover was not associated with that category of deficiencies. Turnover in nursing homes for both licensed nurses and CNAs is associated with quality problems as measured by deficiencies. Copyright © 2014 American Medical Directors Association, Inc. Published by Elsevier Inc. All rights reserved.

Retirement Choice 2015

DTIC Science & Technology

2015-11-01

and Aline Quester November 2015 Copyright © 2015 CNA This document contains the best opinion of CNA at the time of issue. It does...RetirementChoiceCalculator.aspx. 3 The original paper was by Aline O. Quester and Lewis G. Lee, The Retirement Choice: FY 2006, CNA Research

Retirement Choice 2015

DTIC Science & Technology

2015-11-01

and Aline Quester November 2015 Copyright © 2015 CNA This document contains the best opinion of CNA at the time of issue. It does...by Aline O. Quester and Lewis G. Lee, The Retirement Choice: FY 2006, CNA Research Memorandum D0003713.A6/4REV, Oct. 2005. 2 First

75 FR 6682 - Notice of Proposed Information Collection: Comment Request; Comprehensive Needs Assessment (CNA)

Federal Register 2010, 2011, 2012, 2013, 2014

2010-02-10

... Information Collection: Comment Request; Comprehensive Needs Assessment (CNA) AGENCY: Office of the Assistant.... This Notice also lists the following information: Title of Proposal: Capital Needs Assessment (CNA...-96001 Unit Survey Comprehensive Needs Assessment; Form HUD-96002 Project Profile Comprehensive Needs...

Solar flare induced cosmic noise absorption

NASA Astrophysics Data System (ADS)

Ogunmodimu, Olugbenga; Honary, Farideh; Rogers, Neil; Falayi, E. O.; Bolaji, O. S.

2018-06-01

Solar flare events are a major observing emphasis for space weather because they affect the ionosphere and can eject high-energy particles that can adversely affect Earth's technologies. In this study we model 38.2 MHz cosmic noise absorption (CNA) by utilising measurements from the Imaging Riometer for Ionospheric Studies (IRIS) at Kilpisjärvi, Finland obtained during solar cycle 23 (1996-2009). We utilised X-ray archive for the same period from the Geostationary Operational Environmental Satellite (GOES) to study solar flare induced cosmic noise absorption. We identified the threshold of flare (M4 class) that could bear significant influence on CNA. Through epoch analysis, we show the magnitude of absorption that each class of flare could produce. Using the parameters of flare and absorption we present a model that could provide the basis for nowcast of CNA induced by M and X-class solar flares.

78 FR 40310 - 30-Day Notice of Proposed Information Collection: Comprehensive Needs Assessment (CNA)

Federal Register 2010, 2011, 2012, 2013, 2014

2013-07-03

... Information Collection: Comprehensive Needs Assessment (CNA) AGENCY: Office of the Chief Information Officer... Collection Title of Information Collection: Comprehensive Needs Assessment (CNA). OMB Approval Number: 2502... provide a copy to HUD. Description of the need for the information and proposed use: Collecting this...

78 FR 19509 - Notice of Proposed Information Collection: Comment Request; Comprehensive Needs Assessment (CNA)

Federal Register 2010, 2011, 2012, 2013, 2014

2013-04-01

... Information Collection: Comment Request; Comprehensive Needs Assessment (CNA) AGENCY: Office of the Assistant... information: Title of Proposal: Capital Needs Assessment (CNA). OMB Control Number, if applicable: 2502-0505. Description of the need for the information and proposed use: Collecting this information is required for...

Effect of drink flavor and NaCL on voluntary drinking and hydration in boys exercising in the heat.

PubMed

Wilk, B; Bar-Or, O

1996-04-01

This study was intended to assess the influence of drink flavor and composition on voluntary drinking and hydration status in children exercising intermittently at 35 +/- 1 degrees C and 45-50% relative humidity. Twelve boys (9-12 yr) performed three 3-h identical sessions (four 20-min cycling bouts at 50% maximal O2 uptake followed by 25-min rest). One of three beverages (chilled to 8-10 degrees C) was assigned to each session in a Latin-square sequence: unflavored water (W), grape-flavored water (FW), and grape-flavored water plus 6% carbohydrate and 18 mmol/l NaCl (CNa). Drinking was ad libitum. Body weight, heart rate, rectal and skin temperatures, and thirst and stomach fullness perceptions were monitored periodically. Total intake was 610, 882, and 1,157 g in W, FW, and CNa, respectively (CNa-W and CNa-FW; P < 0.05). Hypohydration was observed with W (-0.65% body wt) and FW (-0.32% body wt), but drinking CNa resulted in slight overhydration (+0.47% body wt, CNa-W, CNa-FW; P < 0.05). Other physiological and all perceptual variables were insignificantly different among trails. In conclusion, while flavoring of water reduces children's voluntary dehydration, further addition of 6% carbohydrates and 18 mmol/l NaCl prevents it altogether.

Reasons for referral and findings of clinical neuropsychological assessment in youth with mental illness: A clinical file audit.

PubMed

Proffitt, Tina-Marie; Brewer, Warrick J; Parrish, Emma M; McGorry, Patrick D; Allott, Kelly A

2018-01-01

Study aims were to 1) determine the characteristics and reasons for referral for Clinical Neuropsychological Assessment (CNA) and 2) characterize the findings and recommendations contained in the CNA reports, of clients attending a youth mental health service. File audit of all CNA reports (N = 140) of youth attending a mental health service. Cognitive performances on neuropsychological tests that were administered to >50% of clients were examined. Referral reasons, findings, and recommendations for future treatment were coded and described from neuropsychological files. Age of clients referred for CNA ranged from 13-29, the majority were male (62.5%), referred primarily from the early psychosis clinic (63.2%), and had a mean number of 3.5 presenting problems. Cognitive performances ranged from extremely low to very superior. Mean number of reasons for referral was 2, with treatment recommendation (55%) and diagnostic clarification (50.7%) being the most common. Mean number of findings from CNA was 5.8; most commonly, a diagnosis of clinically meaningful cognitive impairment (85%), followed by a recommendations for additional services/investigations (77.1%). CNA provides diagnostic clarification and treatment recommendations for youth receiving mental health treatment. Future studies should examine the cost-effectiveness, implementation, and objective impact of CNA in clinical practice.

Building on what you know.

PubMed

Patry, Leslie Anne

2006-02-01

The author undertook a project to support nurses participating in study groups as part of their strategy to prepare for the Canadian Nurses Association certification exams. Feedback was obtained from CNA certified nurses, study group participants and facilitators and other key stakeholders to develop a study group resource manual. CNA certification is a voluntary national nursing specialty credential that offers Canadian nurses the opportunity to demonstrate their knowledge and skills by meeting eligibility criteria and successfully writing an examination. Initially, development of a study group manual was the principal aim of the project; however, nurses' insights into their study group experiences became the focal point. Nurses recognized that being part of a study group was an effective learning strategy and a valuable networking experience. The author highlights nurses' study group experiences, describes the use of a nursing leadership conceptual model to frame the project and discusses the concept of continuing competence.

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

Tahvanainen, E.; Karila, E.; Ranta, S.

We report the mapping of the locus for autosomal recessive cornea plana congenita (CNA2; MIM 217300) by linkage analysis to the approximately 10-cM interval between markers D12S82 and D12S327. The recessively inherited disorder studied here is more severe than dominant forms. Its main manifestations are reduced curvature and hazy limbus of the cornea, opacities in the corneal stroma, and marked corneal arcus at early age. Our results provide a starting point for the positional cloning of CNA2 and the elucidation of the pathogenesis of the disease. 20 refs., 1 fig., 2 tabs.

Global copy number profiling of cancer genomes | Office of Cancer Genomics

Cancer.gov

In this article, we introduce a robust and efficient strategy for deriving global and allele-specific copy number alternations (CNA) from cancer whole exome sequencing data based on Log R ratios and B-allele frequencies. Applying the approach to the analysis of over 200 skin cancer samples, we demonstrate its utility for discovering distinct CNA events and for deriving ancillary information such as tumor purity. Availability and implementation: https://github.com/xfwang/CLOSE CONTACT: xuefeng.wang@stonybrook.edu or michael.krauthammer@yale.edu. (Publication Abstract)

Combined treatment with cotylenin A and phenethyl isothiocyanate induces strong antitumor activity mainly through the induction of ferroptotic cell death in human pancreatic cancer cells.

PubMed

Kasukabe, Takashi; Honma, Yoshio; Okabe-Kado, Junko; Higuchi, Yusuke; Kato, Nobuo; Kumakura, Shunichi

2016-08-01

The treatment of pancreatic cancer, one of the most aggressive gastrointestinal tract malignancies, with current chemotherapeutic drugs has had limited success due to its chemoresistance and poor prognosis. Therefore, the development of new drugs or effective combination therapies is urgently needed. Cotylenin A (CN-A) (a plant growth regulator) is a potent inducer of differentiation in myeloid leukemia cells and exhibits potent antitumor activities in several cancer cell lines. In the present study, we demonstrated that CN-A and phenethyl isothiocyanate (PEITC), an inducer of reactive oxygen species (ROS) and a dietary anticarcinogenic compound, synergistically inhibited the proliferation of MIAPaCa-2, PANC-1 and gemcitabine-resistant PANC-1 cells. A combined treatment with CN-A and PEITC also effectively inhibited the anchorage-independent growth of these cancer cells. The combined treatment with CN-A and PEITC strongly induced cell death within 1 day at concentrations at which CN-A or PEITC alone did not affect cell viability. A combined treatment with synthetic CN-A derivatives (ISIR-005 and ISIR-042) or fusicoccin J (CN-A-related natural product) and PEITC did not have synergistic effects on cell death. The combined treatment with CN-A and PEITC synergistically induced the generation of ROS. Antioxidants (N-acetylcysteine and trolox), ferroptosis inhibitors (ferrostatin-1 and liproxstatin), and the lysosomal iron chelator deferoxamine canceled the synergistic cell death. Apoptosis inhibitors (Z-VAD-FMK and Q-VD-OPH) and the necrosis inhibitor necrostatin-1s did not inhibit synergistic cell death. Autophagy inhibitors (3-metyladenine and chloroquine) partially prevented cell death. These results show that synergistic cell death induced by the combined treatment with CN-A and PEITC is mainly due to the induction of ferroptosis. Therefore, the combination of CN-A and PEITC has potential as a novel therapeutic strategy against pancreatic cancer.

Alternating magnetic field-induced hyperthermia increases iron oxide nanoparticle cell association/uptake and flux in blood-brain barrier models.

PubMed

Dan, Mo; Bae, Younsoo; Pittman, Thomas A; Yokel, Robert A

2015-05-01

Superparamagnetic iron oxide nanoparticles (IONPs) are being investigated for brain cancer therapy because alternating magnetic field (AMF) activates them to produce hyperthermia. For central nervous system applications, brain entry of diagnostic and therapeutic agents is usually essential. We hypothesized that AMF-induced hyperthermia significantly increases IONP blood-brain barrier (BBB) association/uptake and flux. Cross-linked nanoassemblies loaded with IONPs (CNA-IONPs) and conventional citrate-coated IONPs (citrate-IONPs) were synthesized and characterized in house. CNA-IONP and citrate-IONP BBB cell association/uptake and flux were studied using two BBB Transwell(®) models (bEnd.3 and MDCKII cells) after conventional and AMF-induced hyperthermia exposure. AMF-induced hyperthermia for 0.5 h did not alter CNA-IONP size but accelerated citrate-IONP agglomeration. AMF-induced hyperthermia for 0.5 h enhanced CNA-IONP and citrate-IONP BBB cell association/uptake. It also enhanced the flux of CNA-IONPs across the two in vitro BBB models compared to conventional hyperthermia and normothermia, in the absence of cell death. Citrate-IONP flux was not observed under these conditions. AMF-induced hyperthermia also significantly enhanced paracellular pathway flux. The mechanism appears to involve more than the increased temperature surrounding the CNA-IONPs. Hyperthermia induced by AMF activation of CNA-IONPs has potential to increase the BBB permeability of therapeutics for the diagnosis and therapy of various brain diseases.

Needs Assessment Studies of Certified Nurse Assistants and Administrators. Volume XXII, No. 7.

ERIC Educational Resources Information Center

Fair, Lillian; And Others

As part of an educational needs assessment, a survey was conducted by William Rainey Harper College (WRHC) in Palatine, Illinois, of Certified Nursing Assistants (CNA) and of administrators at institutions known to employ CNA's. Survey instruments were mailed to two groups. The first group, 153 administrators at institutions employing CNA's, were…

An NRG Oncology/GOG study of molecular classification for risk prediction in endometrioid endometrial cancer

PubMed Central

Cosgrove, Casey M; Tritchler, David L; Cohn, David E; Mutch, David G; Rush, Craig M; Lankes, Heather A; Creasman, William T.; Miller, David S; Ramirez, Nilsa C; Geller, Melissa A; Powell, Matthew A; Backes, Floor J; Landrum, Lisa M; Timmers, Cynthia; Suarez, Adrian A; Zaino, Richard J; Pearl, Michael L; DiSilvestro, Paul A; Lele, Shashikant B; Goodfellow, Paul J

2017-01-01

Objectives The purpose of this study was to assess the prognostic significance of a simplified, clinically accessible classification system for endometrioid endometrial cancers combining Lynch syndrome screening and molecular risk stratification. Methods Tumors from NRG/GOG GOG210 were evaluated for mismatch repair defects (MSI, MMR IHC, and MLH1 methylation), POLE mutations, and loss of heterozygosity. TP53 was evaluated in a subset of cases. Tumors were assigned to four molecular classes. Relationships between molecular classes and clinicopathologic variables were assessed using contingency tests and Cox proportional methods. Results Molecular classification was successful for 982 tumors. Based on the NCI consensus MSI panel assessing MSI and loss of heterozygosity combined with POLE testing, 49% of tumors were classified copy number stable (CNS), 39% MMR deficient, 8% copy number altered (CNA) and 4% POLE mutant. Cancer-specific mortality occurred in 5% of patients with CNS tumors; 2.6% with POLE tumors; 7.6% with MMR deficient tumors and 19% with CNA tumors. The CNA group had worse progression-free (HR 2.31, 95%CI 1.53–3.49) and cancer-specific survival (HR 3.95; 95%CI 2.10–7.44). The POLE group had improved outcomes, but the differences were not statistically significant. CNA class remained significant for cancer-specific survival (HR 2.11; 95%CI 1.04–4.26) in multivariable analysis. The CNA molecular class was associated with TP53 mutation and expression status. Conclusions A simple molecular classification for endometrioid endometrial cancers that can be easily combined with Lynch syndrome screening provides important prognostic information. These findings support prospective clinical validation and further studies on the predictive value of a simplified molecular classification system. PMID:29132872

Three Perspectives on Getting Data Right: An Introduction to CNA Education's IRC Paper Series

ERIC Educational Resources Information Center

Muller, Robert D.

2011-01-01

As a research and technical assistance organization, CNA Education would be the last to deny the importance of good data and the first to applaud efforts to improve the quality and scope of the data available. Solid data are critical to CNA's mission to further general understanding of the efficacy of specific education reform initiatives and to…

Isopeptide bonds of the major pilin protein BcpA influence pilus structure and bundle formation on the surface of Bacillus cereus

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

Hendrickx, Antoni P.A.; Poor, Catherine B.; Jureller, Justin E.

Bacillus cereus strains elaborate pili on their surface using a mechanism of sortase-mediated cross-linking of major and minor pilus components. Here we used a combination of electron microscopy and atomic force microscopy to visualize these structures. Pili occur as single, double or higher order assemblies of filaments formed from monomers of the major pilin, BcpA, capped by the minor pilin, BcpB. Previous studies demonstrated that within assembled pili, four domains of BcpA -- CNA{sub 1}, CNA{sub 2}, XNA and CNA{sub 3} -- each acquire intramolecular lysine-asparagine isopeptide bonds formed via catalytic glutamic acid or aspartic acid residues. Here we showedmore » that mutants unable to form the intramolecular isopeptide bonds in the CNA2 or CNA3 domains retain the ability to form pilus bundles. A mutant lacking the CNA{sub 1} isopeptide bond assembled deformed pilin subunits that failed to associate as bundles. X-ray crystallography revealed that the BcpA variant Asp{sup 312}Ala, lacking an aspartyl catalyst, did not generate the isopeptide bond within the jelly-roll structure of XNA. The Asp{sup 312}Ala mutant was also unable to form bundles and promoted the assembly of deformed pili. Thus, structural integrity of the CNA{sub 1} and XNA domains are determinants for the association of pili into higher order bundle structures and determine native pilus structure.« less

Genotoxic potential of montmorillonite clay mineral and alteration in the expression of genes involved in toxicity mechanisms in the human hepatoma cell line HepG2.

PubMed

Maisanaba, Sara; Hercog, Klara; Filipic, Metka; Jos, Ángeles; Zegura, Bojana

2016-03-05

Montmorillonite, also known as Cloisite(®)Na(+) (CNa(+)), is a natural clay with a wide range of well-documented and novel applications, such as pharmaceutical products or food packaging. Although considered a low toxic product, the expected increased exposure to CNa(+) arises concern on the potential consequences on human and environmental health especially as its genotoxicity has scarcely been investigated so far. Thus, we investigated, for the first time, the influence of non-cytotoxic concentrations of CNa(+) (15.65, 31.25 and 62.5 μg/mL) on genomic instability of human hepatoma cell line (HepG2) by determining the formation of micronuclei (MNi), nucleoplasmic bridges (NPBs) and nuclear buds (NBUDs) with the Cytokinesis block micronucleus cytome assay. Further on we studied the influence of CNa(+) on the expression of several genes involved in toxicity mechanisms using the real-time quantitative PCR. The results showed that CNa(+) increased the number of MNi, while the numbers of NBUDs and NPBs were not affected. In addition it deregulated genes in all the groups studied, mainly after longer time of exposure. These findings provide the evidence that CNa(+) is potentially genotoxic. Therefore further studies that will elucidate the molecular mechanisms involved in toxic activity of CNa(+) are needed for hazard identification and human safety assessment. Copyright © 2015 Elsevier B.V. All rights reserved.

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

Allan, Phoebe K.; Griffin, John M.; Darwiche, Ali

We use operando pair distribution function (PDF) analysis and ex situ 23Na magic-angle spinning solid-state nuclear magnetic resonance (MAS ssNMR) spectroscopy to gain insight into the alloying mechanism of high-capacity antimony anodes for sodium-ion batteries. Subtraction of the PDF of crystalline Na xSb phases from the total PDF, an approach constrained by chemical phase information gained from 23Na ssNMR in reference to relevant model compounds, identifies two previously uncharacterized intermediate species formed electrochemically; a-Na 3–xSb (x ≈ 0.4–0.5), a structure locally similar to crystalline Na 3Sb (c-Na 3Sb) but with significant numbers of sodium vacancies and a limited correlation length,more » and a-Na1.7Sb, a highly amorphous structure featuring some Sb–Sb bonding. The first sodiation breaks down the crystalline antimony to form first a-Na 3–xSb and, finally, crystalline Na 3Sb. Desodiation results in the formation of an electrode formed of a composite of crystalline and amorphous antimony networks. We link the different reactivity of these networks to a series of sequential sodiation reactions manifesting as a cascade of processes observed in the electrochemical profile of subsequent cycles. The amorphous network reacts at higher voltages reforming a-Na 1.7Sb, then a-Na 3–xSb, whereas lower potentials are required for the sodiation of crystalline antimony, which reacts to form a-Na 3–xSb without the formation of a-Na 1.7Sb. a-Na 3–xSb is converted to crystalline Na 3Sb at the end of the second discharge. In the end, we find no evidence of formation of NaSb. Variable temperature 23Na NMR experiments reveal significant sodium mobility within c-Na 3Sb; this is a possible contributing factor to the excellent rate performance of Sb anodes.« less

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

Allan, Phoebe K.; Griffin, John M.; Darwiche, Ali

Operando pair distribution function (PDF) analysis and ex situ Na-23 magic-angle spinning solid-state nuclear magnetic resonance (MAS ssNMR) spectroscopy are used to gain insight into the alloying mechanism of high-capacity antimony anodes for sodium-ion batteries. Subtraction of the PDF of crystalline NaxSb phases from the total PDF, an approach constrained by chemical phase information gained from Na-23 ssNMR in reference to relevant model compounds, identifies two previously uncharacterized intermediate species formed electro-chemically; a-Na3-xSb (x approximate to 0.4-0.5), a structure locally similar to crystalline Na3Sb (c-Na3Sb) but with significant numbers of sodium vacancies and a limited correlation length, and a-Na1.7Sb, amore » highly amorphous structure featuring some Sb-Sb bonding. The first sodiation breaks down the crystalline antimony to form first a-Na3-xSb and, finally, crystalline Na3Sb. Desodiation results in the formation of an electrode formed of a composite of crystalline and amorphous antimony networks. We link the different reactivity of these networks to a series of sequential sodiation reactions manifesting as a cascade of processes observed in the electrochemical profile of subsequent cycles. The amorphofis network reacts at higher voltages reforming a-Na1.7Sb, then a-Na3-xSb, whereas lower potentials are required for the sodiation of crystalline antimony, which reacts to form a-Na3-xSb without the formation of a-Na3-xSb. a-Na3-xSb is converted to crystalline Na3Sb at the end of the second discharge. We find no evidence of formation of NaSb. Variable temperature Na-23 NMR experiments reveal significant sodium mobility within c-Na3Sb; this is a possible contributing factor to the excellent rate performance of Sb anodes.« less

Population Representation in the Military Services: Fiscal Year 2015 Summary Report

DTIC Science & Technology

2017-01-24

efficient. Major areas of research include health research and policy; energy and environment; manpower management; acquisition and cost; infrastructure...document shall be referred to CNA Document Center at inquiries@cna.org. January 2017 Anita Hattiangadi, Research Team Leader Resource...available online at https://www.cna.org/ research /pop-rep. 3 market, which, although improving in FY15, produced a prolonged period of historically

X-ray crystal structures of Staphylococcus aureus collagen adhesin and sortases

NASA Astrophysics Data System (ADS)

Zong, Yinong

For many gram-positive bacteria, adhesion to host tissues is the first critical step in developing an infection. The adhesion is mediated by a superfamily of bacterial surface proteins, called MSCRAMM (microbial surface components recognizing adhesive matrix molecules), which in most cases are covalently attached to the cell wall peptidoglycan. Collagen adhesin (CNA) from Staphylococcus aureus, one of the MSCRAMMs, is responsible for bacterial binding to collagen molecules. CNA and other MSCRAMMs are anchored to the cell wall by a transpeptidase, sortase. The knowledge about how bacterial surface proteins adhere to host molecules and how they are sorted onto the cell wall is crucial for the design of novel antibiotics against bacterial infections. The crystal structures of CNA31--344 (residue 31 to 334), a truncation of CNA's collagen binding region, and CNA31--344 in complex with a collagen peptide were determined. CNA31--344 contains two domains, and between them is a big hole formed by a loop connecting the two domains. In the structure of CNA31--344-collagen complex, the collagen peptide is locked in the hole formed by the two domains of CNA 31--344. We reason that the two domains of CNA31--344 are open in the physiological condition, and close up when binding to collagen. This binding mechanism may be common for other bacterial collagen adhesins. There are two known sortases in Staphylococcus aureus. Sortase A is responsible for anchoring most MSCRAMMs that have a LPXTG (X represents any amino acid) sorting motif and sortase B for a bacterial ion acquisition protein. The crystal structures of both sortases indicate that they share a common catalytic mechanism. Unlike typical cysteine transpeptidases, sortases may use a novel Cys-Arg catalytic dyad instead of a Cys-His pair. All other sortases found in gram-positive bacteria may have similar active site architecture and employ the same catalytic dyad because the critical residues are all conserved among them. The structures of sortases in complex with their substrates and inhibitors are also useful to explain their substrate specificity and catalytic kinetics.

Ab initio investigation on the valence and dipole-bound states of CNa - and SiNa -

NASA Astrophysics Data System (ADS)

Kalcher, Josef; Sax, Alexander F.

2000-08-01

CNa - and SiNa - have been studied by the CAS-ACPF method. The 3Σ- ground states have binding energies of 5420 and 7517 cm -1, respectively. The 5Σ- excited states are 494 and 1551 cm -1 above the respective ground states. The 1Δ , 3Π , and 1Π valence-excited states for SiNa - should be at least metastable. CNa - and SiNa - possess dipole-bound 5Σ- and 3Σ- states. Binding energies of these states in CNa - are 217 and 236 cm -1, respectively. SiNa - has two stable 5Σ- dipole-bound states, whose binding energies are 246 and 118 cm -1, respectively.

Russia’s Approach to Cyber Warfare (1Rev)

DTIC Science & Technology

2017-03-01

Steinitz, CNA. Approved by: March 2017 Ken E. Gause, RTL International Affairs Group Center for Strategic Studies REPORT DOCUMENTATION PAGE...the help of information networks.”7 Russian military thinkers on information operations IO and asymmetric military tactics, Col. S.G. Chekinov (Res...adversaries, influence public opinion, and reduce an opponent’s will to resist.8 Cyber IO affords the Russian government covert means to achieve these

Visualisation of Collagen in fixed skeletal muscle tissue using fluorescently tagged Collagen binding protein CNA35.

PubMed

Mohammadkhah, Melika; Simms, Ciaran K; Murphy, Paula

2017-02-01

Detection and visualisation of Collagen structure are important to understand the relationship between mechanical behaviour and microstructure in skeletal muscle since Collagen is the main structural protein in animal connective tissues, and is primarily responsible for their passive load-bearing properties. In the current study, the direct detection and visualization of Collagen using fluorescently tagged CNA35 binding protein (fused to EGFP or tdTomato) is reported for the first time on fixed skeletal muscle tissue. This Technical Note also establishes a working protocol by examining tissue preparation, dilution factor, exposure time etc. for sensitivity and specificity. Penetration of the binding protein into intact mature skeletal muscle was found to be very limited, but detection works well on tissue sections with higher sensitivity on wax embedded sections compared to frozen sections. CNA35 fused to tdTomato has a higher sensitivity than CNA35 fused to EGFP but both show specific detection. Best results were obtained with 15μm wax embedded sections, with blocking of non-specific binding in 1% BSA and antigen retrieval in Sodium Citrate. There was a play-off between dilution of the binding protein and time of incubation but both CNA35-tdTomato and CNA35-EGFP worked well with approximately 100μg/ml of purified protein with overnight incubation, while CNA35-tdTomato could be utilized at 5 fold less concentration. This approach can be applied to study the relationship between skeletal muscle micro-structure and to observe mechanical response to applied deformation. It can be used more broadly to detect Collagen in a variety of fixed tissues, useful for structure-functions studies, constitutive modelling, tissue engineering and assessment of muscle tissue pathologies. Copyright © 2016 Elsevier Ltd. All rights reserved.

Oxytocin administration in the basolateral and central nuclei of amygdala moderately suppresses food intake.

PubMed

Klockars, Oscar A; Klockars, Anica; Levine, Allen S; Olszewski, Pawel K

2018-04-11

Oxytocin (OT) at acting central nuclei decreases meal size and reduces intake of palatable sweet solutions. It remains largely unclear as to which brain sites mediate OT's effect on palatability versus energy or the combination of those aspects of consumption. Here, we expanded the search for sites that mediate anorexigenic properties of OT by focusing on two subdivisions of the amygdala, its central (CNA) and basolateral (BLA) nuclei. We injected OT directly into the BLA or CNA in rats and assessed intake of standard chow induced by energy deprivation and intake of sweet solutions in nondeprived animals. We examined whether these effects are reversible by OT receptor (OTr) antagonism and whether OT presence in BLA or CNA induces taste aversion. We also determined the effect of energy deprivation and exposure to sweet saccharin on BLA and CNA expression of OTr mRNA. OT administration in BLA at 0.3 μg and in CNA at 1 μg reduced standard chow intake after deprivation by ~25%. Only administration of OT in BLA was effective in suppressing consumption of sucrose and saccharin solutions. The anorexigenic effects of OT in BLA and CNA were attenuated by OTr antagonist, L-368,899, pretreatment. OT at anorexigenic doses did not promote acquisition of taste aversion. BLA OTr mRNA expression was affected by exposure to palatable saccharin, whereas that of CNA OTr, by energy deprivation. OT in the amygdala moderately decreases food intake. The functional relationship between amygdalar OT and energy intake versus palatability-driven intake depends on the discrete localization of the OTr within this complex structure.

Colorful protein-based fluorescent probes for collagen imaging.

PubMed

Aper, Stijn J A; van Spreeuwel, Ariane C C; van Turnhout, Mark C; van der Linden, Ardjan J; Pieters, Pascal A; van der Zon, Nick L L; de la Rambelje, Sander L; Bouten, Carlijn V C; Merkx, Maarten

2014-01-01

Real-time visualization of collagen is important in studies on tissue formation and remodeling in the research fields of developmental biology and tissue engineering. Our group has previously reported on a fluorescent probe for the specific imaging of collagen in live tissue in situ, consisting of the native collagen binding protein CNA35 labeled with fluorescent dye Oregon Green 488 (CNA35-OG488). The CNA35-OG488 probe has become widely used for collagen imaging. To allow for the use of CNA35-based probes in a broader range of applications, we here present a toolbox of six genetically-encoded collagen probes which are fusions of CNA35 to fluorescent proteins that span the visible spectrum: mTurquoise2, EGFP, mAmetrine, LSSmOrange, tdTomato and mCherry. While CNA35-OG488 requires a chemical conjugation step for labeling with the fluorescent dye, these protein-based probes can be easily produced in high yields by expression in E. coli and purified in one step using Ni2+-affinity chromatography. The probes all bind specifically to collagen, both in vitro and in porcine pericardial tissue. Some first applications of the probes are shown in multicolor imaging of engineered tissue and two-photon imaging of collagen in human skin. The fully-genetic encoding of the new probes makes them easily accessible to all scientists interested in collagen formation and remodeling.

Clonal evolution and devolution after chemotherapy in adult acute myelogenous leukemia

PubMed Central

Parkin, Brian; Ouillette, Peter; Li, Yifeng; Keller, Jennifer; Lam, Cindy; Roulston, Diane; Li, Cheng; Shedden, Kerby

2013-01-01

The frequent occurrence of persistent or relapsed disease after induction chemotherapy in AML necessitates a better understanding of the clonal relationship of AML in various disease phases. In this study, we used SNP 6.0 array-based genomic profiling of acquired copy number aberrations (aCNA) and copy neutral LOH (cnLOH) together with sequence analysis of recurrently mutated genes to characterize paired AML genomes. We analyzed 28 AML sample pairs from patients who achieved complete remission with chemotherapy and subsequently relapsed and 11 sample pairs from patients with persistent disease after induction chemotherapy. Through review of aCNA/cnLOH and gene mutation profiles in informative cases, we demonstrate that relapsed AML invariably represents re-emergence or evolution of a founder clone. Furthermore, all individual aCNA or cnLOH detected at presentation persisted at relapse indicating that this lesion type is proximally involved in AML evolution. Analysis of informative paired persistent AML disease samples uncovered cases with 2 coexisting dominant clones of which at least one was chemotherapy sensitive and one resistant, respectively. These data support the conclusion that incomplete eradication of AML founder clones rather than stochastic emergence of fully unrelated novel clones underlies AML relapse and persistence with direct implications for clinical AML research. PMID:23175688

An evidential example of airborne bacteria in a crowded, underground public concourse in Tokyo

NASA Astrophysics Data System (ADS)

Seino, Kaoruko; Takano, Takehito; Nakamura, Keiko; Watanabe, Masafumi

2005-01-01

We examined airborne bacteria in an underground concourse in Tokyo and investigated conditions that influenced bacterial counts. Airborne bacteria were collected by using an impactor sampler. Colonies on plate count agar (PCA) and Columbia colistin-nalidixic acid agar with 5% sheep blood (CNA agar) were enumerated. The range, geometric mean, and 95% CI of the bacterial counts (CFU m-3) on PCA and CNA agar were 150-1380, 456, 382-550 and 50-990, 237, 182-309, respectively. Bacterial counts on PCA significantly correlated with number of the pedestrians (r=0.89), relative humidity (r=0.70) and airborne dust (PM5.0) (r=0.73). Results of a multiple regression indicated independent positive association between the number of pedestrians and bacterial counts on PCA (p<0.01) after excluding the influence of relative humidity and airborne dust. Similar results were obtained with the statistical analysis for the counts of bacteria on CNA agar. Gram-positive cocci were dominant on PCA and CNA agar. Staphylococcus epidermidis and Micrococcus spp. were dominant among the 11 genera and 19 species identified in the present study. Considering the pattern of identified species and the significant independent association between number of pedestrians and bacterial counts, airborne bacteria in a crowded underground concourse were mostly originated from the pedestrians who were walking in the underground concourse. This study gave an evidential example of bacterial conditions in the air of an underground crowded public space in Tokyo.

CLImAT-HET: detecting subclonal copy number alterations and loss of heterozygosity in heterogeneous tumor samples from whole-genome sequencing data.

PubMed

Yu, Zhenhua; Li, Ao; Wang, Minghui

2017-03-15

Copy number alterations (CNA) and loss of heterozygosity (LOH) represent a large proportion of genetic structural variations of cancer genomes. These aberrations are continuously accumulated during the procedure of clonal evolution and patterned by phylogenetic branching. This invariably results in the emergence of multiple cell populations with distinct complement of mutational landscapes in tumor sample. With the advent of next-generation sequencing technology, inference of subclonal populations has become one of the focused interests in cancer-associated studies, and is usually based on the assessment of combinations of somatic single-nucleotide variations (SNV), CNA and LOH. However, cancer samples often have several inherent issues, such as contamination of normal stroma, tumor aneuploidy and intra-tumor heterogeneity. Addressing these critical issues is imperative for accurate profiling of clonal architecture. We present CLImAT-HET, a computational method designed for capturing clonal diversity in the CNA/LOH dimensions by taking into account the intra-tumor heterogeneity issue, in the case where a reference or matched normal sample is absent. The algorithm quantitatively represents the clonal identification problem using a factorial hidden Markov model, and takes an integrated analysis of read counts and allele frequency data. It is able to infer subclonal CNA and LOH events as well as the fraction of cells harboring each event. The results on simulated datasets indicate that CLImAT-HET has high power to identify CNA/LOH segments, it achieves an average accuracy of 0.87. It can also accurately infer proportion of each clonal population with an overall Pearson correlation coefficient of 0.99 and a mean absolute error of 0.02. CLImAT-HET shows significant advantages when compared with other existing methods. Application of CLImAT-HET to 5 primary triple negative breast cancer samples demonstrates its ability to capture clonal diversity in the CAN/LOH dimensions. It detects two clonal populations in one sample, and three clonal populations in one other sample. CLImAT-HET, a novel algorithm is introduced to infer CNA/LOH segments from heterogeneous tumor samples. We demonstrate CLImAT-HET's ability to accurately recover clonal compositions using tumor WGS data without a match normal sample.

Growth of binary organic NLO crystals: m.NA-p.NA and m.NA-CNA system

NASA Technical Reports Server (NTRS)

Singh, N. B.; Henningsen, T.; Hopkins, R. H.; Mazelsky, R.

1993-01-01

Experiments were carried out to grow 3.Nitroaniline (m.NA) crystals doped with 4.Nitroaniline (p.NA) and 2.chloro 4.Nitroaniline (CNA). The measured undercooling for m.NA, p.NA, and CNA were 0.21 tm K, 0.23 tm K, and 0.35 tm K respectively, where tm represents the melting temperature of the pure component. Because of the crystals' large heat of fusion and large undercooling, it was not possible to grow good quality crystals with low thermal gradients. In the conventional two-zone Bridgman furnace we had to raise the temperature of the hot zone above the decomposition temperature of CNA, p.NA, and m.NA to achieve the desired thermal gradient. To avoid decomposition, we used an unconventional Bridgman furnace. Two immiscible liquids, silicone oil and ethylene glycol, were used to build a special two-zone Bridgman furnace. A temperature gradient of 18 K/cm was achieved without exceeding the decomposition temperature of the crystal. The binary crystals, m.NA-p.NA and m.NA-CNA, were grown in centimeter size in this furnace. X-ray and optical characterization showed good optical quality.

Challenges for Navy Officer Personnel Management

DTIC Science & Technology

2014-04-01

Aline Quester, Russell Beland, and William Mulligan. Ship Material Readiness. CNA Professional Paper 467 (Revised). Feb. 1991. 4825 Mark Center Drive, Alexandria, VA 22311-1850 703-824-2000 www.cna.org DAB-2014-U-007152-Final-7

Calcineurin plays key roles in the dimorphic transition and virulence of the human pathogenic zygomycete Mucor circinelloides.

PubMed

Lee, Soo Chan; Li, Alicia; Calo, Silvia; Heitman, Joseph

2013-01-01

Many pathogenic fungi are dimorphic and switch between yeast and filamentous states. This switch alters host-microbe interactions and is critical for pathogenicity. However, in zygomycetes, whether dimorphism contributes to virulence is a central unanswered question. The pathogenic zygomycete Mucor circinelloides exhibits hyphal growth in aerobic conditions but switches to multi-budded yeast growth under anaerobic/high CO₂ conditions. We found that in the presence of the calcineurin inhibitor FK506, Mucor exhibits exclusively multi-budded yeast growth. We also found that M. circinelloides encodes three calcineurin catalytic A subunits (CnaA, CnaB, and CnaC) and one calcineurin regulatory B subunit (CnbR). Mutations in the latch region of CnbR and in the FKBP12-FK506 binding domain of CnaA result in hyphal growth of Mucor in the presence of FK506. Disruption of the cnbR gene encoding the sole calcineurin B subunit necessary for calcineurin activity yielded mutants locked in permanent yeast phase growth. These findings reveal that the calcineurin pathway plays key roles in the dimorphic transition from yeast to hyphae. The cnbR yeast-locked mutants are less virulent than the wild-type strain in a heterologous host system, providing evidence that hyphae or the yeast-hyphal transition are linked to virulence. Protein kinase A activity (PKA) is elevated during yeast growth under anaerobic conditions, in the presence of FK506, or in the yeast-locked cnbR mutants, suggesting a novel connection between PKA and calcineurin. cnaA mutants lacking the CnaA catalytic subunit are hypersensitive to calcineurin inhibitors, display a hyphal polarity defect, and produce a mixture of yeast and hyphae in aerobic culture. The cnaA mutants also produce spores that are larger than wild-type, and spore size is correlated with virulence potential. Our results demonstrate that the calcineurin pathway orchestrates the yeast-hyphal and spore size dimorphic transitions that contribute to virulence of this common zygomycete fungal pathogen.

Cnm is a major virulence factor of invasive Streptococcus mutans and part of a conserved three-gene locus

PubMed Central

Avilés-Reyes, A.; Miller, J.H.; Simpson-Haidaris, P.J.; Lemos, J.A.; Abranches, J.

2014-01-01

SUMMARY Cnm, a collagen- and laminin-binding protein present in a subset of Streptococcus mutans strains, mediates binding to extracellular matrices (ECM), intracellular invasion and virulence in the Galleria mellonella model. Antibodies raised against Cnm were used to confirm expression and the cell surface localization of Cnm in the highly invasive OMZ175 strain. Sequence analysis identified two additional genes (cnaB and cbpA) encoding putative surface proteins immediately upstream of cnm. Inactivation of cnaB and cbpA in OMZ175, individually or in combination, did not decrease the ability of this highly invasive and virulent strain to bind to different ECM proteins, invade human coronary artery endothelial cells (HCAEC), or kill G. mellonella. Similarly, expression of cnaB and cbpA in the cnm− strain UA159 revealed that these genes did not enhance Cnmrelated phenotypes. However, integration of cnm in the chromosome of UA159 significantly increased its ability to bind to collagen and laminin, invade HCAEC, and kill G. mellonella. Moreover, the presence of antibodies against Cnm nearly abolished the ability of OMZ175 to bind to collagen and laminin and invade HCAEC, and significantly protected G. mellonella against OMZ175 infection. We concluded that neither CnaB nor CbpA is necessary for the expression of Cnm-related traits. We also provided definitive evidence that Cnm is an important virulence factor and a suitable target for the development of novel preventive and therapeutic strategies to combat invasive S. mutans strains. PMID:24103776

Helium sequestration at nanoparticle-matrix interfaces in helium + heavy ion irradiated nanostructured ferritic alloys

DOE PAGES

Parish, Chad M.; Unocic, Kinga A.; Tan, Lizhen; ...

2016-10-24

Here we irradiated four ferritic alloys with energetic Fe and He ions: one castable nanostructured alloy (CNA) containing Ti-W-Ta-carbides, and three nanostructured ferritic alloys (NFAs). The NFAs were: 9Cr containing Y-Ti-O nanoclusters, and two Fe-12Cr-5Al NFAs containing Y-Zr-O or Y-Hf-O clusters. All four were subjected to simultaneous dual-beam Fe + He ion implantation (650 °C, ~50 dpa, ~15 appm He/dpa), simulating fusion-reactor conditions. Examination using scanning/transmission electron microscopy (STEM) revealed high-number-density helium bubbles of ~8 nm, ~10 21 m -3 (CNA), and of ~3 nm, 10 23 m -3 (NFAs). STEM combined with multivariate statistical analysis data mining suggests thatmore » the precipitate-matrix interfaces in all alloys survived ~50 dpa at 650 °C and serve as effective helium trapping sites. All alloys appear viable structural material candidates for fusion or advanced fission energy systems. Finally, among these developmental alloys the NFAs appear to sequester the helium into smaller bubbles and away from the grain boundaries more effectively than the early-generation CNA.« less

Assessment of immigrant certified nursing assistants' communication when responding to standardized care challenges.

PubMed

Massey, Meredith; Roter, Debra L

2016-01-01

Certified nursing assistants (CNAs) provide 80% of the hands-on care in US nursing homes; a significant portion of this work is performed by immigrants with limited English fluency. This study is designed to assess immigrant CNA's communication behavior in response to a series of virtual simulated care challenges. A convenience sample of 31 immigrant CNAs verbally responded to 9 care challenges embedded in an interactive computer platform. The responses were coded with the Roter Interaction Analysis System (RIAS), CNA instructors rated response quality and spoken English was rated. CNA communication behaviors varied across care challenges and a broad repertoire of communication was used; 69% of response content was characterized as psychosocial. Communication elements (both instrumental and psychosocial) were significant predictors of response quality for 5 of 9 scenarios. Overall these variables explained between 13% and 36% of the adjusted variance in quality ratings. Immigrant CNAs responded to common care challenges using a variety of communication strategies despite fluency deficits. Virtual simulation-based observation is a feasible, acceptable and low cost method of communication assessment with implications for supervision, training and evaluation of a para-professional workforce. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Recognizing and Responding to the "Toxic" Work Environment: Worker Safety, Patient Safety, and Abuse/Neglect in Nursing Homes.

PubMed

Pickering, Carolyn E Z; Nurenberg, Katie; Schiamberg, Lawrence

2017-10-01

This grounded theory study examined how the certified nursing assistant (CNA) understands and responds to bullying in the workplace. Constant comparative analysis was used to analyze data from in-depth telephone interviews with CNAs ( N = 22) who experienced bullying while employed in a nursing home. The result of the analysis is a multistep model describing CNA perceptions of how, over time, they recognized and responded to the "toxic" work environment. The strategies used in responding to the "toxic" environment affected their care provision and were attributed to the development of several resident and worker safety outcomes. The data suggest that the etiology of abuse and neglect in nursing homes may be better explained by institutional cultures rather than individual traits of CNAs. Findings highlight the relationship between worker and patient safety, and suggest worker safety outcomes may be an indicator of quality in nursing homes.

Cooling rate dependence and local structure in aluminum monatomic metallic glass

NASA Astrophysics Data System (ADS)

Kbirou, M.; Trady, S.; Hasnaoui, A.; Mazroui, M.

2017-10-01

The local atomic structure in aluminium monatomic metallic glass is studied using molecular dynamics simulations combined with the embedded atom method (EAM). We have used a variety of analytical methods to characterise the atomic configurations of our system: the Pair Distribution Function (PDF), the Common Neighbour Analysis (CNA) and the Voronoi Tessellation Analysis. CNA was used to investigate the order change from liquid to amorphous phases, recognising that the amount of icosahedral clusters increases with the decrease of temperature. The Voronoi analysis revealed that the icosahedral-like polyhedral are the predominant ones. It has been observed that the PDF function shows a splitting in the second peak, which cannot be attributed to the only ideal icosahedral polyhedron 〈0, 0, 12, 0〉, but also to the formation of other Voronoi polyhedra 〈0, 1, 10, 2〉 . Further, the PDFs were then integrated giving the cumulative coordination number in order to compute the fractal dimension (df).

Effect of dry heat and steam sterilization on load-deflection characteristics of β-titanium wires: An in vitro study

PubMed Central

Alavi, Shiva; Sinaee, Neda

2012-01-01

Background: Sterilization techniques could affect the characteristics of orthodontic wires. The aim of the present study was to evaluate the effect of steam and dry heat sterilization techniques on load-deflection behavior of five types of β-titanium alloy wires. Materials and Methods: The samples consisted of 30 straight lengths of five types of β-titanium alloy wires: Titanium Molybdenum Alloy (TMA) Low Friction (TMAL), TMA Low Friction Colored (HONE), Resolve (RES), BetaForce (BETA), and BETA CNA (CNA). Thirty wire segments were divided into three groups of 10. Group 1 was the control group and the group 2 samples were sterilized by dry heat in an oven (60 minutes at 160°C) and group 3 by steam in an autoclave (15 minutes at 121°C). Then all the wire samples underwent a three-point bending test in a testing machine to evaluate load-deflection properties. Data was analyzed by repeated measures ANOVA and Scheffé's test (α = 0.05). Results: The results showed that dry heat sterilization significantly increased force levels during both loading and unloading of CNA, BETA and RES and during loading of HONE (P < 0.05). Steam sterilization significantly increased force levels during both loading and unloading of BETA and during unloading of HONE (P < 0.05), with no effects on the load-deflection characteristics of TMAL, CNA and RES (P > 0.05). Conclusion: It appears dry heat sterilization increases stiffness of RES, BETA, CNA and HONE but autoclave sterilization did not have any effect on load-deflection characteristics of most of the β-titanium wires tested, indicating that clinicians who want to provide maximum safety for their patients can autoclave TMAL, RES and CNA before applying them. PMID:23559917

Deciphering the associations between gene expression and copy number alteration using a sparse double Laplacian shrinkage approach

PubMed Central

Shi, Xingjie; Zhao, Qing; Huang, Jian; Xie, Yang; Ma, Shuangge

2015-01-01

Motivation: Both gene expression levels (GEs) and copy number alterations (CNAs) have important biological implications. GEs are partly regulated by CNAs, and much effort has been devoted to understanding their relations. The regulation analysis is challenging with one gene expression possibly regulated by multiple CNAs and one CNA potentially regulating the expressions of multiple genes. The correlations among GEs and among CNAs make the analysis even more complicated. The existing methods have limitations and cannot comprehensively describe the regulation. Results: A sparse double Laplacian shrinkage method is developed. It jointly models the effects of multiple CNAs on multiple GEs. Penalization is adopted to achieve sparsity and identify the regulation relationships. Network adjacency is computed to describe the interconnections among GEs and among CNAs. Two Laplacian shrinkage penalties are imposed to accommodate the network adjacency measures. Simulation shows that the proposed method outperforms the competing alternatives with more accurate marker identification. The Cancer Genome Atlas data are analysed to further demonstrate advantages of the proposed method. Availability and implementation: R code is available at http://works.bepress.com/shuangge/49/ Contact: shuangge.ma@yale.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:26342102

Tracing the origin of disseminated tumor cells in breast cancer using single-cell sequencing.

PubMed

Demeulemeester, Jonas; Kumar, Parveen; Møller, Elen K; Nord, Silje; Wedge, David C; Peterson, April; Mathiesen, Randi R; Fjelldal, Renathe; Zamani Esteki, Masoud; Theunis, Koen; Fernandez Gallardo, Elia; Grundstad, A Jason; Borgen, Elin; Baumbusch, Lars O; Børresen-Dale, Anne-Lise; White, Kevin P; Kristensen, Vessela N; Van Loo, Peter; Voet, Thierry; Naume, Bjørn

2016-12-09

Single-cell micro-metastases of solid tumors often occur in the bone marrow. These disseminated tumor cells (DTCs) may resist therapy and lay dormant or progress to cause overt bone and visceral metastases. The molecular nature of DTCs remains elusive, as well as when and from where in the tumor they originate. Here, we apply single-cell sequencing to identify and trace the origin of DTCs in breast cancer. We sequence the genomes of 63 single cells isolated from six non-metastatic breast cancer patients. By comparing the cells' DNA copy number aberration (CNA) landscapes with those of the primary tumors and lymph node metastasis, we establish that 53% of the single cells morphologically classified as tumor cells are DTCs disseminating from the observed tumor. The remaining cells represent either non-aberrant "normal" cells or "aberrant cells of unknown origin" that have CNA landscapes discordant from the tumor. Further analyses suggest that the prevalence of aberrant cells of unknown origin is age-dependent and that at least a subset is hematopoietic in origin. Evolutionary reconstruction analysis of bulk tumor and DTC genomes enables ordering of CNA events in molecular pseudo-time and traced the origin of the DTCs to either the main tumor clone, primary tumor subclones, or subclones in an axillary lymph node metastasis. Single-cell sequencing of bone marrow epithelial-like cells, in parallel with intra-tumor genetic heterogeneity profiling from bulk DNA, is a powerful approach to identify and study DTCs, yielding insight into metastatic processes. A heterogeneous population of CNA-positive cells is present in the bone marrow of non-metastatic breast cancer patients, only part of which are derived from the observed tumor lineages.

75 FR 27805 - Comprehensive Needs Assessment (CNA)

Federal Register 2010, 2011, 2012, 2013, 2014

2010-05-18

... Comprehensive Needs Assessment is a description of current and future needs and resources of certain multifamily...: Comprehensive Needs Assessment (CNA). OMB Approval Number: 2502-0505. Form Numbers: HUD-96001, HUD-96002, HUD..., sanitary, and in good repair. The Comprehensive Needs Assessment is a description of current and future...

Trends in Operational Fuel Use

DTIC Science & Technology

2016-08-01

Wikipedia, The Free Encyclopedia. Chow Test. Viewed July 18, 2016 at: https://en.wikipedia.org/wiki/Chow_test 8. CNA Research Memorandum CRM 86-178. Ship...Gren Landry and Gregory Suess. May 2006 10. CNA, CRM D0026186.A2/Final. Vessel Traffic in the Hawaii-Southern California and Atlantic Fleet Testing

The Energy Conversation: The First 3 Years

DTIC Science & Technology

2009-07-01

Office of Naval Research CNA Robert J. Murray, CNA President and CEO Mitzi Wertheim, Director of The Energy Conversation Printed in the United States of... Mitzi Wertheim and flew out to Washington, DC to meet her for lunch. Wertheim had been Woolsey’s Deputy Under Secretary of the Navy. She is also the

Genome analysis of Clostridium perfringens isolates from healthy and necrotic enteritis infected chickens and turkeys.

PubMed

Ronco, Troels; Stegger, Marc; Ng, Kim Lee; Lilje, Berit; Lyhs, Ulrike; Andersen, Paal Skytt; Pedersen, Karl

2017-07-11

Clostridium perfringens causes gastrointestinal diseases in both humans and domestic animals. Type A strains expressing the NetB toxin are the main cause of necrotic enteritis (NE) in chickens, which has remarkable impact on animal welfare and production economy in the international poultry industry. Three pathogenicity loci NELoc-1, -2 and -3 and a collagen adhesion gene cnaA have been found to be associated with NE in chickens, whereas the presence of these has not been investigated in diseased turkeys. The purpose was to investigate the virulence associated genome content and the genetic relationship among 30 C. perfringens isolates from both healthy and NE infected chickens and turkeys, applying whole-genome sequencing. NELoc-1, -3, netB and cnaA were significantly associated with NE isolates from chickens, whereas only NELoc-2 was commonly observed in both diseased turkeys and chickens. A putative collagen adhesion gene that encodes a von Willebrand Factor (vWF) domain was identified in all diseased turkeys and designated as cnaD. The phylogenetic analysis based on single nucleotide polymorphisms showed that the isolates generally were not closely related. These results indicate that virulence factors and pathogenicity loci associated with NE in chickens are not important to the same extent in diseased turkeys except for NELoc-2. A putative collagen adhesion gene which potentially could be of importance in regard to the NE pathogenesis in turkeys was identified and need to be further investigated. Thus, the pathogenesis of NE in turkeys appears to be different from that of broiler chickens.

Life Satisfaction: The Richard Cory Syndrome.

ERIC Educational Resources Information Center

Gatz, Margaret; And Others

This study of life satisfaction and competence was part of the Individual and Community Competence Project (Gatz and others, 1976). It included two groups of people, community workers (N=21) and non-workers (N=22), from each of two settings, Model Neighborhoods Areas (MNA) and Central Area (CNA). The MNA is a black area, while the CNA is a white…

Bov-tA short interspersed nucleotide element sequences in circulating nucleic acids from sera of cattle with bovine spongiform encephalopathy (BSE) and sera of cattle exposed to BSE.

PubMed

Schütz, Ekkehard; Urnovitz, Howard B; Iakoubov, Leonid; Schulz-Schaeffer, Walter; Wemheuer, Wilhelm; Brenig, Bertram

2005-07-01

Circulating nucleic acids (CNA) are known to be enriched in repetitive DNA sequences in humans. Here, bovine sera CNA were analyzed to determine if cell stress-related short interspersed nucleotide elements (SINEs) could be detected in sera from cattle associated with bovine spongiform encephalopathy (BSE). Nucleic acids were extracted, amplified, cloned, and sequenced from the sera of protease-resistant prion protein (PrP(res))-positive cattle (n = 2) and sera from BSE-cohort cows (n = 6); 150 out of 163 clones revealed the presence of, on average, an 80-bp sequence from the 3' region of Bov-tA SINE. A PCR protocol was developed that differentially identified SINE-associated CNA in BSE-exposed versus normal cattle. CNA were extracted from a serum vesicular fraction after controlled blood collection and processing procedures. Sera from four confirmed cases of BSE, 137 BSE-exposed cohort animals associated with eight confirmed BSE cases, and 845 healthy, PrP(res)-negative control cows were tested. All four sera from confirmed BSE cases were repeatedly reactive in the assay. BSE-exposed cohorts had a 100-fold higher occurrence of repeatedly reactive individuals per cohort (average = 63%; range = 33% to 91%), compared to healthy controls (average = 0.6%; P < 0.001). This study shows that BSE-confirmed and cohort animals possess a unique profile of SINE-associated serum CNA that can be utilized as a marker that highly correlates to BSE exposure.

Bov-tA Short Interspersed Nucleotide Element Sequences in Circulating Nucleic Acids from Sera of Cattle with Bovine Spongiform Encephalopathy (BSE) and Sera of Cattle Exposed to BSE

PubMed Central

Schütz, Ekkehard; Urnovitz, Howard B.; Iakoubov, Leonid; Schulz-Schaeffer, Walter; Wemheuer, Wilhelm; Brenig, Bertram

2005-01-01

Circulating nucleic acids (CNA) are known to be enriched in repetitive DNA sequences in humans. Here, bovine sera CNA were analyzed to determine if cell stress-related short interspersed nucleotide elements (SINEs) could be detected in sera from cattle associated with bovine spongiform encephalopathy (BSE). Nucleic acids were extracted, amplified, cloned, and sequenced from the sera of protease-resistant prion protein (PrPres)-positive cattle (n = 2) and sera from BSE-cohort cows (n = 6); 150 out of 163 clones revealed the presence of, on average, an 80-bp sequence from the 3′ region of Bov-tA SINE. A PCR protocol was developed that differentially identified SINE-associated CNA in BSE-exposed versus normal cattle. CNA were extracted from a serum vesicular fraction after controlled blood collection and processing procedures. Sera from four confirmed cases of BSE, 137 BSE-exposed cohort animals associated with eight confirmed BSE cases, and 845 healthy, PrPres-negative control cows were tested. All four sera from confirmed BSE cases were repeatedly reactive in the assay. BSE-exposed cohorts had a 100-fold higher occurrence of repeatedly reactive individuals per cohort (average = 63%; range = 33% to 91%), compared to healthy controls (average = 0.6%; P < 0.001). This study shows that BSE-confirmed and cohort animals possess a unique profile of SINE-associated serum CNA that can be utilized as a marker that highly correlates to BSE exposure. PMID:16002628

Pulsating aurora and cosmic noise absorption associated with growth-phase arcs

NASA Astrophysics Data System (ADS)

McKay, Derek; Partamies, Noora; Vierinen, Juha

2018-01-01

The initial stage of a magnetospheric substorm is the growth phase, which typically lasts 1-2 h. During the growth phase, an equatorward moving, east-west extended, optical auroral arc is observed. This is called a growth-phase arc. This work aims to characterize the optical emission and riometer absorption signatures associated with growth-phase arcs of isolated substorms. This is done using simultaneous all-sky camera and imaging riometer observations. The optical and riometric observations allow determination of the location of the precipitation within growth-phase arcs of low- (< 10 keV) and high- (> 10 keV) energy electrons, respectively. The observations indicate that growth-phase arcs have the following characteristics: 1. The peak of the cosmic noise absorption (CNA) arc is equatorward of the optical emission arc. This CNA is contained within the region of diffuse aurora on the equatorward side.2. Optical pulsating aurora are seen in the border region between the diffuse emission region on the equatorward side and the bright growth-phase arc on the poleward side. CNA is detected in the same region. 3. There is no evidence of pulsations in the CNA. 4. Once the equatorward drift starts, it proceeds at constant speed, with uniform separation between the growth-phase arc and CNA of 40 ± 10 km. Optical pulsating aurora are known to be prominent in the post-onset phase of a substorm. The fact that pulsations are also seen in a fairly localized region during the growth phase shows that the substorm expansion-phase dynamics are not required to closely precede the pulsating aurora.

The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups.

PubMed

Curtis, Christina; Shah, Sohrab P; Chin, Suet-Feung; Turashvili, Gulisa; Rueda, Oscar M; Dunning, Mark J; Speed, Doug; Lynch, Andy G; Samarajiwa, Shamith; Yuan, Yinyin; Gräf, Stefan; Ha, Gavin; Haffari, Gholamreza; Bashashati, Ali; Russell, Roslin; McKinney, Steven; Langerød, Anita; Green, Andrew; Provenzano, Elena; Wishart, Gordon; Pinder, Sarah; Watson, Peter; Markowetz, Florian; Murphy, Leigh; Ellis, Ian; Purushotham, Arnie; Børresen-Dale, Anne-Lise; Brenton, James D; Tavaré, Simon; Caldas, Carlos; Aparicio, Samuel

2012-04-18

The elucidation of breast cancer subgroups and their molecular drivers requires integrated views of the genome and transcriptome from representative numbers of patients. We present an integrated analysis of copy number and gene expression in a discovery and validation set of 997 and 995 primary breast tumours, respectively, with long-term clinical follow-up. Inherited variants (copy number variants and single nucleotide polymorphisms) and acquired somatic copy number aberrations (CNAs) were associated with expression in ~40% of genes, with the landscape dominated by cis- and trans-acting CNAs. By delineating expression outlier genes driven in cis by CNAs, we identified putative cancer genes, including deletions in PPP2R2A, MTAP and MAP2K4. Unsupervised analysis of paired DNA–RNA profiles revealed novel subgroups with distinct clinical outcomes, which reproduced in the validation cohort. These include a high-risk, oestrogen-receptor-positive 11q13/14 cis-acting subgroup and a favourable prognosis subgroup devoid of CNAs. Trans-acting aberration hotspots were found to modulate subgroup-specific gene networks, including a TCR deletion-mediated adaptive immune response in the ‘CNA-devoid’ subgroup and a basal-specific chromosome 5 deletion-associated mitotic network. Our results provide a novel molecular stratification of the breast cancer population, derived from the impact of somatic CNAs on the transcriptome.

The role of certified nursing assistants in nursing homes.

PubMed

Pennington, Karen; Scott, Jill; Magilvy, Kathy

2003-11-01

OBJECTIVE Pilot study to examine the experiences of the certified nursing assistants (CNAs) in Colorado nursing homes. CNAs provide 80% to 90% of the care to residents in nursing homes. Their reported turnover rate is as high as 400% in some studies, and the potential pool of CNAs is dwindling. As the demand for CNAs increases, their experiences must be understood to effectively address recruitment and retention issues. Minimally structured interviews of 12 CNAs in 6 Colorado nursing homes and observations of care provided were conducted. Atlas/Ti software was used as a data management tool for analyzing and coding data. The overriding theme that emerged from the interviews was "we love our jobs." Three patterns of thought and behavior emerged: attributes of the CNA, working conditions of the CNA, and future success of the CNA and the nursing home. Issues important to CNAs revolved around basic motivational factors, such as job enrichment opportunities, personal growth opportunities, recognition, responsibility, and sense of achievement. Leadership must become creative and build on that base, providing CNAs with job mobility, job enrichment opportunities, recognition, and increased job responsibility, producing positive outcomes not only for the CNA but also for the resident and the facility.

[Copy number alterations in adult patients with mature B acute lymphoblastic leukemia treated with specific immunochemotherapy].

PubMed

Ribera, Jordi; Zamora, Lurdes; García, Olga; Hernández-Rivas, Jesús-María; Genescà, Eulàlia; Ribera, Josep-Maria

2016-12-02

Unlike Burkitt lymphoma, molecular abnormalities other than C-MYC rearrangements have scarcely been studied in patients with mature B acute lymphoblastic leukemia (B-ALL). The aim of this study was to analyze the frequency and prognostic significance of copy number alterations (CNA) in genes involved in lymphoid differentiation, cell cycle and tumor suppression in adult patients with B-ALL. We have analyzed by multiplex ligation-dependent probe amplification the genetic material from bone marrow at diagnosis from 25 adult B-ALL patients treated with rituximab and specific chemotherapy. The most frequent CNA were alterations in the 14q32.33 region (11 cases, 44%) followed by alterations in the cell cycle regulator genes CDKN2A/B and RB1 (16%). No correlation between the presence of specific CNA and the clinical-biologic features or the response to therapy was found. The high frequency of CNA in the 14q32.33 region, CDKN2A/B and RB1 found in our study could contribute to the aggressiveness and invasiveness of mature B-ALL. Copyright © 2016 Elsevier España, S.L.U. All rights reserved.

First-principles investigation of the physical properties of cubic and orthorhombic phase Na3UO4

NASA Astrophysics Data System (ADS)

Chen, Haichuan; Tian, Wenyan

2017-11-01

The anisotropic elastic properties, Vickers hardness, Debye temperature and the minimum thermal conductivity of c-Na3UO4 and o-Na3UO4 have been investigated by means of the first principles calculations. The lattice parameters are in good agreement with the available experimental data and the theoretical results. The elastic constants satisfy the mechanical stability criteria show that both of them are mechanically stable. The value of B / G and Cauchy pressure reveal that the c-Na3UO4 holds a ductile behavior while the o-Na3UO4 behaves a brittle manner. The elastic anisotropy of c-Na3UO4 is less weak than that of o-Na3UO4. The hardness shows that both of them can be classified as ;soft materials;. Finally, the Debye temperature is 452.6 K and 388.4 K, and the minimum thermal conductivities kmin is 0.883 W m-1 K-1 and 0.753 W m-1 K-1 of c-Na3UO4 and o-Na3UO4, respectively. Due to relatively lower thermal conductivity, and thereby they are suitable to be used as thermal insulating materials.

2002 CNA Code of Ethics: some recommendations.

PubMed

Kikuchi, June F

2004-07-01

The Canadian Nurses Association (CNA) recently revised its 1997 Code of Ethics for Registered Nurses to reflect the context within which nurses practise today. Given the unprecedented changes that have taken place within the profession, healthcare and society, it was timely for the CNA to review and revise its Code. But the revisions were relatively minor; important problematic, substantive aspects of the Code were essentially left untouched and persist in the updated 2002 Code. In this paper, three of those aspects are examined and discussed: the 2002 Code's (a) definition of health and well-being, (b) notion of respect and (c) conception of justice. Recommendations are made. It is hoped that these comments will encourage nurse leaders in Canada to initiate discussion of the Code now, in preparation for its next planned revision in 2007.

Radicals and molecular products from the gas-phase pyrolysis of lignin model compounds. Cinnamyl alcohol

PubMed Central

Khachatryan, Lavrent; Xu, Meng-xia; Wu, Ang-jian; Pechagin, Mikhail; Asatryan, Rubik

2016-01-01

The experimental results on detection and identification of intermediate radicals and molecular products from gas-phase pyrolysis of cinnamyl alcohol (CnA), the simplest non-phenolic lignin model compound, over the temperature range of 400–800 °C are reported. The low temperature matrix isolation – electron paramagnetic resonance (LTMI-EPR) experiments along with the theoretical calculations, provided evidences on the generation of the intermediate carbon and oxygen centered as well as oxygen-linked, conjugated radicals. A mechanistic analysis is performed based on density functional theory to explain formation of the major products from CnA pyrolysis; cinnamaldehyde, indene, styrene, benzaldehyde, 1-propynyl benzene, and 2-propenyl benzene. The evaluated bond dissociation patterns and unimolecular decomposition pathways involve dehydrogenation, dehydration, 1,3-sigmatropic H-migration, 1,2-hydrogen shift, C—O and C—C bond cleavage processes. PMID:28344372

Abu Sayyaf Group (ASG): An Al-Qaeda Associate Case Study

DTIC Science & Technology

2017-10-01

completed in August 2017. In order to conduct this assessment, CNA used a comparative methodology that included eight case studies on groups affiliated...assessment, CNA used a comparative methodology that included eight case studies on groups affiliated or associated with Al-Qaeda. These case studies ...Case Study P. Kathleen Hammerberg and Pamela G. Faber With contributions from Alexander Powell October 2017 This work was performed

U.S. Navy Capstone Strategies and Concepts: Introduction, Background and Analyses

DTIC Science & Technology

2011-12-01

Zumwalt  Jun 1974 ADM James Holloway  Jul 1978 ADM Thomas Hayward  Jun 1982 ADM James Watkins  Jul 1986 ADM Carlisle Trost  Jun 1990 ADM Frank...RDML Bill Center USN (Ret) • Dr. Eugene Cobble (CNA) • CAPT Bud Cole USN (Ret) • Mr. Tim Colton • Dr. Greg Cox (CNA) • Hon. Seth Cropsey • RDML

Improving Naval Aviation Depot Responsiveness

DTIC Science & Technology

1992-01-01

for Naval Analyses (CNA) has researched the construc- tion of AVCALs (Evanovich, 1987; Evanovich and Measell , 1986). It produced a readiness-based AVCAL...improvements, a finding that is consistent with the CNA findings on readiness-based sparing AVCALs (Evanovich and Measell , 1986; Evanovich et al., 1987).3...Aviation Components: Contractor vs. Organic Repair, RAND, N-2225-NAVY, March 1985. Evanovich, Peter J., and Barbara H. Measell , Full Airwing

Applying geo-spatial analysis in community needs assessment: Implications for planning and prioritizing based on data.

PubMed

Baig, Kamran; Shaw-Ridley, Mary; Munoz, Oscar J

2016-10-01

Colonias are sub standardized and unincorporated areas located along the US-Mexico border, with severely lacking infrastructure. Residents have poor health and limited availability, accessibility and/or utilization of healthcare services in the region. Using 2006-2007 community needs assessment (CNA) surveys collected by the Center for Housing and Urban Development of Texas A&M University, 410 randomly selected surveys from Hidalgo County, Texas were analyzed. Descriptive and spatial analyses were performed and Odds ratio (OR) was calculated. Out of 410 surveys, 333 were geo-coded to identify areas most in need of dental and vision care. Two hospitals existed within 5 miles radius of the mean centers for the two areas. Distance to health care facility was not statistically predictive of the need of dental care OR=0.96 (95% CI=0.855-1.078, p value=0.492) and vision care OR=1.083 (95% CI=0.968-1.212, p value=0.164). Integrating spatial analysis and CNA enhances planning to improve service accessibility and utilization in underserved areas. Copyright © 2016 Elsevier Ltd. All rights reserved.

Evaluation of the Navys Sea/Shore Flow Policy

DTIC Science & Technology

2016-06-01

Std. Z39.18 i Abstract CNA developed an independent Discrete -Event Simulation model to evaluate and assess the effect of...a more steady manning level, but the variability remains, even if the system is optimized. In building a Discrete -Event Simulation model, we...steady-state model. In FY 2014, CNA developed a Discrete -Event Simulation model to evaluate the impact of sea/shore flow policy (the DES-SSF model

Insurgency in Greater Baluchistan: A CNA Small Group Discussion, March 29, 2013

DTIC Science & Technology

2013-06-01

Insurgency in Greater Baluchistan A CNA Small Group Discussion March 29, 2013 Cleared for public release DCP-2013-U-004988-Final... Baluchistan , one of the most remote and least developed areas of southwest Asia, stretches north from Karachi in Pakistan, along the arid and... Baluchistan and the implications for U.S. interests and regional stability. Bottom line up front  Successive generations of ethnic Baluch living along

Copy number aberrations landscape of a breast tumor, connection with the efficiency of neoadjuvant chemotherapy

NASA Astrophysics Data System (ADS)

Ibragimova, M. K.; Tsyganov, M. M.; Slonimskaya, E. M.; Litviakov, N. V.

2017-09-01

The research involved 80 patients diagnosed with breast cancer (BC). Each patient had their tumor biopsy material sampled before their treatment. We studied the tumor tissue using the CytoScan HD Array (Affymetrix, USA) microarray to evaluate the CNA landscape. We studied the frequency of segmental and numerical CNA occurrence, their association with the efficiency of neoadjuvant chemotherapy (NAC). We found that the biggest number of amplifications (with frequency over 60%) were found on in the following locuses; 1q32.1 1q32.3, 1q42.13, 1q42.2, 1q43. The biggest frequency of deletions (more than in 58% of the patients) was found in these locuses: 16q21, 16q23.2, 16q23.3, 17p12, 17p13.1. However, we found the locuses with full absence of segmental chromosome anomalies. We observed trisomy most frequently in the 7, 8, 12, and 17 chromosomes, and monosomy in the 3, 4, 9, 11, 18, and X-chromosomes. We demonstrated the connection between the high frequency of cytobands with CNA in the patients' tumors and the efficiency of NAC. We also identified the cytobands, whose CNA are linked to the response to NAC.

Certified Nurse Aide scope of practice: state-by-state differences in allowable delegated activities.

PubMed

McMullen, Tara L; Resnick, Barbara; Chin-Hansen, Jennie; Geiger-Brown, Jeanne M; Miller, Nancy; Rubenstein, Robert

2015-01-01

To gain a better understanding of the state-by-state differences in allowable delegated activities for Certified Nurse Aides (CNAs) working in long-term care settings, this exploratory descriptive study assessed what are the allowable tasks for CNAs based on findings from each state board of nursing. Specifically, findings from each state determined whether the care tasks allowed were consistent with those delineated by the 42 CFR § 483. This descriptive study included data drawn from all 50 states' regulatory offices or health care services agencies. Data were obtained from the regulations listed on each state's board of nursing, department of health, department of aging, department of health professions, department of commerce, and office of long-term care, among like agencies. The Code of Federal regulations (42 CFR § 483) listed 9 tasks that are allowable by each state. These tasks are identified as items 1 to 9: (1) personal care skills, (2) safety/emergency procedures, (3) basic nursing skills, (4) infection control, (5) communication and interpersonal skills, (6) care of cognitively impaired residents, (7) basic restorative care, (8) mental health and social service needs, and (9) residents' rights. Nine tasks delineated in the 42 CFR § 483 were identified as allowable in each state. On data analysis, it was found that 11 states noted that CNAs were able to perform workplace tasks that could be considered "expanded" care tasks, tasks beyond the basic care tasks listed in the 42 CFR § 483. Findings from this exploratory study aid in limiting the confusion around the application of workplace duties across states, providing a useful description of the care tasks CNAs are allowed to perform in an attempt to find uniformity state-by-state. Overall, states reported considering expanding the scope of practice or authorized duties for CNAs to strengthen patient care and safety. States may choose to expand CNA authorized duties so as to equip CNAs with specific training so that the CNA is able to provide a certain level of care when or if he or she is needed to do so. Without uniformity of CNA authorized duties, it is difficult to interpret whether expanding the scope of the CNA can result in outcomes such as improved patient care. State regulations vary and there were state boards of nursing that were not sure about the true extent of CNA workplace responsibilities. Copyright © 2015 AMDA – The Society for Post-Acute and Long-Term Care Medicine. Published by Elsevier Inc. All rights reserved.

Intramolecular amide bonds stabilize pili on the surface of bacilli

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

Budzik, Jonathan M.; Poor, Catherine B.; Faull, Kym F.

Gram-positive bacteria elaborate pili and do so without the participation of folding chaperones or disulfide bond catalysts. Sortases, enzymes that cut pilin precursors, form covalent bonds that link pilin subunits and assemble pili on the bacterial surface. We determined the x-ray structure of BcpA, the major pilin subunit of Bacillus cereus. The BcpA precursor encompasses 2 Ig folds (CNA{sub 2} and CNA{sub 3}) and one jelly-roll domain (XNA) each of which synthesizes a single intramolecular amide bond. A fourth amide bond, derived from the Ig fold of CNA{sub 1}, is formed only after pilin subunits have been incorporated into pili.more » We report that the domains of pilin precursors have evolved to synthesize a discrete sequence of intramolecular amide bonds, thereby conferring structural stability and protease resistance to pili.« less

On the meaning of meaning when being mean: commentary on Berkowitz's "on the consideration of automatic as well as controlled psychological processes in aggression".

PubMed

Dodge, Kenneth A

2008-01-01

Berkowitz (this issue) makes a cogent case for his cognitive neo-associationist (CNA) model that some aggressive behaviors occur automatically, emotionally, and through conditioned association with other stimuli. He also proposes that they can occur without "processing," that is, without meaning. He contrasts his position with that of social information processing (SIP) models, which he casts as positing only controlled processing mechanisms for aggressive behavior. However, both CNA and SIP models posit automatic as well as controlled processes in aggressive behavior. Most aggressive behaviors occur through automatic processes, which are nonetheless rule governed. SIP models differ from the CNA model in asserting the essential role of meaning (often through nonconscious, automatic, and emotional processes) in mediating the link between a stimulus and an angry aggressive behavioral response. Copyright 2008 Wiley-Liss, Inc.

Characteristics and Recruitment Paths of Certified Nursing Assistants in Rural and Urban Nursing Homes

ERIC Educational Resources Information Center

Probst, Janice C.; Baek, Jong-Deuk; Laditka, Sarah B.

2009-01-01

Context: Most nursing home care is provided by certified nursing assistants (CNAs), but little is known about rural CNAs. Purpose: To develop a representative geographic profile of the CNA workforce, focusing on paths leading to present job. Methods: Cross-sectional analysis of data from the 2004 National Nursing Assistant Survey (NNAS), a…

The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups

PubMed Central

Curtis, Christina; Shah, Sohrab P.; Chin, Suet-Feung; Turashvili, Gulisa; Rueda, Oscar M.; Dunning, Mark J.; Speed, Doug; Lynch, Andy G.; Samarajiwa, Shamith; Yuan, Yinyin; Gräf, Stefan; Ha, Gavin; Haffari, Gholamreza; Bashashati, Ali; Russell, Roslin; McKinney, Steven; Langerød, Anita; Green, Andrew; Provenzano, Elena; Wishart, Gordon; Pinder, Sarah; Watson, Peter; Markowetz, Florian; Murphy, Leigh; Ellis, Ian; Purushotham, Arnie; Børresen-Dale, Anne-Lise; Brenton, James D.; Tavaré, Simon; Caldas, Carlos; Aparicio, Samuel

2012-01-01

The elucidation of breast cancer subgroups and their molecular drivers requires integrated views of the genome and transcriptome from representative numbers of patients. We present an integrated analysis of copy number and gene expression in a discovery and validation set of 997 and 995 primary breast tumours, respectively, with long-term clinical follow-up. Inherited variants (copy number variants and single nucleotide polymorphisms) and acquired somatic copy number aberrations (CNAs) were associated with expression in ~40% of genes, with the landscape dominated by cis- and trans-acting CNAs. By delineating expression outlier genes driven in cis by CNAs, we identified putative cancer genes, including deletions in PPP2R2A, MTAP and MAP2K4. Unsupervised analysis of paired DNA–RNA profiles revealed novel subgroups with distinct clinical outcomes, which reproduced in the validation cohort. These include a high-risk, oestrogen-receptor-positive 11q13/14 cis-acting subgroup and a favourable prognosis subgroup devoid of CNAs. Trans-acting aberration hotspots were found to modulate subgroup-specific gene networks, including a TCR deletion-mediated adaptive immune response in the ‘CNA-devoid’ subgroup and a basal-specific chromosome 5 deletion-associated mitotic network. Our results provide a novel molecular stratification of the breast cancer population, derived from the impact of somatic CNAs on the transcriptome. PMID:22522925

CNA’s Integrated Ship Database, Fourth Quarter 2011 Update

DTIC Science & Technology

2012-09-01

CNA’s Integrated Ship Database Fourth Quarter 2011 Update Gregory N. Suess, Lynette A . McClain, and Rhea Stone CNA Interactive Software DIS-2012-U...194) during a replenishment at sea (RAS).” Navy.mil Official Website of the United States Navy, last accessed May 24, 2012, at http://www.navy.mil...that notwithstanding any other provision of law, no person shall be subject to any penalty for failing to comply with a collection of information if

GeneBreak: detection of recurrent DNA copy number aberration-associated chromosomal breakpoints within genes.

PubMed

van den Broek, Evert; van Lieshout, Stef; Rausch, Christian; Ylstra, Bauke; van de Wiel, Mark A; Meijer, Gerrit A; Fijneman, Remond J A; Abeln, Sanne

2016-01-01

Development of cancer is driven by somatic alterations, including numerical and structural chromosomal aberrations. Currently, several computational methods are available and are widely applied to detect numerical copy number aberrations (CNAs) of chromosomal segments in tumor genomes. However, there is lack of computational methods that systematically detect structural chromosomal aberrations by virtue of the genomic location of CNA-associated chromosomal breaks and identify genes that appear non-randomly affected by chromosomal breakpoints across (large) series of tumor samples. 'GeneBreak' is developed to systematically identify genes recurrently affected by the genomic location of chromosomal CNA-associated breaks by a genome-wide approach, which can be applied to DNA copy number data obtained by array-Comparative Genomic Hybridization (CGH) or by (low-pass) whole genome sequencing (WGS). First, 'GeneBreak' collects the genomic locations of chromosomal CNA-associated breaks that were previously pinpointed by the segmentation algorithm that was applied to obtain CNA profiles. Next, a tailored annotation approach for breakpoint-to-gene mapping is implemented. Finally, dedicated cohort-based statistics is incorporated with correction for covariates that influence the probability to be a breakpoint gene. In addition, multiple testing correction is integrated to reveal recurrent breakpoint events. This easy-to-use algorithm, 'GeneBreak', is implemented in R ( www.cran.r-project.org ) and is available from Bioconductor ( www.bioconductor.org/packages/release/bioc/html/GeneBreak.html ).

The adherent abilities of Clostridium perfringens strains are critical for the pathogenesis of avian necrotic enteritis.

PubMed

Wade, Ben; Keyburn, Anthony L; Haring, Volker; Ford, Mark; Rood, Julian I; Moore, Robert J

2016-12-25

Necrotic enteritis of poultry is an emerging disease of substantial economic importance, but aspects of the pathogenesis of this multi-factorial disease are still unclear. We recently demonstrated that the ability of avian strains of the causative bacterium, Clostridium perfringens, to bind to specific collagen types correlated strongly with their virulence and we postulated that binding of the pathogen to collagen types IV and V and gelatin may involve the putative adhesin-encoding gene cnaA, which is found in the VR-10B locus. In this study we have used site-directed mutagenesis to demonstrate that disruption of the cnaA gene leads to a reduction in the expression of the three genes immediately downstream of cnaA and reduced adherence to collagen types IV and V and gelatin. In addition, a cnaA mutant of strain EHE-NE18 was no longer capable of causing necrotic enteritis in a chicken disease induction model and had a significantly reduced ability to colonise the chicken intestinal mucosa. These results were confirmed by generating and analysing a similar mutant in an independent necrotic enteritis causing C. perfringens strain. This study expands our understanding of the mechanisms involved in necrotic enteritis pathogenesis by demonstrating the importance of C. perfringens adherence to extracellular matrix proteins. Copyright © 2016. Published by Elsevier B.V.

Single-Nucleotide Polymorphism Array-Based Karyotyping of Acute Promyelocytic Leukemia

PubMed Central

Gómez-Seguí, Inés; Sánchez-Izquierdo, Dolors; Barragán, Eva; Such, Esperanza; Luna, Irene; López-Pavía, María; Ibáñez, Mariam; Villamón, Eva; Alonso, Carmen; Martín, Iván; Llop, Marta; Dolz, Sandra; Fuster, Óscar; Montesinos, Pau; Cañigral, Carolina; Boluda, Blanca; Salazar, Claudia

2014-01-01

Acute promyelocytic leukemia (APL) is characterized by the t(15;17)(q22;q21), but additional chromosomal abnormalities (ACA) and other rearrangements can contribute in the development of the whole leukemic phenotype. We hypothesized that some ACA not detected by conventional techniques may be informative of the onset of APL. We performed the high-resolution SNP array (SNP-A) 6.0 (Affymetrix) in 48 patients diagnosed with APL on matched diagnosis and remission sample. Forty-six abnormalities were found as an acquired event in 23 patients (48%): 22 duplications, 23 deletions and 1 Copy-Neutral Loss of Heterozygocity (CN-LOH), being a duplication of 8(q24) (23%) and a deletion of 7(q33-qter) (6%) the most frequent copy-number abnormalities (CNA). Four patients (8%) showed CNAs adjacent to the breakpoints of the translocation. We compared our results with other APL series and found that, except for dup(8q24) and del(7q33-qter), ACA were infrequent (≤3%) but most of them recurrent (70%). Interestingly, having CNA or FLT3 mutation were mutually exclusive events. Neither the number of CNA, nor any specific CNA was associated significantly with prognosis. This study has delineated recurrent abnormalities in addition to t(15;17) that may act as secondary events and could explain leukemogenesis in up to 40% of APL cases with no ACA by conventional cytogenetics. PMID:24959826

Single-nucleotide polymorphism array-based karyotyping of acute promyelocytic leukemia.

PubMed

Gómez-Seguí, Inés; Sánchez-Izquierdo, Dolors; Barragán, Eva; Such, Esperanza; Luna, Irene; López-Pavía, María; Ibáñez, Mariam; Villamón, Eva; Alonso, Carmen; Martín, Iván; Llop, Marta; Dolz, Sandra; Fuster, Oscar; Montesinos, Pau; Cañigral, Carolina; Boluda, Blanca; Salazar, Claudia; Cervera, Jose; Sanz, Miguel A

2014-01-01

Acute promyelocytic leukemia (APL) is characterized by the t(15;17)(q22;q21), but additional chromosomal abnormalities (ACA) and other rearrangements can contribute in the development of the whole leukemic phenotype. We hypothesized that some ACA not detected by conventional techniques may be informative of the onset of APL. We performed the high-resolution SNP array (SNP-A) 6.0 (Affymetrix) in 48 patients diagnosed with APL on matched diagnosis and remission sample. Forty-six abnormalities were found as an acquired event in 23 patients (48%): 22 duplications, 23 deletions and 1 Copy-Neutral Loss of Heterozygocity (CN-LOH), being a duplication of 8(q24) (23%) and a deletion of 7(q33-qter) (6%) the most frequent copy-number abnormalities (CNA). Four patients (8%) showed CNAs adjacent to the breakpoints of the translocation. We compared our results with other APL series and found that, except for dup(8q24) and del(7q33-qter), ACA were infrequent (≤3%) but most of them recurrent (70%). Interestingly, having CNA or FLT3 mutation were mutually exclusive events. Neither the number of CNA, nor any specific CNA was associated significantly with prognosis. This study has delineated recurrent abnormalities in addition to t(15;17) that may act as secondary events and could explain leukemogenesis in up to 40% of APL cases with no ACA by conventional cytogenetics.

CYP2D6 polymorphisms as predictors of outcome in breast cancer patients treated with tamoxifen: expanded polymorphism coverage improves risk stratification.

PubMed

Schroth, Werner; Hamann, Ute; Fasching, Peter A; Dauser, Silke; Winter, Stefan; Eichelbaum, Michel; Schwab, Matthias; Brauch, Hiltrud

2010-09-01

This study aimed to validate matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS)/Taqman copy number assay (CNA) CYP2D6 genotyping by AmpliChip CYP450 Test for the prediction of tamoxifen metabolizer phenotypes in breast cancer, and to investigate the influence of CYP2D6 variant coverage on genotype-phenotype relationships and tamoxifen outcome. Hormone receptor-positive postmenopausal breast cancer patients (n = 492) treated with adjuvant tamoxifen, previously analyzed by MALDI-TOF MS/CNA, were reanalyzed by AmpliChip CYP450 Test and validated by independent methods. Cox proportional hazard ratios (HR) were calculated for recurrence of poor (PM) relative to extensive metabolizer (EM) phenotypes with increasing numbers of CYP2D6 variants. Kaplan-Meier distributions were calculated for different phenotype classifications. Concordance was 99.2% to 99.5% for CNA and 99.8% to 100% per CYP2D6 allele (*3, *4, *5, *9, *10, and *41). The prevalence of predicted phenotypes was 1.2% for ultrarapid metabolizer (UM), 37.2% for EM without variant, 43.5% for heterozygous EM, 9.7% for intermediate metabolizer (IM), and 8.3% for PM. Approximately, one third of patients were misclassified based on a *4 analysis only, but inclusion of all reduced-function alleles increased the PM-associated HR from 1.33 (P = 0.58) to 2.87 (P = 0.006). Kaplan-Meier analyses showed highest and lowest clinical benefit for UM and PM with respect to both the AmpliChip-based and a redefined phenotype assignment. The latter revealed significant allele-dose-dependent associations (P = 0.011) and largest effect size (HR(PM_EM) = 2.77; 95% confidence interval, 1.31-5.89). MALDI-TOF MS/CNA is suitable for accurate CYP2D6 genotyping. For tamoxifen pharmacogenetics, broad CYP2D6 allele coverage is recommended to reduce phenotype misclassification. Classification based on refined EM and reduced-function metabolizers is advisable. AACR.

Interplay between calcineurin and the Slt2 MAP-kinase in mediating cell wall integrity, conidiation and virulence in the insect fungal pathogen Beauveria bassiana.

PubMed

Huang, Shuaishuai; He, Zhangjiang; Zhang, Shiwei; Keyhani, Nemat O; Song, Yulin; Yang, Zhi; Jiang, Yahui; Zhang, Wenli; Pei, Yan; Zhang, Yongjun

2015-10-01

The entomopathogenic fungus, Beauveria bassiana, is of environmental and economic importance as an insect pathogen, currently used for the biological control of a number of pests. Cell wall integrity and conidiation are critical parameters for the ability of the fungus to infect insects and for production of the infectious propagules. The contribution of calcineurin and the Slt2 MAP kinase to cell wall integrity and development in B. bassiana was investigated. Gene knockouts of either the calcineurin CNA1 subunit or the Slt2 MAP kinase resulted in decreased tolerance to calcofluor white and high temperature. In contrast, the Δcna1 strain was more tolerant to Congo red but more sensitive to osmotic stress (NaCl, sorbitol) than the wild type, whereas the Δslt2 strain had the opposite phenotype. Changes in cell wall structure and composition were seen in the Δslt2 and Δcna1 strains during growth under cell wall stress as compared to the wild type. Both Δslt2 and Δcna1 strains showed significant alterations in growth, conidiation, and viability. Elevation of intracellular ROS levels, and decreased conidial hydrophobicity and adhesion to hydrophobic surfaces, were also seen for both mutants, as well as decreased virulence. Under cell wall stress conditions, inactivation of Slt2 significantly repressed CN-mediated phosphatase activity suggesting some level of cross talk between the two pathways. Comparative transcriptome profiling of the Δslt2 and Δcna1 strains revealed alterations in the expression of distinct gene sets, with overlap in transcripts involved in cell wall integrity, stress response, conidiation and virulence. These data illustrate convergent and divergent phenotypes and targets of the calcineurin and Slt2 pathways in B. bassiana. Copyright © 2015 Elsevier Inc. All rights reserved.

Tomorrow’s Handgun: Ensuring the Right Gun for All Military Law Enforcement Officers

DTIC Science & Technology

2016-02-01

www.military.com/equipment/m9-pistol. 23 Ibid. 24 Russell, Sara M. Soldier Perspectives on Small Arms in Combat. Tech. no. CRM D0015259.A2. Alexandria...pistol-of- choice-1749620057. Russell, Sara M. Soldier Perspectives on Small Arms in Combat. Tech. no. CRM D0015259.A2. Alexandria, VA: CNA...Tech. no. CRM D0015259.A2. Alexandria, VA: CNA, 2006. Print. "The Avalon Project: Laws of War - Declaration on the Use of Bullets Which Expand or

Effects of solid-medium type on routine identification of bacterial isolates by use of matrix-assisted laser desorption ionization-time of flight mass spectrometry.

PubMed

Anderson, Neil W; Buchan, Blake W; Riebe, Katherine M; Parsons, Lauren N; Gnacinski, Stacy; Ledeboer, Nathan A

2012-03-01

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is a rapid method for the identification of bacteria. Factors that may alter protein profiles, including growth conditions and presence of exogenous substances, could hinder identification. Bacterial isolates identified by conventional methods were grown on various media and identified using the MALDI Biotyper (Bruker Daltonics, Billerica, MA) using a direct smear method and an acid extraction method. Specimens included 23 Pseudomonas isolates grown on blood agar, Pseudocel (CET), and MacConkey agar (MAC); 20 Staphylococcus isolates grown on blood agar, colistin-nalidixic acid agar (CNA), and mannitol salt agar (MSA); and 25 enteric isolates grown on blood agar, xylose lysine deoxycholate agar (XLD), Hektoen enteric agar (HE), salmonella-shigella agar (SS), and MAC. For Pseudomonas spp., the identification rate to genus using the direct method was 83% from blood, 78% from MAC, and 94% from CET. For Staphylococcus isolates, the identification rate to genus using the direct method was 95% from blood, 75% from CNA, and 95% from MSA. For enteric isolates, the identification rate to genus using the direct method was 100% from blood, 100% from MAC, 100% from XLD, 92% from HE, and 87% from SS. Extraction enhanced identification rates. The direct method of MALDI-TOF analysis of bacteria from selective and differential media yields identifications of varied confidence. Notably, Staphylococci spp. from CNA exhibit low identification rates. Extraction enhances identification rates and is recommended for colonies from this medium.

Navy Manpower Planning

DTIC Science & Technology

2017-03-31

requirements based on valid, approved workload. • Link peacetime and mobilization manpower requirements. 16 Moreover, the purpose of the SMRD is to... research and policy; energy and environment; manpower management; acquisition and cost; infrastructure; and military readiness . CPP-2017 -U-015038-Final...CNA ANALYSIS & SOLUTIONS 31st March 2017 Subject: NAVY MANPOWER PLANNING MONOGRAPH Navy manpower planning is a rich and complex topic that has a

A cryptographic hash function based on chaotic network automata

NASA Astrophysics Data System (ADS)

Machicao, Jeaneth; Bruno, Odemir M.

2017-12-01

Chaos theory has been used to develop several cryptographic methods relying on the pseudo-random properties extracted from simple nonlinear systems such as cellular automata (CA). Cryptographic hash functions (CHF) are commonly used to check data integrity. CHF “compress” arbitrary long messages (input) into much smaller representations called hash values or message digest (output), designed to prevent the ability to reverse the hash values into the original message. This paper proposes a chaos-based CHF inspired on an encryption method based on chaotic CA rule B1357-S2468. Here, we propose an hybrid model that combines CA and networks, called network automata (CNA), whose chaotic spatio-temporal outputs are used to compute a hash value. Following the Merkle and Damgård model of construction, a portion of the message is entered as the initial condition of the network automata, so that the rest parts of messages are iteratively entered to perturb the system. The chaotic network automata shuffles the message using flexible control parameters, so that the generated hash value is highly sensitive to the message. As demonstrated in our experiments, the proposed model has excellent pseudo-randomness and sensitivity properties with acceptable performance when compared to conventional hash functions.

Effect of staff turnover on staffing: A closer look at registered nurses, licensed vocational nurses, and certified nursing assistants.

PubMed

Kash, Bita A; Castle, Nicholas G; Naufal, George S; Hawes, Catherine

2006-10-01

We examined the effects of facility and market-level characteristics on staffing levels and turnover rates for direct care staff, and we examined the effect of staff turnover on staffing levels. We analyzed cross-sectional data from 1,014 Texas nursing homes. Data were from the 2002 Texas Nursing Facility Medicaid Cost Report and the Area Resource File for 2003. After examining factors associated with staff turnover, we tested the significance and impact of staff turnover on staffing levels for registered nurses (RNs), licensed vocational nurses (LVNs) and certified nursing assistants (CNAs). All three staff types showed strong dependency on resources, such as reimbursement rates and facility payor mix. The ratio of contracted to employed nursing staff as well as RN turnover increased LVN turnover rates. CNA turnover was reduced by higher administrative expenditures and higher CNA wages. Turnover rates significantly reduced staffing levels for RNs and CNAs. LVN staffing levels were not affected by LVN turnover but were influenced by market factors such as availability of LVNs in the county and women in the labor force. Staffing levels are not always associated with staff turnover. We conclude that staff turnover is a predictor of RN and CNA staffing levels but that LVN staffing levels are associated with market factors rather than turnover. Therefore, it is important to focus on management initiatives that help reduce CNA and RN turnover and ultimately result in higher nurse staffing levels in nursing homes.

Integrated Analysis of Genome-wide Copy Number Alterations and Gene Expression in MSS, CIMP-negative Colon Cancer

PubMed Central

Loo, Lenora WM; Tiirikainen, Maarit; Cheng, Iona; Lum-Jones, Annette; Seifried, Ann; Church, James M; Gryfe, Robert; Weisenberger, Daniel J; Lindor, Noralane M; Gallinger, Steven; Haile, Robert W; Duggan, David J; Thibodeau, Stephen N; Casey, Graham; Le Marchand, Loïc

2014-01-01

Microsatellite stable (MSS), CpG island methylator phenotype (CIMP)-negative colorectal tumors, the most prevalent molecular subtype of colorectal cancer, are associated with extensive copy number alteration (CNA) events and aneuploidy. We report on the identification of characteristic recurrent CNA (with frequency >25%) events and associated gene expression profiles for a total of 40 paired tumor and adjacent normal colon tissues using genome-wide microarrays. We observed recurrent CNAs, namely gains at 1q, 7p, 7q, 8p12-11, 8q, 12p13, 13q, 20p, 20q, Xp, and Xq and losses at 1p36, 1p31, 1p21, 4p15-12, 4q12-35, 5q21-22, 6q26, 8p, 14q, 15q11-12, 17p, 18p, 18q, 21q21-22, and 22q. Within these genomic regions we identified 356 genes with significant differential expression (P<0.0001 and ±1.5 fold change) in the tumor compared to adjacent normal tissue. Gene ontology and pathway analyses indicated that many of these genes were involved in functional mechanisms that regulate cell cycle, cell death, and metabolism. An amplicon present in >70% of the tumor samples at 20q11-20q13 contained several cancer-related genes (AHCY, POFUT1, RPN2, TH1L and PRPF6) that were up-regulated and demonstrated a significant linear correlation (P<0.05) for gene dosage and gene expression. Copy number loss at 8p, a CNA associated with adenocarcinoma and poor prognosis, was observed in >50% of the tumor samples and demonstrated a significant linear correlation for gene dosage and gene expression for two potential tumor suppressor genes, MTUS1 (8p22) and PPP2CB (8p12). The results from our integration analysis illustrate the complex relationship between genomic alterations and gene expression in colon cancer. PMID:23341073

The shaping and functional consequences of the dosage effect landscape in multiple myeloma.

PubMed

Samur, Mehmet K; Shah, Parantu K; Wang, Xujun; Minvielle, Stéphane; Magrangeas, Florence; Avet-Loiseau, Hervé; Munshi, Nikhil C; Li, Cheng

2013-10-02

Multiple myeloma (MM) is a malignant proliferation of plasma B cells. Based on recurrent aneuploidy such as copy number alterations (CNAs), myeloma is divided into two subtypes with different CNA patterns and patient survival outcomes. How aneuploidy events arise, and whether they contribute to cancer cell evolution are actively studied. The large amount of transcriptomic changes resultant of CNAs (dosage effect) pose big challenges for identifying functional consequences of CNAs in myeloma in terms of specific driver genes and pathways. In this study, we hypothesize that gene-wise dosage effect varies as a result from complex regulatory networks that translate the impact of CNAs to gene expression, and studying this variation can provide insights into functional effects of CNAs. We propose gene-wise dosage effect score and genome-wide karyotype plot as tools to measure and visualize concordant copy number and expression changes across cancer samples. We find that dosage effect in myeloma is widespread yet variable, and it is correlated with gene expression level and CNA frequencies in different chromosomes. Our analysis suggests that despite the enrichment of differentially expressed genes between hyperdiploid MM and non-hyperdiploid MM in the trisomy chromosomes, the chromosomal proportion of dosage sensitive genes is higher in the non-trisomy chromosomes. Dosage-sensitive genes are enriched by genes with protein translation and localization functions, and dosage resistant genes are enriched by apoptosis genes. These results point to future studies on differential dosage sensitivity and resistance of pro- and anti-proliferation pathways and their variation across patients as therapeutic targets and prognosis markers. Our findings support the hypothesis that recurrent CNAs in myeloma are selected by their functional consequences. The novel dosage effect score defined in this work will facilitate integration of copy number and expression data for identifying driver genes in cancer genomics studies. The accompanying R code is available at http://www.canevolve.org/dosageEffect/.

The Education and Development of Strategic Planners in the Navy

DTIC Science & Technology

1990-12-01

MANAGEMENT .................. 23 C. SUBSEQUENT TOURS .......... .............. ....... 24 V. GRADUATE LEVEL EDUCATION FOR STRATEGIC PLANNERS .... 26 A...experience coded officers. A comparison was conducted in an attempt to determine any trends that may prove beneficial for creating better career management ...plans, which the Center for Naval Analysis (CNA) manages for OP-07 (Director of Naval Warfare) [Ref. i] In addition to the master plans, the CNO has

Clonal evolution in paired endometrial intraepithelial neoplasia/atypical hyperplasia and endometrioid adenocarcinoma.

PubMed

Russo, Mariano; Broach, James; Sheldon, Kathryn; Houser, Kenneth R; Liu, Dajiang J; Kesterson, Joshua; Phaeton, Rebecca; Hossler, Carrie; Hempel, Nadine; Baker, Maria; Newell, Jordan M; Zaino, Richard; Warrick, Joshua I

2017-09-01

Endometrial intraepithelial neoplasia (EIN) and atypical endometrial hyperplasia (AH) are histomorphologically defined precursors to endometrioid adenocarcinoma, which are unified as EIN/AH by the World Health Organization. EIN/AH harbors a constellation of molecular alterations similar to those found in endometrioid adenocarcinoma. However, the process of clonal evolution from EIN/AH to carcinoma is poorly characterized. To investigate, we performed next-generation sequencing, copy number alteration (CNA) analysis, and immunohistochemistry for mismatch repair protein expression on EIN/AH and endometrioid adenocarcinoma samples from 6 hysterectomy cases with spatially distinct EIN/AH and carcinoma. In evaluating all samples, EIN/AH and carcinoma did not differ in mutational burden, CNA burden, or specific genes mutated (all P>.1). All paired EIN/AH and carcinoma samples shared at least one identical somatic mutation, frequently in PI(3)K pathway members. Large CNAs (>10 genes in length) were identified in 83% of cases; paired EIN/AH and carcinoma samples shared at least one identical CNA in these cases. Mismatch repair protein expression matched in all paired EIN/AH and carcinoma samples. All paired EIN/AH and carcinoma samples had identical The Cancer Genome Atlas subtype, with 3 classified as "copy number low endometrioid" and 3 classified as "microsatellite instability hypermutated." Although paired EIN/AH and carcinoma samples were clonal, private mutations (ie, present in only one sample) were identified in EIN/AH and carcinoma in all cases, frequently in established cancer-driving genes. These findings indicate that EIN/AH gives rise to endometrioid adenocarcinoma by a complex process of subclone evolution, not a linear accumulation of molecular events. Copyright © 2017 Elsevier Inc. All rights reserved.

Pressure ulcer prevention in long-term-care facilities: a pilot study implementing standardized nurse aide documentation and feedback reports.

PubMed

Horn, Susan D; Sharkey, Siobhan S; Hudak, Sandra; Gassaway, Julie; James, Roberta; Spector, William

2010-03-01

To design and facilitate implementation of practice-based evidence changes associated with decreases in pressure ulcer (PrU) development in long-term-care (LTC) facilities and promote these practices as part of routine care. Pre/post observational study. Frail older adult residents in 11 US LTC facilities. Project facilitators assisted frontline multidisciplinary teams (certified nurse aides [CNAs], nurses, and dietitians/dietary aides) to develop streamlined standardized CNA documentation and weekly reports to identify high-risk residents and to integrate clinical reports into day-to-day practice and clinical decision making. The program was called "Real-Time Optimal Care Plans for Nursing Home QI" (Real-Time). Prevalence of PrUs using Centers for Medicare & Medicaid Services (CMS) quality measures (QMs), number of in-house-acquired PrUs, and number and completeness of CNA documentation forms. Seven study LTC facilities that reported data to CMS experienced a combined 33% (SD, 36.1%) reduction in the CMS high-risk PrU QM in 18 months and reduction in newly occurring PrUs (number of ulcers in the fourth quarter of 2003: range, 2-19; and in the third quarter of 2005: range, 1-6). Five of these LTC facilities that fully implemented Real-Time experienced a combined 48.1% (SD, 23.4%) reduction in the CMS high-risk PrU QM. Ten facilities reduced by an average of 2 to 5 their number of CNA documentation forms; CNA weekly documentation completeness reached a consistent level of 90% to 95%, and 8 facilities integrated the use of 2 to 4 weekly project reports in routine clinical decision making. Quality improvement efforts that provide access to focused and timely clinical information, facilitate change, and promote staff working together in multidisciplinary teams impacted clinical outcomes. Prevention of PrUs showed a trend of improvement in facilities that fully integrated tools to identify high-risk residents into day-to-day practice. CNA documentation facilitated better information for clinical decision making. More than 70 additional LTC facilities across the United States are implementing this QI program.

Vitamin C and sodium bicarbonate enhance the antioxidant ability of H9C2 cells and induce HSPs to relieve heat stress.

PubMed

Yin, Bin; Tang, Shu; Sun, Jiarui; Zhang, Xiaohui; Xu, Jiao; Di, Liangjiao; Li, Zhihong; Hu, Yurong; Bao, Endong

2018-02-13

Heat stress is exacerbated by global warming and affects human and animal health, leading to heart damage caused by imbalances in reactive oxygen species (ROS) and the antioxidant system, acid-base chemistry, electrolytes and respiratory alkalosis. Vitamin C scavenges excess ROS, and sodium bicarbonate maintains acid-base and electrolyte balance, and alleviates respiratory alkalosis. Herein, we explored the ability of vitamin C alone and in combination with equimolar sodium bicarbonate (Vitamin C-Na) to stimulate endogenous antioxidants and heat shock proteins (HSPs) to relieve heat stress in H9C2 cells. Control, vitamin C (20 μg/ml vitamin C for 16 h) and vitamin C-Na (20 μg/ml vitamin C-Na for 16 h) groups were heat-stressed for 1, 3 or 5 h. Granular and vacuolar degeneration, karyopyknosis and damage to nuclei and mitochondria were clearly reduced in treatment groups, as were apoptosis, lactate dehydrogenase activity and ROS and malondialdehyde levels, while superoxide dismutase activity was increased. Additionally, CRYAB, Hsp27, Hsp60 and Hsp70 mRNA levels were upregulated at 3 h (p < 0.01), and protein levels were increased for CRYAB at 0 h (p < 0.05) and 1 h (p < 0.01), and for Hsp70 at 3 and 5 h (p < 0.01). Thus, pre-treatment with vitamin C or vitamin C-Na might protect H9C2 cells against heat damage by enhancing the antioxidant ability and upregulating CRYAB and Hsp70.

Comparison between POES energetic electron precipitation observations and riometer absorptions: Implications for determining true precipitation fluxes

NASA Astrophysics Data System (ADS)

Rodger, Craig J.; Kavanagh, Andrew J.; Clilverd, Mark A.; Marple, Steve R.

2013-12-01

electron precipitation (EEP) impacts the chemistry of the middle atmosphere with growing evidence of coupling to surface temperatures at high latitudes. To better understand this link, it is essential to have realistic observations to properly characterize precipitation and which can be incorporated into chemistry-climate models. The Polar-orbiting Operational Environmental Satellite (POES) detectors measure precipitating particles but only integral fluxes and only in a fraction of the bounce loss cone. Ground-based riometers respond to precipitation from the whole bounce loss cone; they measure the cosmic radio noise absorption (CNA), a qualitative proxy with scant direct information on the energy flux of EEP. POES observations should have a direct relationship with ΔCNA and comparing the two will clarify their utility in studies of atmospheric change. We determined ionospheric changes produced by the EEP measured by the POES spacecraft in ~250 overpasses of an imaging riometer in northern Finland. The ΔCNA modeled from the POES data is 10-15 times less than the observed ΔCNA when the >30 keV flux is reported as <106 cm-2 s-1 sr-1. Above this level, there is relatively good agreement between the space-based and ground-based measurements. The discrepancy occurs mostly during periods of low geomagnetic activity, and we contend that weak diffusion is dominating the pitch angle scattering into the bounce loss cone at these times. A correction to the calculation using measurements of the trapped flux considerably reduces the discrepancy and provides further support to our hypothesis that weak diffusion leads to underestimates of the EEP.

TITAN: inference of copy number architectures in clonal cell populations from tumor whole-genome sequence data

PubMed Central

Roth, Andrew; Khattra, Jaswinder; Ho, Julie; Yap, Damian; Prentice, Leah M.; Melnyk, Nataliya; McPherson, Andrew; Bashashati, Ali; Laks, Emma; Biele, Justina; Ding, Jiarui; Le, Alan; Rosner, Jamie; Shumansky, Karey; Marra, Marco A.; Gilks, C. Blake; Huntsman, David G.; McAlpine, Jessica N.; Aparicio, Samuel

2014-01-01

The evolution of cancer genomes within a single tumor creates mixed cell populations with divergent somatic mutational landscapes. Inference of tumor subpopulations has been disproportionately focused on the assessment of somatic point mutations, whereas computational methods targeting evolutionary dynamics of copy number alterations (CNA) and loss of heterozygosity (LOH) in whole-genome sequencing data remain underdeveloped. We present a novel probabilistic model, TITAN, to infer CNA and LOH events while accounting for mixtures of cell populations, thereby estimating the proportion of cells harboring each event. We evaluate TITAN on idealized mixtures, simulating clonal populations from whole-genome sequences taken from genomically heterogeneous ovarian tumor sites collected from the same patient. In addition, we show in 23 whole genomes of breast tumors that the inference of CNA and LOH using TITAN critically informs population structure and the nature of the evolving cancer genome. Finally, we experimentally validated subclonal predictions using fluorescence in situ hybridization (FISH) and single-cell sequencing from an ovarian cancer patient sample, thereby recapitulating the key modeling assumptions of TITAN. PMID:25060187

Single-cell sequencing deciphers a convergent evolution of copy number alterations from primary to circulating tumor cells.

PubMed

Gao, Yan; Ni, Xiaohui; Guo, Hua; Su, Zhe; Ba, Yi; Tong, Zhongsheng; Guo, Zhi; Yao, Xin; Chen, Xixi; Yin, Jian; Yan, Zhao; Guo, Lin; Liu, Ying; Bai, Fan; Xie, X Sunney; Zhang, Ning

2017-08-01

Copy number alteration (CNA) is a major contributor to genome instability, a hallmark of cancer. Here, we studied genomic alterations in single primary tumor cells and circulating tumor cells (CTCs) from the same patient. Single-nucleotide variants (SNVs) in single cells from both samples occurred sporadically, whereas CNAs among primary tumor cells emerged accumulatively rather than abruptly, converging toward the CNA in CTCs. Focal CNAs affecting the MYC gene and the PTEN gene were observed only in a minor portion of primary tumor cells but were present in all CTCs, suggesting a strong selection toward metastasis. Single-cell structural variant (SV) analyses revealed a two-step mechanism, a complex rearrangement followed by gene amplification, for the simultaneous formation of anomalous CNAs in multiple chromosome regions. Integrative CNA analyses of 97 CTCs from 23 patients confirmed the convergence of CNAs and revealed single, concurrent, and mutually exclusive CNAs that could be the driving events in cancer metastasis. © 2017 Gao et al.; Published by Cold Spring Harbor Laboratory Press.

Littoral Combat Ship Open Ocean Anti-Submarine Warfare

DTIC Science & Technology

2014-06-01

maintain stealth and its defense in order to properly conduct an attack on a surface vessel (Sternhell and Thorndike 2014, 102). This statement...its target, the surface combatants can counter by increasing their speed (Sternhell and Thorndike 2014). While the maximum speed of the current...120316_PS.pdf Sternhell, Charles M, and Alan M Thorndike . 2014. “Antisubmarine Warfare in World War II.” CNA Analysis & Solutions. Accessed April 14, 2014

Small-scale nuclear reactors for remote military operations: opportunities and challenges

DTIC Science & Technology

2015-08-25

study – Report was published in March 2011  CNA study identified challenges to deploy small modular reactors (SMRs) at a base – Identified First-of...forward operating bases. The availability of deployable, cost-effective, regulated, and secure small modular reactors with a modest output electrical...defense committees on the challenges, operational requirements, constraints, cost, and life cycle analysis for a small modular reactor of less than 10

CNA’s Integrated Ship Database: Third Quarter CY 2012 Update

DTIC Science & Technology

2013-11-01

rogram!- -;OJ"’T’-" A "’K"C~¥-go"Shi"~P:----------------t---’~;;1~ ® T- AKR Veh icle-Car o 9 S T- ADT Tran rt 0i1er 1 9 Mitita.y Sealift Command (MSC). in...CNA’s Integrated Ship Database Third Quarter CY 2012 Update Gregory N. Suess • Lynette A . McClain • Linette O. Neal CNA Interactive Software DIS...law, no person shall be subject to a penalty for failing to comply with a collection of information if it does not display a currently valid OMB

CNA’s Integrated Ship Database, Fourth Quarter 2011 Update

DTIC Science & Technology

2012-09-01

AKR300 G T-AKR301 G T-AKR302 8 T-AKR303 A 8 T-AKR304 G T-AKR305 G T-AKR30S 8 T- AKR 31l R - G T- AKR 312 G T- AKR 313 8 T- AKR 314 G T- AKR 315...CNA’s Integrated Ship Database Fourth Quarter 2011 Update Gregory N. Suess, Lynette A . McClain, and Rhea Stone CNA Interactive Software DIS-2012-U...no person shall be subject to a penalty for failing to comply with a collection of information if it does not display a currently valid OMB control

Dioxaphosphorinane-constrained nucleic Acid dinucleotides as tools for structural tuning of nucleic acids.

PubMed

Catana, Dan-Andrei; Renard, Brice-Loïc; Maturano, Marie; Payrastre, Corinne; Tarrat, Nathalie; Escudier, Jean-Marc

2012-01-01

We describe a rational approach devoted to modulate the sugar-phosphate backbone geometry of nucleic acids. Constraints were generated by connecting one oxygen of the phosphate group to a carbon of the sugar moiety. The so-called dioxaphosphorinane rings were introduced at key positions along the sugar-phosphate backbone allowing the control of the six-torsion angles α to ζ defining the polymer structure. The syntheses of all the members of the D-CNA family are described, and we emphasize the effect on secondary structure stabilization of a couple of diastereoisomers of α,β-D-CNA exhibiting wether B-type canonical values or not.

TITAN: inference of copy number architectures in clonal cell populations from tumor whole-genome sequence data.

PubMed

Ha, Gavin; Roth, Andrew; Khattra, Jaswinder; Ho, Julie; Yap, Damian; Prentice, Leah M; Melnyk, Nataliya; McPherson, Andrew; Bashashati, Ali; Laks, Emma; Biele, Justina; Ding, Jiarui; Le, Alan; Rosner, Jamie; Shumansky, Karey; Marra, Marco A; Gilks, C Blake; Huntsman, David G; McAlpine, Jessica N; Aparicio, Samuel; Shah, Sohrab P

2014-11-01

The evolution of cancer genomes within a single tumor creates mixed cell populations with divergent somatic mutational landscapes. Inference of tumor subpopulations has been disproportionately focused on the assessment of somatic point mutations, whereas computational methods targeting evolutionary dynamics of copy number alterations (CNA) and loss of heterozygosity (LOH) in whole-genome sequencing data remain underdeveloped. We present a novel probabilistic model, TITAN, to infer CNA and LOH events while accounting for mixtures of cell populations, thereby estimating the proportion of cells harboring each event. We evaluate TITAN on idealized mixtures, simulating clonal populations from whole-genome sequences taken from genomically heterogeneous ovarian tumor sites collected from the same patient. In addition, we show in 23 whole genomes of breast tumors that the inference of CNA and LOH using TITAN critically informs population structure and the nature of the evolving cancer genome. Finally, we experimentally validated subclonal predictions using fluorescence in situ hybridization (FISH) and single-cell sequencing from an ovarian cancer patient sample, thereby recapitulating the key modeling assumptions of TITAN. © 2014 Ha et al.; Published by Cold Spring Harbor Laboratory Press.

A safe and reliable neutralization assay based on pseudovirus to measure neutralizing antibody titer against poliovirus.

PubMed

Liu, Shaohua; Song, Dongmei; Bai, Han; Lu, Weiwei; Dai, Xinxian; Hao, Chunsheng; Zhang, Zhongyang; Guo, Huijie; Zhang, Yue; Li, Xiuling

2017-12-01

With the promotion of inactivated poliomyelitis vaccine (IPV) and live attenuated oral poliomyelitis vaccine (OPV), the global reported cases of poliomyelitis have reduced sharply from 0.35 million in 1988 to 74 in 2015. The Polio Eradication & Endgame Strategic Plan published by WHO in 2013 included the strategy of implementation of poliovirus safe handling and containment measures to minimize the risks of facility-associated reintroduction of virus into the polio-free community to prevent the re-import of poliovirus. Toward this strategy, we produced replication-incompetent pseudovirus of poliovirus type 1, 2, 3 attenuated strains by constructing poliovirus capsid expression vectors and poliovirus replicon then transfecting HEK293T cells and developed a pseudovirus-based neutralization assay (pNA) to determine neutralizing antibody titer which is more secure, time-saving and reliable than conventional neutralization assay (cNA). By using anti-poliovirus rat serum, we demonstrated excellent correlation between neutralizing antibody titers measured by cNA and pNA. It was concluded that pNA can be a potential alternative to replace cNA as a safe and time-saving system for titer determination after live poliovirus's safekeeping. © 2017 Wiley Periodicals, Inc.

Comparison of different sampling techniques and of different culture methods for detection of group B streptococcus carriage in pregnant women.

PubMed

El Aila, Nabil A; Tency, Inge; Claeys, Geert; Saerens, Bart; Cools, Piet; Verstraelen, Hans; Temmerman, Marleen; Verhelst, Rita; Vaneechoutte, Mario

2010-09-29

Streptococcus agalactiae (group B streptococcus; GBS) is a significant cause of perinatal and neonatal infections worldwide. To detect GBS colonization in pregnant women, the CDC recommends isolation of the bacterium from vaginal and anorectal swab samples by growth in a selective enrichment medium, such as Lim broth (Todd-Hewitt broth supplemented with selective antibiotics), followed by subculture on sheep blood agar. However, this procedure may require 48 h to complete. We compared different sampling and culture techniques for the detection of GBS. A total of 300 swabs was taken from 100 pregnant women at 35-37 weeks of gestation. For each subject, one rectovaginal, one vaginal and one rectal ESwab were collected. Plating onto Columbia CNA agar (CNA), group B streptococcus differential agar (GBSDA) (Granada Medium) and chromID Strepto B agar (CA), with and without Lim broth enrichment, were compared. The isolates were confirmed as S. agalactiae using the CAMP test on blood agar and by molecular identification with tDNA-PCR or by 16S rRNA gene sequence determination. The overall GBS colonization rate was 22%. GBS positivity for rectovaginal sampling (100%) was significantly higher than detection on the basis of vaginal sampling (50%), but not significantly higher than for rectal sampling (82%). Direct plating of the rectovaginal swab on CNA, GBSDA and CA resulted in detection of 59, 91 and 95% of the carriers, respectively, whereas subculturing of Lim broth yielded 77, 95 and 100% positivity, respectively. Lim broth enrichment enabled the detection of only one additional GBS positive subject. There was no significant difference between GBSDA and CA, whereas both were more sensitive than CNA. Direct culture onto GBSDA or CA (91 and 95%) detected more carriers than Lim broth enrichment and subculture onto CNA (77%). One false negative isolate was observed on GBSDA, and three false positives on CA. In conclusion, rectovaginal sampling increased the number GBS positive women detected, compared to vaginal and/or rectal sampling. Direct plating on CA and/or GBSDA provided rapid detection of GBS that was at least as sensitive and specific as the CDC recommended method of Lim broth subcultured onto non chromogenic agar.

Global analysis of community-associated methicillin-resistant Staphylococcus aureus exoproteins reveals molecules produced in vitro and during infection

PubMed Central

Burlak, Christopher; Hammer, Carl H; Robinson, Mary-Ann; Whitney, Adeline R; McGavin, Martin J; Kreiswirth, Barry N; DeLeo, Frank R

2007-01-01

Community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) is a threat to human health worldwide. Although progress has been made, mechanisms of CA-MRSA pathogenesis are poorly understood and a comprehensive analysis of CA-MRSA exoproteins has not been conducted. To address that deficiency, we used proteomics to identify exoproteins made by MW2 (USA400) and LAC (USA300) during growth in vitro. Two hundred and fifty unique exoproteins were identified by 2-dimensional gel electrophoresis coupled with automated direct infusion-tandem mass spectrometry (ADI-MS/MS) analysis. Eleven known virulence-related exoproteins differed in abundance between the strains, including alpha-haemolysin (Hla), collagen adhesin (Cna), staphylokinase (Sak), coagulase (Coa), lipase (Lip), enterotoxin C3 (Sec3), enterotoxin Q (Seq), V8 protease (SspA) and cysteine protease (SspB). Mice infected with MW2 or LAC produced antibodies specific for known or putative virulence factors, such as autolysin (Atl), Cna, Ear, ferritin (Ftn), Lip, 1-phosphatidylinositol phosphodiesterase (Plc), Sak, Sec3 and SspB, indicating the exoproteins are made during infection in vivo. We used confocal microscopy to demonstrate aureolysin (Aur), Hla, SspA and SspB are produced following phagocytosis by human neutrophils, thereby linking exoprotein production in vitro with that during host–pathogen interaction. We conclude that the exoproteins identified herein likely account in part for the success of CA-MRSA as a human pathogen. PMID:17217429

Identification of constrained cancer driver genes based on mutation timing.

PubMed

Sakoparnig, Thomas; Fried, Patrick; Beerenwinkel, Niko

2015-01-01

Cancer drivers are genomic alterations that provide cells containing them with a selective advantage over their local competitors, whereas neutral passengers do not change the somatic fitness of cells. Cancer-driving mutations are usually discriminated from passenger mutations by their higher degree of recurrence in tumor samples. However, there is increasing evidence that many additional driver mutations may exist that occur at very low frequencies among tumors. This observation has prompted alternative methods for driver detection, including finding groups of mutually exclusive mutations and incorporating prior biological knowledge about gene function or network structure. Dependencies among drivers due to epistatic interactions can also result in low mutation frequencies, but this effect has been ignored in driver detection so far. Here, we present a new computational approach for identifying genomic alterations that occur at low frequencies because they depend on other events. Unlike passengers, these constrained mutations display punctuated patterns of occurrence in time. We test this driver-passenger discrimination approach based on mutation timing in extensive simulation studies, and we apply it to cross-sectional copy number alteration (CNA) data from ovarian cancer, CNA and single-nucleotide variant (SNV) data from breast tumors and SNV data from colorectal cancer. Among the top ranked predicted drivers, we find low-frequency genes that have already been shown to be involved in carcinogenesis, as well as many new candidate drivers. The mutation timing approach is orthogonal and complementary to existing driver prediction methods. It will help identifying from cancer genome data the alterations that drive tumor progression.

Identification of Constrained Cancer Driver Genes Based on Mutation Timing

PubMed Central

Sakoparnig, Thomas; Fried, Patrick; Beerenwinkel, Niko

2015-01-01

Cancer drivers are genomic alterations that provide cells containing them with a selective advantage over their local competitors, whereas neutral passengers do not change the somatic fitness of cells. Cancer-driving mutations are usually discriminated from passenger mutations by their higher degree of recurrence in tumor samples. However, there is increasing evidence that many additional driver mutations may exist that occur at very low frequencies among tumors. This observation has prompted alternative methods for driver detection, including finding groups of mutually exclusive mutations and incorporating prior biological knowledge about gene function or network structure. Dependencies among drivers due to epistatic interactions can also result in low mutation frequencies, but this effect has been ignored in driver detection so far. Here, we present a new computational approach for identifying genomic alterations that occur at low frequencies because they depend on other events. Unlike passengers, these constrained mutations display punctuated patterns of occurrence in time. We test this driver–passenger discrimination approach based on mutation timing in extensive simulation studies, and we apply it to cross-sectional copy number alteration (CNA) data from ovarian cancer, CNA and single-nucleotide variant (SNV) data from breast tumors and SNV data from colorectal cancer. Among the top ranked predicted drivers, we find low-frequency genes that have already been shown to be involved in carcinogenesis, as well as many new candidate drivers. The mutation timing approach is orthogonal and complementary to existing driver prediction methods. It will help identifying from cancer genome data the alterations that drive tumor progression. PMID:25569148

Genome-wide comparison of paired fresh frozen and formalin-fixed paraffin-embedded gliomas by custom BAC and oligonucleotide array comparative genomic hybridization: facilitating analysis of archival gliomas.

PubMed

Mohapatra, Gayatry; Engler, David A; Starbuck, Kristen D; Kim, James C; Bernay, Derek C; Scangas, George A; Rousseau, Audrey; Batchelor, Tracy T; Betensky, Rebecca A; Louis, David N

2011-04-01

Array comparative genomic hybridization (aCGH) is a powerful tool for detecting DNA copy number alterations (CNA). Because diffuse malignant gliomas are often sampled by small biopsies, formalin-fixed paraffin-embedded (FFPE) blocks are often the only tissue available for genetic analysis; FFPE tissues are also needed to study the intratumoral heterogeneity that characterizes these neoplasms. In this paper, we present a combination of evaluations and technical advances that provide strong support for the ready use of oligonucleotide aCGH on FFPE diffuse gliomas. We first compared aCGH using bacterial artificial chromosome (BAC) arrays in 45 paired frozen and FFPE gliomas, and demonstrate a high concordance rate between FFPE and frozen DNA in an individual clone-level analysis of sensitivity and specificity, assuring that under certain array conditions, frozen and FFPE DNA can perform nearly identically. However, because oligonucleotide arrays offer advantages to BAC arrays in genomic coverage and practical availability, we next developed a method of labeling DNA from FFPE tissue that allows efficient hybridization to oligonucleotide arrays. To demonstrate utility in FFPE tissues, we applied this approach to biphasic anaplastic oligoastrocytomas and demonstrate CNA differences between DNA obtained from the two components. Therefore, BAC and oligonucleotide aCGH can be sensitive and specific tools for detecting CNAs in FFPE DNA, and novel labeling techniques enable the routine use of oligonucleotide arrays for FFPE DNA. In combination, these advances should facilitate genome-wide analysis of rare, small and/or histologically heterogeneous gliomas from FFPE tissues.

A Simulation Analysis of Work Based Navy Manpower Requirements

DTIC Science & Technology

2012-09-01

Workweek is also the subject of greater discussion in the 2002 CNA study. At the time, the Navy Standard Workweek was 67 hours of...policies, states that the Navy Standard Workweek includes 8 hours of sleep a day (Navy, 2007). To properly model this while also treating...system during these non-scheduled hours . Figure 4 shows an example of a sailor’s schedule as built into Arena. The graph’s x-axis represents the

In vitro mutagenicity, NMR metabolite characterization of azo and triphenylmethanes dyes by adherents bacteria and the role of the "cna" adhesion gene in activated sludge.

PubMed

Ayed, Lamia; Bakir, Karima; Ben Mansour, Hedi; Hammami, Saousen; Cheref, Abdelkrim; Bakhrouf, Amina

2017-02-01

Staphylococcus aureus, showing the greatest decolorization ability, was further investigated for Methyl Red (MR) Congo Red (CR), Crystal Violet (CV) and Malachite Green (MG) decolorization using response surface methodology (RSM). The chemometric methods use, based on statistical design of experiments (DOEs) such as RSM is becoming increasingly widespread in several sciences such as analytical chemistry, engineering and environmental chemistry. Stapphylococcus aureus ATCC 25923, Stapphylococcus aureus (S1) and Stapphylococcus aureus (S2), were isolated from textile wastewater plant located in KsarHellal, Tunisia and were tested for their decolorization capacity. PCR technique was utilized to identify the 3 bacterial strains and to detect the adhesin gene "cna". Biodegradation of MR, CR, CV and MG (750 ppm), were investigated under shaking condition in Mineral Salt Medium (MSM) solution at pH 7.5 and temperature 30 °C, using a 3.7 × 10 5  CFU/ml as inoculum size. Our results showed that Staphylococcus aureus had a high decolorization capacity. Nuclear magnetic resonance (NMR) spectroscopy analysis confirmed the biodegradation of dyes. The four dyes mutagenicity with the S9 metabolizing system decreased significantly after biodegradation and totally disappeared. Nuclear magnetic resonance (NMR) spectroscopy analysis confirmed the biodegradation of dyes. Copyright © 2016 Elsevier Ltd. All rights reserved.

Identification of Novel Genomic Aberrations in AML-M5 in a Level of Array CGH

PubMed Central

Zhang, Rui; Lee, Ji-Yun; Wang, Xianfu; Xu, Weihong; Hu, Xiaoxia; Lu, Xianglan; Niu, Yimeng; Tang, Rurong; Li, Shibo; Li, Yan

2014-01-01

To assess the possible existence of unbalanced chromosomal abnormalities and delineate the characterization of copy number alterations (CNAs) of acute myeloid leukemia-M5 (AML-M5), R-banding karyotype, oligonucelotide array CGH and FISH were performed in 24 patients with AML-M5. A total of 117 CNAs with size ranging from 0.004 to 146.263 Mb was recognized in 12 of 24 cases, involving all chromosomes other than chromosome 1, 4, X and Y. Cryptic CNAs with size less than 5 Mb accounted for 59.8% of all the CNAs. 12 recurrent chromosomal alterations were mapped. Seven out of them were described in the previous AML studies and five were new candidate AML-M5 associated CNAs, including gains of 3q26.2-qter and 13q31.3 as well as losses of 2q24.2, 8p12 and 14q32. Amplication of 3q26.2-qter was the sole large recurrent chromosomal anomaly and the pathogenic mechanism in AML-M5 was possibly different from the classical recurrent 3q21q26 abnormality in AML. As a tumor suppressor gene, FOXN3, was singled out from the small recurrent CNA of 14q32, however, it is proved that deletion of FOXN3 is a common marker of myeloid leukemia rather than a specific marker for AML-M5 subtype. Moreover, the concurrent amplication of MLL and deletion of CDKN2A were noted and it might be associated with AML-M5. The number of CNA did not show a significant association with clinico-biological parameters and CR number of the 22 patients received chemotherapy. This study provided the evidence that array CGH served as a complementary platform for routine cytogenetic analysis to identify those cryptic alterations in the patients with AML-M5. As a subtype of AML, AML-M5 carries both common recurrent CNAs and unique CNAs, which may harbor novel oncogenes or tumor suppressor genes. Clarifying the role of these genes will contribute to the understanding of leukemogenic network of AML-M5. PMID:24727659

Evodiamine Inhibits Angiotensin II-Induced Rat Cardiomyocyte Hypertrophy.

PubMed

He, Na; Gong, Qi-Hai; Zhang, Feng; Zhang, Jing-Yi; Lin, Shu-Xian; Hou, Hua-Hua; Wu, Qin; Sun, An-Sheng

2018-05-01

To investigate the effects of evodiamine (Evo), a component of Evodiaminedia rutaecarpa (Juss.) Benth, on cardiomyocyte hypertrophy induced by angiotensin II (Ang II) and further explore the potential mechanisms. Cardiomyocytes from neonatal Sprague Dawley rats were isolated and characterized, and then the cadiomyocyte cultures were randomly divided into control, model (Ang II 0.1 μmol/L), and Evo (0.03, 0.3, 3 μmol/L) groups. The cardiomyocyte surface area, protein level, intracellular free calcium ([Ca 2+ ] i ) concentration, activity of nitric oxide synthase (NOS) and content of nitric oxide (NO) were measured, respectively. The mRNA expressions of atrial natriuretic factor (ANF), calcineurin (CaN), extracellular signal-regulated kinase-2 (ERK-2), and endothelial nitric oxide synthase (eNOS) of cardiomyocytes were analyzed by real-time reverse transcriptionpolymerase chain reaction. The protein expressions of calcineurin catalytic subunit (CnA) and mitogen-activated protein kinase phosphatase-1 (MKP-1) were detected by Western blot analysis. Compared with the control group, Ang II induced cardiomyocytes hypertrophy, as evidenced by increased cardiomyocyte surface area, protein content, and ANF mRNA expression; increased intracellular free calcium ([Ca 2+ ] i ) concentration and expressions of CaN mRNA, CnA protein, and ERK-2 mRNA, but decreased MKP-1 protein expression (P<0.05 or P<0.01). Compared with Ang II, Evo (0.3, 3 μmol/L) significantly attenuated Ang II-induced cardiomyocyte hypertrophy, decreased the [Ca 2+ ] i concentration and expressions of CaN mRNA, CnA protein, and ERK-2 mRNA, but increased MKP-1 protein expression (P<0.05 or P<0.01). Most interestingly, Evo increased the NOS activity and NO production, and upregulated the eNOS mRNA expression (P<0.05). Evo signifificantly attenuated Ang II-induced cardiomyocyte hypertrophy, and this effect was partly due to promotion of NO production, reduction of [Ca 2+ ]i concentration, and inhibition of CaN and ERK-2 signal transduction pathways.

The U.S. Navy in the World (1981-1990): Context for U.S. Navy Capstone Strategies and Concepts

DTIC Science & Technology

2011-12-01

shall be subject to a penalty for failing to comply with a collection of information if it does not display a currently valid OMB control number. 1...NAME OF RESPONSIBLE PERSON a . REPORT unclassified b. ABSTRACT unclassified c. THIS PAGE unclassified Standard Form 298 (Rev. 8-98) Prescribed by...ANSI Std Z39-18 CNA is a not-for-profit organization whose professional staff of over 700 provides in-depth analysis and results-oriented solutions

A constructive nonlinear array (CNA) method for barely visible impact detection in composite materials

NASA Astrophysics Data System (ADS)

Malfense Fierro, Gian Piero; Meo, Michele

2017-04-01

Currently there are numerous phased array techniques such as Full Matrix Capture (FMC) and Total Focusing Method (TFM) that provide good damage assessment for composite materials. Although, linear methods struggle to evaluate and assess low levels of damage, while nonlinear methods have shown great promise in early damage detection. A sweep and subtraction evaluation method coupled with a constructive nonlinear array method (CNA) is proposed in order to assess damage specific nonlinearities, address issues with frequency selection when using nonlinear ultrasound imaging techniques and reduce equipment generated nonlinearities. These methods were evaluated using multiple excitation locations on an impacted composite panel with a complex damage (barely visible impact damage). According to various recent works, damage excitation can be accentuated by exciting at local defect resonance (LDR) frequencies; although these frequencies are not always easily determinable. The sweep methodology uses broadband excitation to determine both local defect and material resonances, by assessing local defect generated nonlinearities using a laser vibrometer it is possible to assess which frequencies excite the complex geometry of the crack. The dual effect of accurately determining local defect resonances, the use of an image subtraction method and the reduction of equipment based nonlinearities using CNA result in greater repeatability and clearer nonlinear imaging (NIM).

Genomic copy number analysis of Chernobyl papillary thyroid carcinoma in the Ukrainian–American Cohort

PubMed Central

Selmansberger, Martin; Braselmann, Herbert; Hess, Julia; Bogdanova, Tetiana; Abend, Michael; Tronko, Mykola; Brenner, Alina; Zitzelsberger, Horst; Unger, Kristian

2015-01-01

One of the major consequences of the 1986 Chernobyl reactor accident was a dramatic increase in papillary thyroid carcinoma (PTC) incidence, predominantly in patients exposed to the radioiodine fallout at young age. The present study is the first on genomic copy number alterations (CNAs) of PTCs of the Ukrainian–American cohort (UkrAm) generated by array comparative genomic hybridization (aCGH). Unsupervised hierarchical clustering of CNA profiles revealed a significant enrichment of a subgroup of patients with female gender, long latency (>17 years) and negative lymph node status. Further, we identified single CNAs that were significantly associated with latency, gender, radiation dose and BRAF V600E mutation status. Multivariate analysis revealed no interactions but additive effects of parameters gender, latency and dose on CNAs. The previously identified radiation-associated gain of the chromosomal bands 7q11.22-11.23 was present in 29% of cases. Moreover, comparison of our radiation-associated PTC data set with the TCGA data set on sporadic PTCs revealed altered copy numbers of the tumor driver genes NF2 and CHEK2. Further, we integrated the CNA data with transcriptomic data that were available on a subset of the herein analyzed cohort and did not find statistically significant associations between the two molecular layers. However, applying hierarchical clustering on a ‘BRAF-like/RAS-like’ transcriptome signature split the cases into four groups, one of which containing all BRAF-positive cases validating the signature in an independent data set. PMID:26320103

Tracing the Origin of Non-ferrous Oxides in Lamination Defects on Hot-Rolled Coils: Mold Slag Entrainment vs Submerged Entry Nozzle Reaction Products

NASA Astrophysics Data System (ADS)

Sengo, Sabri; Romano Triguero, Patricia; Zinngrebe, Enno; Mensonides, Fokko

2017-06-01

In this work, lamination defects (slivers) on hot-rolled coils of Ca-treated steel were investigated for microstructure and composition using optical and scanning electron microscopy combined with microanalysis (SEM/EDS). The goal was to identify possible origins for the observed defects which contain a complex assemblage of phases, such as different types of calcium aluminates (CA, CA2, CA6), melilite (C2AS), spinel (MA), and a newly identified phase, CNA2. Mold slag similar to that employed during the cast was absent. Analysis of the bulk composition of some of the defects indicated these to be too rich in alumina to be derived from mold slag through steel-slag redox exchange. In contrast, microstructural observation of the inner side of the submerged entry nozzles (SEN) used during casting showed deposits with compositions comparable to those of the defect material. Based on an estimation of the chemical evolution of mold slag interacting with steel, it is found that the defects are not likely to be entrained mold slag but remobilized SEN deposits, as supported by several microstructural and trace phase criteria. However, it should be noted that extensive reduction of mold slag by steel can lead to compositions rich in sodic-calcic aluminates (CNA2). Therefore, differentiation between specific locations of the defect materials within a casting system requires detailed analysis from the potential sources of origin as well as from the materials found in the defects.

Parity-Dependent Rotational Energy Transfer in CN(A2Π, ν = 4, jF1ε) + N2, O2, and CO2 Collisions

PubMed Central

2015-01-01

We report state-resolved total removal cross sections and state-to-state rotational energy transfer (RET) cross sections for collisions of CN(A2Π, ν = 4, jF1ε) with N2, O2, and CO2. CN(X2Σ+) was produced by 266 nm photolysis of ICN in a thermal bath (296 K) of the collider gas. A circularly polarized pulse from a dye laser prepared CN(A2Π, ν = 4) in a range of F1e rotational states, j = 2.5, 3.5, 6.5, 11.5, 13.5, and 18.5. These prepared states were monitored using the circularly polarized output of an external cavity diode laser by frequency-modulated (FM) spectroscopy on the CN(A–X)(4,2) band. The FM Doppler profiles were analyzed as a function of pump–probe delay to determine the time dependence of the population of the initially prepared states. Kinetic analysis of the resulting time dependences was used to determine total removal cross sections from the initially prepared levels. In addition, a range of j′ F1e and j′ F2f product states resulting from rotational energy transfer out of the j = 6.5 F1e initial state were probed, from which state-to-state RET cross sections were measured. The total removal cross sections lie in the order CO2 > N2 > O2, with evidence for substantial cross sections for electronic and/or reactive quenching of CN(A, ν = 4) to unobserved products with CO2 and O2. This is supported by the magnitude of the state-to-state RET cross sections, where a deficit of transferred population is apparent for CO2 and O2. A strong propensity for conservation of rotational parity in RET is observed for all three colliders. Spin–orbit-changing cross sections are approximately half of those of the respective conserving cross sections. These results are in marked disagreement with previous experimental observations with N2 as a collider but are in good agreement with quantum scattering calculations from the same study (Khachatrian et al. J. Phys. Chem. A2009, 113, 392219215110). Our results with CO2 as a collider are similarly in strong disagreement with a related experimental study (Khachatrian et al. J. Phys. Chem. A2009, 113, 1339019405498). We therefore propose that the previous experiments substantially underestimated the spin–orbit-changing cross sections for collisions with both N2 and CO2, suggesting that even approximate quantum scattering calculations may be more successful for such molecule–molecule systems than was previously concluded. PMID:24552624

Baroreceptors mask sympathetic responses to high intraocular pressure in dogs.

PubMed

Yahagi, Toru; Koyama, Shozo; Osaka, Kazumasa; Koyama, Haruhide

2008-05-30

These experiments were designed to investigate whether increasing intraocular pressure (IOP) in anesthetized dogs produces differential control of sympathetic nerve activities to various organs (heart, kidney, liver, and spleen) and if these sympathetic responses are modified by baroreceptors. We performed simultaneous multi-recordings of cardiac, renal, hepatic and splenic sympathetic nerve activities (CNA, RNA, HNA and SpNA, respectively) during 2 min of increasing IOP to a mean pressure of 30 mmHg. After increasing IOP in dogs with the intact baroreceptors, all of measured nerve activities did not change significantly throughout the experiment. In dogs with denervation of baroreceptors (cervical vagotomy with denervation of the carotid sinus and aortic nerves), only RNA and CNA showed significant increases in response to the increased IOP. However, time course changes in HNA and SpNA did not show any significant differences as compared with the baseline or that of the control group. These results indicate that systemic sympathetic nerve responses to increasing IOP are masked by systemic baroreceptors. As animals were denervated of their systemic baroreceptors, the unidirectional sympathoexcitatory responses to increased IOP were observed on CNA and RNA, but not on HNA and SpNA. These sympathetic outflow, when systemic baroreceptors are impaired as observed in old age, may play an important role in management of glaucoma attack with the use of adrenolytic drugs.

Sparse representation and Bayesian detection of genome copy number alterations from microarray data.

PubMed

Pique-Regi, Roger; Monso-Varona, Jordi; Ortega, Antonio; Seeger, Robert C; Triche, Timothy J; Asgharzadeh, Shahab

2008-02-01

Genomic instability in cancer leads to abnormal genome copy number alterations (CNA) that are associated with the development and behavior of tumors. Advances in microarray technology have allowed for greater resolution in detection of DNA copy number changes (amplifications or deletions) across the genome. However, the increase in number of measured signals and accompanying noise from the array probes present a challenge in accurate and fast identification of breakpoints that define CNA. This article proposes a novel detection technique that exploits the use of piece wise constant (PWC) vectors to represent genome copy number and sparse Bayesian learning (SBL) to detect CNA breakpoints. First, a compact linear algebra representation for the genome copy number is developed from normalized probe intensities. Second, SBL is applied and optimized to infer locations where copy number changes occur. Third, a backward elimination (BE) procedure is used to rank the inferred breakpoints; and a cut-off point can be efficiently adjusted in this procedure to control for the false discovery rate (FDR). The performance of our algorithm is evaluated using simulated and real genome datasets and compared to other existing techniques. Our approach achieves the highest accuracy and lowest FDR while improving computational speed by several orders of magnitude. The proposed algorithm has been developed into a free standing software application (GADA, Genome Alteration Detection Algorithm). http://biron.usc.edu/~piquereg/GADA

A struggle for equality: resistance to commissioning of male nurses in the Canadian military, 1952-1967.

PubMed

Care, D; Gregory, D; English, J; Venkatesh, P

1996-01-01

Historical research was conducted to explore and describe the forces of resistance that prevented male registered nurses from being employed and conferred officer status in the Nursing Division of the Canadian military. Prior to 1967, only female nurses were permitted to join the Nursing Division. A 25-year struggle by the Registered Nurses Association of Ontario (RNAO), its Male Nurses Committee (MNC), and the Canadian Nurses Association (CNA) was required to change this discriminatory policy. The struggle for equality on behalf of Canadian male nurses was successfully resolved because of the united stand taken by the MNC, the RNAO, and the CNA. The study also demonstrates the need to move beyond matriarchal history perspectives in nursing to more completely understand the evolution of the profession in Canada.

Clinical isolates of Enterococcus faecium exhibit strain-specific collagen binding mediated by Acm, a new member of the MSCRAMM family.

PubMed

Nallapareddy, Sreedhar R; Weinstock, George M; Murray, Barbara E

2003-03-01

A collagen-binding adhesin of Enterococcus faecium, Acm, was identified. Acm shows 62% similarity to the Staphylococcus aureus collagen adhesin Cna over the entire protein and is more similar to Cna (60% and 75% similarity with Cna A and B domains respectively) than to the Enterococcus faecalis collagen-binding adhesin, Ace, which shares homology with Acm only in the A domain. Despite the detection of acm in 32 out of 32 E. faecium isolates, only 11 of these (all clinical isolates, including four vancomycin-resistant endocarditis isolates and seven other isolates) exhibited binding to collagen type I (CI). Although acm from three CI-binding vancomycin-resistant E. faecium clinical isolates showed 100% identity, analysis of acm genes and their promoter regions from six non-CI-binding strains identified deletions or mutations that introduced stop codons and/or IS elements within the gene or the promoter region in five out of six strains, suggesting that the presence of an intact functional acm gene is necessary for binding of E. faecium strains to CI. Recombinant Acm A domain showed specific and concentration-dependent binding to collagen, and this protein competed with E. faecium binding to immobilized CI. Consistent with the adherence phenotype and sequence data, probing with Acm-specific IgGs purified from anti-recombinant Acm A polyclonal rabbit serum confirmed the surface expression of Acm in three out of three collagen-binding clinical isolates of E. faecium tested, but in none of the strains with a non-functional pseudo acm gene. Introduction of a functional acm gene into two non-CI-binding natural acm mutant strains conferred a CI-binding phenotype, further confirming that native Acm is sufficient for the binding of E. faecium to CI. These results demonstrate that acm, which encodes a potential virulence factor, is functional only in certain infection-derived clinical isolates of E. faecium, and suggest that Acm is the primary adhesin responsible for the ability of E. faecium to bind collagen.

Superposed Epoch Studies of the Response of the High-Latitude Magnetosphere-Ionosphere-Thermosphere System to Solar Wind High-Speed Stream Driving

NASA Astrophysics Data System (ADS)

Grandin, M.; Aikio, A. T.; Kozlovsky, A.; Ulich, T.; Raita, T.

2016-12-01

During the declining phase of the solar cycle, the Earth's magnetosphere-ionosphere-thermosphere system is mainly disturbed by solar wind high-speed streams (HSSs). Their ionospheric response, especially at high latitudes, is not fully understood yet. The perturbations in the ionosphere last for several days. We have examined the effect of HSS in two studies, which apply the superposed epoch method to data to reveal the statistical response in the ionospheric F, E and D regions to such perturbations. We use ionosonde, geomagnetic and cosmic noise absorption data obtained from Finnish stations during 95 high-speed stream events detected between 2006 and 2008. Results show a long-lasting decrease in the F layer critical frequency foF2 between 12 and 23 MLT in summer and equinox. This depletion of the F layer is interpreted as a result of enhanced electric fields inducing ion-neutral frictional heating in the auroral and subauroral regions. The response near noon is different, since foF2 is increased shortly upon arrival of the co-rotating stream interaction region (CIR), possibly because of precipitation of particles from the dayside plasma sheet provoked by the associated solar wind pressure pulse. In the morning sector, both foF2 and foEs show increases for several days, indicating particle precipitation having a soft component. In the study of cosmic noise absorption (CNA), we observe a different response depending on the L-value of the station. Within the auroral oval (L=5-6), CNA gets maximum values in the morning sector 0-12 MLT during the first and second day following the zero epoch. Values are greater during events with longer-lasting high solar wind speed. The CNA maximum shifts to later MLT at lower L values, and in JYV (L=3.8), the maximum takes place at 14 MLT during day 4. Substorm energization events dominate during the first days at 00-01 MLT. We also address the role of Pc5 geomagnetic pulsations observed in association with CNA events. These results may contribute to improve nowcasting and forecasting of space weather activity during high-speed stream events.

Changes in presynaptic release, but not reuptake, of bioamines induced by long-term antidepressant treatment

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

Dolzhenko, A.T.; Komissarov, I.V.

1986-10-01

This paper describes an investigation into the effect of long-term administration of antidepressants on neuronal uptake of NA and 5-HT and on their release, induced by electrical stimulation, in rat brain slices. The effects of the test substances on neuronal uptake of /sup 14/C-NA and /sup 3/H-5-HT by the slices was investigated. Values of IC/sub 50/ and EC/sub 2/ were found and compared in the experiments and control. The inhibitory effect of clonidine (10/sup -4/ M) and of 5-HT (10/sup -5/ M) on presynaptic release of /sup 14/C-NA and /sup 3/H-5-HT also was studied in brain slices from intact ratsmore » and rats treated for two weeks with antidepressants.« less

A WUSCHEL-Independent Stem Cell Specification Pathway Is Repressed by PHB, PHV and CNA in Arabidopsis.

PubMed

Lee, Chunghee; Clark, Steven E

2015-01-01

The homeostatic maintenance of stem cells that carry out continuous organogenesis at the shoot meristem is crucial for plant development. Key known factors act to signal between the stem cells and an underlying group of cells thought to act as the stem cell niche. In Arabidopsis thaliana the homeodomain transcription factor WUSCHEL (WUS) is essential for stem cell initiation and maintenance at shoot and flower meristems. Recent data suggest that the WUS protein may move from the niche cells directly into the stem cells to maintain stem cell identity. Here we provide evidence for a second, previously unknown, pathway for stem cell specification at shoot and flower meristems that bypasses the requirement for WUS. We demonstrate that this novel stem cell specification pathway is normally repressed by the activity of the HD-zip III transcription factors PHABULOSA (PHB), PHAVOLUTA (PHV) and CORONA (CNA). When de-repressed, this second stem cell pathway leads to an accumulation of stem cells and an enlargement of the stem cell niche. When de-repressed in a wus mutant background, this second stem cell pathway leads to functional meristems with largely normal cell layering and meristem morphology, activation of WUS cis regulatory elements, and extensive, but not indeterminate, organogenesis. Thus, WUS is largely dispensable for stem cell specification and meristem function, suggesting a set of key stem cell specification factors, competitively regulated by WUS and PHB/PHV/CNA, remain unidentified.

A WUSCHEL-Independent Stem Cell Specification Pathway Is Repressed by PHB, PHV and CNA in Arabidopsis

PubMed Central

Lee, Chunghee; Clark, Steven E.

2015-01-01

The homeostatic maintenance of stem cells that carry out continuous organogenesis at the shoot meristem is crucial for plant development. Key known factors act to signal between the stem cells and an underlying group of cells thought to act as the stem cell niche. In Arabidopsis thaliana the homeodomain transcription factor WUSCHEL (WUS) is essential for stem cell initiation and maintenance at shoot and flower meristems. Recent data suggest that the WUS protein may move from the niche cells directly into the stem cells to maintain stem cell identity. Here we provide evidence for a second, previously unknown, pathway for stem cell specification at shoot and flower meristems that bypasses the requirement for WUS. We demonstrate that this novel stem cell specification pathway is normally repressed by the activity of the HD-zip III transcription factors PHABULOSA (PHB), PHAVOLUTA (PHV) and CORONA (CNA). When de-repressed, this second stem cell pathway leads to an accumulation of stem cells and an enlargement of the stem cell niche. When de-repressed in a wus mutant background, this second stem cell pathway leads to functional meristems with largely normal cell layering and meristem morphology, activation of WUS cis regulatory elements, and extensive, but not indeterminate, organogenesis. Thus, WUS is largely dispensable for stem cell specification and meristem function, suggesting a set of key stem cell specification factors, competitively regulated by WUS and PHB/PHV/CNA, remain unidentified. PMID:26011610

Medicaid payment rates, case-mix reimbursement, and nursing home staffing--1996-2004.

PubMed

Feng, Zhanlian; Grabowski, David C; Intrator, Orna; Zinn, Jacqueline; Mor, Vincent

2008-01-01

We examined the impact of state Medicaid payment rates and case-mix reimbursement on direct care staffing levels in US nursing homes. We used a recent time series of national nursing home data from the Online Survey Certification and Reporting system for 1996-2004, merged with annual state Medicaid payment rates and case-mix reimbursement information. A 5-category response measure of total staffing levels was defined according to expert recommended thresholds, and examined in a multinomial logistic regression model. Facility fixed-effects models were estimated separately for Registered Nurse (RN), Licensed Practical Nurse (LPN), and Certified Nurse Aide (CNA) staffing levels measured as average hours per resident day. Higher Medicaid payment rates were associated with increases in total staffing levels to meet a higher recommended threshold. However, these gains in overall staffing were accompanied by a reduction of RN staffing and an increase in both LPN and CNA staffing levels. Under case-mix reimbursement, the likelihood of nursing homes achieving higher recommended staffing thresholds decreased, as did levels of professional staffing. Independent of the effects of state, market, and facility characteristics, there was a significant downward trend in RN staffing and an upward trend in both LPN and CNA staffing. Although overall staffing may increase in response to more generous Medicaid reimbursement, it may not translate into improvements in the skill mix of staff. Adjusting for reimbursement levels and resident acuity, total staffing has not increased after the implementation of case-mix reimbursement.

Intra-Tumor Genetic Heterogeneity in Wilms Tumor: Clonal Evolution and Clinical Implications.

PubMed

Cresswell, George D; Apps, John R; Chagtai, Tasnim; Mifsud, Borbala; Bentley, Christopher C; Maschietto, Mariana; Popov, Sergey D; Weeks, Mark E; Olsen, Øystein E; Sebire, Neil J; Pritchard-Jones, Kathy; Luscombe, Nicholas M; Williams, Richard D; Mifsud, William

2016-07-01

The evolution of pediatric solid tumors is poorly understood. There is conflicting evidence of intra-tumor genetic homogeneity vs. heterogeneity (ITGH) in a small number of studies in pediatric solid tumors. A number of copy number aberrations (CNA) are proposed as prognostic biomarkers to stratify patients, for example 1q+ in Wilms tumor (WT); current clinical trials use only one sample per tumor to profile this genetic biomarker. We multisampled 20 WT cases and assessed genome-wide allele-specific CNA and loss of heterozygosity, and inferred tumor evolution, using Illumina CytoSNP12v2.1 arrays, a custom analysis pipeline, and the MEDICC algorithm. We found remarkable diversity of ITGH and evolutionary trajectories in WT. 1q+ is heterogeneous in the majority of tumors with this change, with variable evolutionary timing. We estimate that at least three samples per tumor are needed to detect >95% of cases with 1q+. In contrast, somatic 11p15 LOH is uniformly an early event in WT development. We find evidence of two separate tumor origins in unilateral disease with divergent histology, and in bilateral WT. We also show subclonal changes related to differential response to chemotherapy. Rational trial design to include biomarkers in risk stratification requires tumor multisampling and reliable delineation of ITGH and tumor evolution. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

Investigations on the photoreactions of phenothiazine and phenoxazine in presence of 9-cyanoanthracene by using steady state and time resolved spectroscopic techniques.

PubMed

Bardhan, Munmun; Mandal, Paulami; Tzeng, Wen-Bih; Ganguly, Tapan

2010-09-01

By using electrochemical, steady state and time resolved (fluorescence lifetime and transient absorption) spectroscopic techniques, detailed investigations were made to reveal the mechanisms of charge separation or forward electron transfer reactions within the electron donor phenothiazine (PTZH) or phenoxazine (PXZH) and well known electron acceptor 9-cyanoanthracene (CNA). The transient absorption spectra suggest that the charge separated species formed in the excited singlet state resulted from intermolecular photoinduced electron transfer reactions within the donor PTZH (or PXZH) and CNA acceptor relaxes to the corresponding triplet state. Though alternative mechanisms of via formations of contact neutral radical by H-transfer reaction have been proposed but the observed results obtained from the time resolved measurements indicate that the regeneration of ground state reactants is primarily responsible due to direct recombination of triplet contact ion-pair (CIP) or solvent-separated ion-pair (SSIP).

Shortening of the Lactobacillus paracasei subsp. paracasei BGNJ1-64 AggLb Protein Switches Its Activity from Auto-aggregation to Biofilm Formation.

PubMed

Miljkovic, Marija; Bertani, Iris; Fira, Djordje; Jovcic, Branko; Novovic, Katarina; Venturi, Vittorio; Kojic, Milan

2016-01-01

AggLb is the largest (318.6 kDa) aggregation-promoting protein of Lactobacillus paracasei subsp. paracasei BGNJ1-64 responsible for forming large cell aggregates, which causes auto-aggregation, collagen binding and pathogen exclusion in vitro. It contains an N-terminus leader peptide, followed by six successive collagen binding domains, 20 successive repeats (CnaB-like domains) and an LPXTG sorting signal at the C-terminus for cell wall anchoring. Experimental information about the roles of the domains of AggLb is currently unknown. To define the domain that confers cell aggregation and the key domains for interactions of specific affinity between AggLb and components of the extracellular matrix, we constructed a series of variants of the aggLb gene and expressed them in Lactococcus lactis subsp. lactis BGKP1-20 using a lactococcal promoter. All of the variants contained a leader peptide, an inter collagen binding-CnaB domain region (used to raise an anti-AggLb antibody), an anchor domain and a different number of collagen binding and CnaB-like domains. The role of the collagen binding repeats of the N-terminus in auto-aggregation and binding to collagen and fibronectin was confirmed. Deletion of the collagen binding repeats II, III, and IV resulted in a loss of the strong auto-aggregation, collagen and fibronectin binding abilities whereas the biofilm formation capability was increased. The strong auto-aggregation, collagen and fibronectin binding abilities of AggLb were negatively correlated to biofilm formation.

Unraveling Gardnerella vaginalis Surface Proteins Using Cell Shaving Proteomics.

PubMed

Marín, Elvira; Haesaert, Annelies; Padilla, Laura; Adán, Jaume; Hernáez, María L; Monteoliva, Lucía; Gil, Concha

2018-01-01

Gardnerella vaginalis is one of the main etiologic agents of bacterial vaginosis (BV). This infection is responsible for a wide range of public health costs and is associated with several adverse outcomes during pregnancy. Improving our understanding of G. vaginalis protein cell surface will assist in BV diagnosis. This study represents the first proteomic approach that has analyzed the exposed proteins on G. vaginalis cell surface using a shaving approach. The 261 G. vaginalis proteins identified using this approach were analyzed with bioinformatic tools to detect characteristic motifs from surface-exposed proteins, such as signal peptides (36 proteins), lipobox domains (17 proteins), LPXTG motifs (5 proteins) and transmembrane alpha-helices (66 proteins). One third of the identified proteins were found to have at least one typical motif of surface-exposed proteins. Furthermore, the subcellular location was examined using two predictors (PSORT and Gpos-mPLoc). These bioinformatic tools classified 17% of the identified proteins as surface-associated proteins. Interestingly, we identified 13 members of the ATP-binding cassette (ABC) superfamily, which were mainly involved in the translocation of various substrates across membranes. To validate the location of the G. vaginalis surface-exposed proteins, an immunofluorescence assay with antibodies against Escherichia coli GroEL was performed to reveal the extracellular location of the moonlighting GroEL. In addition, monoclonal antibodies (mAb) against G. vaginalis Cna protein were produced and used to validate the location of Cna on the surface of the G. vaginalis . These high affinity anti-Cna mAb represent a useful tool for the study of this pathogenic microorganism and the BV.

Unraveling Gardnerella vaginalis Surface Proteins Using Cell Shaving Proteomics

PubMed Central

Marín, Elvira; Haesaert, Annelies; Padilla, Laura; Adán, Jaume; Hernáez, María L.; Monteoliva, Lucía; Gil, Concha

2018-01-01

Gardnerella vaginalis is one of the main etiologic agents of bacterial vaginosis (BV). This infection is responsible for a wide range of public health costs and is associated with several adverse outcomes during pregnancy. Improving our understanding of G. vaginalis protein cell surface will assist in BV diagnosis. This study represents the first proteomic approach that has analyzed the exposed proteins on G. vaginalis cell surface using a shaving approach. The 261 G. vaginalis proteins identified using this approach were analyzed with bioinformatic tools to detect characteristic motifs from surface-exposed proteins, such as signal peptides (36 proteins), lipobox domains (17 proteins), LPXTG motifs (5 proteins) and transmembrane alpha-helices (66 proteins). One third of the identified proteins were found to have at least one typical motif of surface-exposed proteins. Furthermore, the subcellular location was examined using two predictors (PSORT and Gpos-mPLoc). These bioinformatic tools classified 17% of the identified proteins as surface-associated proteins. Interestingly, we identified 13 members of the ATP-binding cassette (ABC) superfamily, which were mainly involved in the translocation of various substrates across membranes. To validate the location of the G. vaginalis surface-exposed proteins, an immunofluorescence assay with antibodies against Escherichia coli GroEL was performed to reveal the extracellular location of the moonlighting GroEL. In addition, monoclonal antibodies (mAb) against G. vaginalis Cna protein were produced and used to validate the location of Cna on the surface of the G. vaginalis. These high affinity anti-Cna mAb represent a useful tool for the study of this pathogenic microorganism and the BV. PMID:29867878

The Relationship Between Colocation and Reenlistment in the Navy. Volume 1

DTIC Science & Technology

of a larger CNA project titled The Effects of Personnel Policy Changes on Budgets and Manpower Inventories sponsored by the Office of the Assistant Secretary of the Navy (Financial Management and Comptroller)(ASN(FM and C)).

Prognostic relevance of aberrant DNA methylation in g1 and g2 pancreatic neuroendocrine tumors.

PubMed

Stefanoli, Michele; La Rosa, Stefano; Sahnane, Nora; Romualdi, Chiara; Pastorino, Roberta; Marando, Alessandro; Capella, Carlo; Sessa, Fausto; Furlan, Daniela

2014-01-01

The occurrence and clinical relevance of DNA hypermethylation and global hypomethylation in pancreatic neuroendocrine tumours (PanNETs) are still unknown. We evaluated the frequency of both epigenetic alterations in PanNETs to assess the relationship between methylation profiles and chromosomal instability, tumour phenotypes and prognosis. In a well-characterized series of 56 sporadic G1 and G2 PanNETs, methylation-sensitive multiple ligation-dependent probe amplification was performed to assess hypermethylayion of 33 genes and copy number alterations (CNAs) of 53 chromosomal regions. Long interspersed nucleotide element-1 (LINE-1) hypomethylation was quantified by pyrosequencing. Unsupervised hierarchical clustering allowed to identify a subset of 22 PanNETs (39%) exhibiting high frequency of gene-specific methylation and low CNA percentages. This tumour cluster was significantly associated with stage IV (p = 0.04) and with poor prognosis in univariable analysis (p = 0.004). LINE-1 methylation levels in PanNETs were significantly lower than in normal samples (p < 0.01) and were approximately normally distributed. 12 tumours (21%) were highly hypomethylated, showing variable levels of CNA. Interestingly, only 5 PanNETs (9%) were observed to show simultaneously LINE-1 hypomethylation and high frequency of gene-specific methylation. LINE-1 hypomethylation was strongly correlated with advanced stage (p = 0.002) and with poor prognosis (p < 0.0001). In the multivariable analysis, low LINE-1 methylation status and methylation clusters were the only independent significant predictors of outcome (p = 0.034 and p = 0.029, respectively). The combination of global DNA hypomethylation and gene hypermethylation analyses may be useful to define distinct subsets of PanNETs. Both alterations are common in PanNETs and could be directly correlated with tumour progression. © 2014 S. Karger AG, Basel.

A genomic copy number signature predicts radiation exposure in post-Chernobyl breast cancer.

PubMed

Wilke, Christina M; Braselmann, Herbert; Hess, Julia; Klymenko, Sergiy V; Chumak, Vadim V; Zakhartseva, Liubov M; Bakhanova, Elena V; Walch, Axel K; Selmansberger, Martin; Samaga, Daniel; Weber, Peter; Schneider, Ludmila; Fend, Falko; Bösmüller, Hans C; Zitzelsberger, Horst; Unger, Kristian

2018-04-16

Breast cancer is the second leading cause of cancer death among women worldwide and besides life style, age and genetic risk factors, exposure to ionizing radiation is known to increase the risk for breast cancer. Further, DNA copy number alterations (CNAs), which can result from radiation-induced double-strand breaks, are frequently occurring in breast cancer cells. We set out to identify a signature of CNAs discriminating breast cancers from radiation-exposed and non-exposed female patients. We analyzed resected breast cancer tissues from 68 exposed female Chernobyl clean-up workers and evacuees and 68 matched non-exposed control patients for CNAs by array comparative genomic hybridization analysis (aCGH). Using a stepwise forward-backward selection approach a non-complex CNA signature, that is, less than ten features, was identified in the training data set, which could be subsequently validated in the validation data set (p value < 0.05). The signature consisted of nine copy number regions located on chromosomal bands 7q11.22-11.23, 7q21.3, 16q24.3, 17q21.31, 20p11.23-11.21, 1p21.1, 2q35, 2q35, 6p22.2. The signature was independent of any clinical characteristics of the patients. In all, we identified a CNA signature that has the potential to allow identification of radiation-associated breast cancer at the individual level. © 2018 UICC.

Efficacy of low-level laser therapy on hair regrowth in dogs with noninflammatory alopecia: a pilot study.

PubMed

Olivieri, Lara; Cavina, Damiano; Radicchi, Giada; Miragliotta, Vincenzo; Abramo, Francesca

2015-02-01

Canine noninflammatory alopecia (CNA) is a heterogeneous group of skin diseases with different underlying pathogenesis. The therapeutic approach is challenging, and new options for treatment are desirable. To test the clinical efficacy of low-level laser therapy (LLLT) on hair regrowth in CNA. Seven dogs of different ages, breeds and genders with a clinical and histopathological diagnosis of noninflammatory alopecia. Each dog was treated twice weekly for a maximum of 2 months with a therapeutic laser producing the following three different wavelengths emerging simultaneously from 21 foci: 13 × 16 mW, 470 nm; 4 × 50 mW, 685 nm; and 4 × 200 mW, 830 nm. The fluence given was 3 J/cm(2) , frequency 5 Hz, amplitude of the irradiated area was 25 cm(2) and application time was 1.34 min. A predetermined alopecic area was left untreated and served as a control area. From one dog, post-treatment biopsies of treated and untreated sites were obtained for histological evaluation of hair density and the percentage of haired and nonhaired follicles. At the end of the study, coat regrowth was greatly improved in six of seven animals and improved in one of seven. By morphometry, the area occupied by hair follicles was 18% in the treated sample and 11% in the untreated one (11%); haired follicles were (per area) 93% in the treated sample and only 9% in the control sample. Our clinical and histological data document promising effects of LLLT on hair regrowth in CNA. Further studies investigating the biological mechanism underlying the effect of LLLT on hair follicle cycling are warranted. © 2014 ESVD and ACVD.

The Value of Clinical Needs Assessments for Point-of-Care Diagnostics

PubMed Central

Weigl, Bernhard H.; Gaydos, Charlotte A.; Kost, Gerald; Beyette, Fred R.; Sabourin, Stephanie; Rompalo, Anne; de los Santos, Tala; McMullan, Jason T.; Haller, John

2013-01-01

Most entrepreneurial ventures fail long before the core technology can be brought to the marketplace because of disconnects in performance and usability measures such as accuracy, cost, complexity, assay stability, and time requirements between technology developers’ specifications and needs of the end-users. By going through a clinical needs assessment (CNA) process, developers will gain vital information and a clear focus that will help minimize the risks associated with the development of new technologies available for use within the health care system. This article summarizes best practices of the principal investigators of the National Institute of Biomedical Imaging and Bioengineering point-of-care (POC) centers within the National Institute of Biomedical Imaging and Bioengineering POC Technologies Research Network. Clinical needs assessments are particularly important for product development areas that do not sufficiently benefit from traditional market research, such as grant-funded research and development, new product lines using cutting-edge technologies developed in start-up companies, and products developed through product development partnerships for low-resource settings. The objectives of this article were to (1) highlight the importance of CNAs for development of POC devices, (2) discuss methods applied by POC Technologies Research Network for assessing clinical needs, and (3) provide a road map for future CNAs. PMID:23935405

NFATc1 affects mouse splenic B cell function by controlling the calcineurin–NFAT signaling network

PubMed Central

Bhattacharyya, Sankar; Deb, Jolly; Patra, Amiya K.; Thuy Pham, Duong Anh; Chen, Wen; Vaeth, Martin; Berberich-Siebelt, Friederike; Klein-Hessling, Stefan; Lamperti, Edward D.; Reifenberg, Kurt; Jellusova, Julia; Schweizer, Astrid; Nitschke, Lars; Leich, Ellen; Rosenwald, Andreas; Brunner, Cornelia; Engelmann, Swen; Bommhardt, Ursula; Avots, Andris; Müller, Martin R.; Kondo, Eisaku

2011-01-01

By studying mice in which the Nfatc1 gene was inactivated in bone marrow, spleen, or germinal center B cells, we show that NFATc1 supports the proliferation and suppresses the activation-induced cell death of splenic B cells upon B cell receptor (BCR) stimulation. BCR triggering leads to expression of NFATc1/αA, a short isoform of NFATc1, in splenic B cells. NFATc1 ablation impaired Ig class switch to IgG3 induced by T cell–independent type II antigens, as well as IgG3+ plasmablast formation. Mice bearing NFATc1−/− B cells harbor twofold more interleukin 10–producing B cells. NFATc1−/− B cells suppress the synthesis of interferon-γ by T cells in vitro, and these mice exhibit a mild clinical course of experimental autoimmune encephalomyelitis. In large part, the defective functions of NFATc1−/− B cells are caused by decreased BCR-induced Ca2+ flux and calcineurin (Cn) activation. By affecting CD22, Rcan1, CnA, and NFATc1/αA expression, NFATc1 controls the Ca2+-dependent Cn–NFAT signaling network and, thereby, the fate of splenic B cells upon BCR stimulation. PMID:21464221

Readiness Based Sparing: A Research Summary

DTIC Science & Technology

2012-07-01

TIGER and SESAME. Retrieved from Defense Technical Information Center. (ADA283943) Geis, M. B., Camper, V. S., Measell , B. H., & Oi, J. S. (1995...Camper, V. S., & Measell , B. H. (1993). Aviation logistics support: Retail sparing issues. Retrieved from CNA. (2793002000) Kinskie, S. W. (1997). An

Plasmonic and SERS performances of compound nanohole arrays fabricated by shadow sphere lithography

NASA Astrophysics Data System (ADS)

Skehan, Connor; Ai, Bin; Larson, Steven R.; Stone, Keenan M.; Dennis, William M.; Zhao, Yiping

2018-03-01

Several plasmonic compound nanohole arrays (CNAs), such as triangular nanoholes and fan-like nanoholes with multiple nanotips and nanogaps, are designed by a simple and efficient shadow sphere lithography technique by tuning the sphere mask size, the deposition and azimuthal angles, substrate temperature T S , and the number of deposition steps N. Compared with conventional circular nanohole arrays, the CNAs show more hot spots and exhibit new transmission speaks. Systematic finite-difference time-domain calculations indicate that different resonance modes excited by the various shaped and sized nanoholes are responsible for the enhanced plasmonic performances of CNAs. Compared to the CNA samples with only one circular hole in the unit cell, the Raman scattering intensity of the CNA with multiple triangular nanoholes, nanogaps, and nanotips can be enhanced up to 5-fold. These CNAs, due to the strong resonance due to the multiple structural features, are promising applications as optical filters, plasmonic sensors, and surface-enhanced spectroscopies.

Age-Specific Gene Expression Signatures for Breast Tumors and Cross-Species Conserved Potential Cancer Progression Markers in Young Women

PubMed Central

Colak, Dilek; Nofal, Asmaa; AlBakheet, AlBandary; Nirmal, Maimoona; Jeprel, Hatim; Eldali, Abdelmoneim; AL-Tweigeri, Taher; Tulbah, Asma; Ajarim, Dahish; Malik, Osama Al; Kaya, Namik; Park, Ben H.; Bin Amer, Suad M.

2013-01-01

Breast cancer in young women is more aggressive with a poorer prognosis and overall survival compared to older women diagnosed with the disease. Despite recent research, the underlying biology and molecular alterations that drive the aggressive nature of breast tumors associated with breast cancer in young women have yet to be elucidated. In this study, we performed transcriptomic profile and network analyses of breast tumors arising in Middle Eastern women to identify age-specific gene signatures. Moreover, we studied molecular alterations associated with cancer progression in young women using cross-species comparative genomics approach coupled with copy number alterations (CNA) associated with breast cancers from independent studies. We identified 63 genes specific to tumors in young women that showed alterations distinct from two age cohorts of older women. The network analyses revealed potential critical regulatory roles for Myc, PI3K/Akt, NF-κB, and IL-1 in disease characteristics of breast tumors arising in young women. Cross-species comparative genomics analysis of progression from pre-invasive ductal carcinoma in situ (DCIS) to invasive ductal carcinoma (IDC) revealed 16 genes with concomitant genomic alterations, CCNB2, UBE2C, TOP2A, CEP55, TPX2, BIRC5, KIAA0101, SHCBP1, UBE2T, PTTG1, NUSAP1, DEPDC1, HELLS, CCNB1, KIF4A, and RRM2, that may be involved in tumorigenesis and in the processes of invasion and progression of disease. Array findings were validated using qRT-PCR, immunohistochemistry, and extensive in silico analyses of independently performed microarray datasets. To our knowledge, this study provides the first comprehensive genomic analysis of breast cancer in Middle Eastern women in age-specific cohorts and potential markers for cancer progression in young women. Our data demonstrate that cancer appearing in young women contain distinct biological characteristics and deregulated signaling pathways. Moreover, our integrative genomic and cross-species analysis may provide robust biomarkers for the detection of disease progression in young women, and lead to more effective treatment strategies. PMID:23704896

Age-specific gene expression signatures for breast tumors and cross-species conserved potential cancer progression markers in young women.

PubMed

Colak, Dilek; Nofal, Asmaa; Albakheet, Albandary; Nirmal, Maimoona; Jeprel, Hatim; Eldali, Abdelmoneim; Al-Tweigeri, Taher; Tulbah, Asma; Ajarim, Dahish; Malik, Osama Al; Inan, Mehmet S; Kaya, Namik; Park, Ben H; Bin Amer, Suad M

2013-01-01

Breast cancer in young women is more aggressive with a poorer prognosis and overall survival compared to older women diagnosed with the disease. Despite recent research, the underlying biology and molecular alterations that drive the aggressive nature of breast tumors associated with breast cancer in young women have yet to be elucidated. In this study, we performed transcriptomic profile and network analyses of breast tumors arising in Middle Eastern women to identify age-specific gene signatures. Moreover, we studied molecular alterations associated with cancer progression in young women using cross-species comparative genomics approach coupled with copy number alterations (CNA) associated with breast cancers from independent studies. We identified 63 genes specific to tumors in young women that showed alterations distinct from two age cohorts of older women. The network analyses revealed potential critical regulatory roles for Myc, PI3K/Akt, NF-κB, and IL-1 in disease characteristics of breast tumors arising in young women. Cross-species comparative genomics analysis of progression from pre-invasive ductal carcinoma in situ (DCIS) to invasive ductal carcinoma (IDC) revealed 16 genes with concomitant genomic alterations, CCNB2, UBE2C, TOP2A, CEP55, TPX2, BIRC5, KIAA0101, SHCBP1, UBE2T, PTTG1, NUSAP1, DEPDC1, HELLS, CCNB1, KIF4A, and RRM2, that may be involved in tumorigenesis and in the processes of invasion and progression of disease. Array findings were validated using qRT-PCR, immunohistochemistry, and extensive in silico analyses of independently performed microarray datasets. To our knowledge, this study provides the first comprehensive genomic analysis of breast cancer in Middle Eastern women in age-specific cohorts and potential markers for cancer progression in young women. Our data demonstrate that cancer appearing in young women contain distinct biological characteristics and deregulated signaling pathways. Moreover, our integrative genomic and cross-species analysis may provide robust biomarkers for the detection of disease progression in young women, and lead to more effective treatment strategies.

Cognitive and Noncognitive Improvements Among Cadets at the Washington Youth Academy (WYA)

DTIC Science & Technology

2014-12-01

including affecting one’s success in the labor market [6]. Other researchers have shown that noncognitive skills are also related to outcomes, such as...Robert Shuford. 2008. Variation in Participants and Policies Across ChalleNGe Programs. CNA Corporation. CRM D0016643.A2/Final. [10] Rosen, Jeffrey

Genomic characterization of Imatinib resistance in CD34+ cell populations from chronic myeloid leukaemia patients.

PubMed

Joha, Sami; Dauphin, Véronique; Leprêtre, Frédéric; Corm, Sélim; Nicolini, Franck E; Roumier, Christophe; Nibourel, Olivier; Grardel, Nathalie; Maguer-Satta, Véronique; Idziorek, Thierry; Figeac, Martin; Laï, Jean-Luc; Quesnel, Bruno; Etienne, Gabriel; Guilhot, François; Lippert, Eric; Preudhomme, Claude; Roche-Lestienne, Catherine

2011-04-01

To ascertain genomic alterations associated with Imatinib resistance in chronic myeloid leukaemia, we performed high resolution genomic analysis of CD34(+) cells from 25 Imatinib (IM) resistant and 11 responders CML patients. Using patients' T-cells as reference, we found significant association between number of acquired cryptic copy number alterations (CNA) and disease phase (p=0.036) or loss of IM response for patients diagnosed in chronic phase (CP) (p=0.04). Recurrent cryptic losses were identified on chromosomes 7, 12 and 13. On chromosome 7, recurrent deletions of the IKZF1 locus were detected, for the first time, in 4 patients in CP. Copyright © 2010 Elsevier Ltd. All rights reserved.

The Nine Planets Solar System Tour

Science.gov Websites

Astronomy news section which gives news, notes and general observations, we also have an interactive tour of ; Notes Astronomy picture of the day. For a full list of contents please see here. cna classes online Professional Astronomy research paper writing help can be found at AdvancedWriters.com. Solar system tour

A Preliminary Qualitative Evaluation of the Virginia Gold Quality Improvement Program

ERIC Educational Resources Information Center

Craver, Gerald A.; Burkett, Amy K.

2012-01-01

Certified nursing assistants (CNAs) perform an important role in the long-term care system because they provide the majority of paid care to nursing facility residents. Unfortunately, annual CNA turnover often exceeds 100 percent nationally. Many factors account for this, including stressful working conditions, low pay, and limited benefits. The…

Peer Mentoring in Long-Term Care: Rational, Design, and Retention

ERIC Educational Resources Information Center

Hegeman, Carol; Hoskinson, Debi; Munro, Heather; Maiden, Patricia; Pillemer, Karl

2007-01-01

This article describes two successful peer-mentoring programs designed to improve the quality of care in nursing homes and retention rates among direct care staff. The first program, "Growing Strong Roots," examined CNA retention rates and the second program, "Peer Mentoring for Long Term Charge Nurses," examined RN and LPN retention rates. These…

Collaborating for Success: Team Teaching the Engineering Technical Thesis

ERIC Educational Resources Information Center

Keating, Terrence; Long, Mike

2012-01-01

This paper will examine the collaborative teaching process undertaken at College of the North Atlantic-Qatar (CNA-Q) by Engineering and the Communication faculties to improve the overall quality of engineering students' capstone projects known as the Technical Thesis. The Technical Thesis is divided into two separate components: a proposal stage…

Innovative Contextualized Curriculum for a CNA to LPN Bridge Course. Promising Practice

ERIC Educational Resources Information Center

Office of Community College Research and Leadership, 2010

2010-01-01

As a pilot site selected to participate in Illinois' Shifting Gears (SG) initiative in 2007, Oakton Community College (OCC) partnered with Presbyterian Homes to develop a bridge course to prepare a cadre of their employed Certified Nursing Assistants (CNAs) to enter college-credit prerequisite courses to a Practical Nursing program. Oakton…

Scalable whole-exome sequencing of cell-free DNA reveals high concordance with metastatic tumors.

PubMed

Adalsteinsson, Viktor A; Ha, Gavin; Freeman, Samuel S; Choudhury, Atish D; Stover, Daniel G; Parsons, Heather A; Gydush, Gregory; Reed, Sarah C; Rotem, Denisse; Rhoades, Justin; Loginov, Denis; Livitz, Dimitri; Rosebrock, Daniel; Leshchiner, Ignaty; Kim, Jaegil; Stewart, Chip; Rosenberg, Mara; Francis, Joshua M; Zhang, Cheng-Zhong; Cohen, Ofir; Oh, Coyin; Ding, Huiming; Polak, Paz; Lloyd, Max; Mahmud, Sairah; Helvie, Karla; Merrill, Margaret S; Santiago, Rebecca A; O'Connor, Edward P; Jeong, Seong H; Leeson, Rachel; Barry, Rachel M; Kramkowski, Joseph F; Zhang, Zhenwei; Polacek, Laura; Lohr, Jens G; Schleicher, Molly; Lipscomb, Emily; Saltzman, Andrea; Oliver, Nelly M; Marini, Lori; Waks, Adrienne G; Harshman, Lauren C; Tolaney, Sara M; Van Allen, Eliezer M; Winer, Eric P; Lin, Nancy U; Nakabayashi, Mari; Taplin, Mary-Ellen; Johannessen, Cory M; Garraway, Levi A; Golub, Todd R; Boehm, Jesse S; Wagle, Nikhil; Getz, Gad; Love, J Christopher; Meyerson, Matthew

2017-11-06

Whole-exome sequencing of cell-free DNA (cfDNA) could enable comprehensive profiling of tumors from blood but the genome-wide concordance between cfDNA and tumor biopsies is uncertain. Here we report ichorCNA, software that quantifies tumor content in cfDNA from 0.1× coverage whole-genome sequencing data without prior knowledge of tumor mutations. We apply ichorCNA to 1439 blood samples from 520 patients with metastatic prostate or breast cancers. In the earliest tested sample for each patient, 34% of patients have ≥10% tumor-derived cfDNA, sufficient for standard coverage whole-exome sequencing. Using whole-exome sequencing, we validate the concordance of clonal somatic mutations (88%), copy number alterations (80%), mutational signatures, and neoantigens between cfDNA and matched tumor biopsies from 41 patients with ≥10% cfDNA tumor content. In summary, we provide methods to identify patients eligible for comprehensive cfDNA profiling, revealing its applicability to many patients, and demonstrate high concordance of cfDNA and metastatic tumor whole-exome sequencing.

The somatic mutation profiles of 2,433 breast cancers refines their genomic and transcriptomic landscapes

PubMed Central

Pereira, Bernard; Chin, Suet-Feung; Rueda, Oscar M.; Vollan, Hans-Kristian Moen; Provenzano, Elena; Bardwell, Helen A.; Pugh, Michelle; Jones, Linda; Russell, Roslin; Sammut, Stephen-John; Tsui, Dana W. Y.; Liu, Bin; Dawson, Sarah-Jane; Abraham, Jean; Northen, Helen; Peden, John F.; Mukherjee, Abhik; Turashvili, Gulisa; Green, Andrew R.; McKinney, Steve; Oloumi, Arusha; Shah, Sohrab; Rosenfeld, Nitzan; Murphy, Leigh; Bentley, David R.; Ellis, Ian O.; Purushotham, Arnie; Pinder, Sarah E.; Børresen-Dale, Anne-Lise; Earl, Helena M.; Pharoah, Paul D.; Ross, Mark T.; Aparicio, Samuel; Caldas, Carlos

2016-01-01

The genomic landscape of breast cancer is complex, and inter- and intra-tumour heterogeneity are important challenges in treating the disease. In this study, we sequence 173 genes in 2,433 primary breast tumours that have copy number aberration (CNA), gene expression and long-term clinical follow-up data. We identify 40 mutation-driver (Mut-driver) genes, and determine associations between mutations, driver CNA profiles, clinical-pathological parameters and survival. We assess the clonal states of Mut-driver mutations, and estimate levels of intra-tumour heterogeneity using mutant-allele fractions. Associations between PIK3CA mutations and reduced survival are identified in three subgroups of ER-positive cancer (defined by amplification of 17q23, 11q13–14 or 8q24). High levels of intra-tumour heterogeneity are in general associated with a worse outcome, but highly aggressive tumours with 11q13–14 amplification have low levels of intra-tumour heterogeneity. These results emphasize the importance of genome-based stratification of breast cancer, and have important implications for designing therapeutic strategies. PMID:27161491

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas.

PubMed

Campbell, Joshua D; Yau, Christina; Bowlby, Reanne; Liu, Yuexin; Brennan, Kevin; Fan, Huihui; Taylor, Alison M; Wang, Chen; Walter, Vonn; Akbani, Rehan; Byers, Lauren Averett; Creighton, Chad J; Coarfa, Cristian; Shih, Juliann; Cherniack, Andrew D; Gevaert, Olivier; Prunello, Marcos; Shen, Hui; Anur, Pavana; Chen, Jianhong; Cheng, Hui; Hayes, D Neil; Bullman, Susan; Pedamallu, Chandra Sekhar; Ojesina, Akinyemi I; Sadeghi, Sara; Mungall, Karen L; Robertson, A Gordon; Benz, Christopher; Schultz, Andre; Kanchi, Rupa S; Gay, Carl M; Hegde, Apurva; Diao, Lixia; Wang, Jing; Ma, Wencai; Sumazin, Pavel; Chiu, Hua-Sheng; Chen, Ting-Wen; Gunaratne, Preethi; Donehower, Larry; Rader, Janet S; Zuna, Rosemary; Al-Ahmadie, Hikmat; Lazar, Alexander J; Flores, Elsa R; Tsai, Kenneth Y; Zhou, Jane H; Rustgi, Anil K; Drill, Esther; Shen, Ronglei; Wong, Christopher K; Stuart, Joshua M; Laird, Peter W; Hoadley, Katherine A; Weinstein, John N; Peto, Myron; Pickering, Curtis R; Chen, Zhong; Van Waes, Carter

2018-04-03

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smoking and/or human papillomavirus (HPV). SCCs harbor 3q, 5p, and other recurrent chromosomal copy-number alterations (CNAs), DNA mutations, and/or aberrant methylation of genes and microRNAs, which are correlated with the expression of multi-gene programs linked to squamous cell stemness, epithelial-to-mesenchymal differentiation, growth, genomic integrity, oxidative damage, death, and inflammation. Low-CNA SCCs tended to be HPV(+) and display hypermethylation with repression of TET1 demethylase and FANCF, previously linked to predisposition to SCC, or harbor mutations affecting CASP8, RAS-MAPK pathways, chromatin modifiers, and immunoregulatory molecules. We uncovered hypomethylation of the alternative promoter that drives expression of the ΔNp63 oncogene and embedded miR944. Co-expression of immune checkpoint, T-regulatory, and Myeloid suppressor cells signatures may explain reduced efficacy of immune therapy. These findings support possibilities for molecular classification and therapeutic approaches. Published by Elsevier Inc.

Method of using 5,10,15,20-tetrakis(carboxyphenyl)porphine for detecting cancers of the lung

DOEpatents

Cole, Dean A.; Moody, III, David C.; Ellinwood, L. Edward; Klein, M. Gerard

1992-01-01

Method using tetra-aryl porphyrins for and, in particular, 5,10,15,20-tetrakis(4-carboxyphenyl)porphine as a fluorescent tracer for cancers of the lung, and as a radiotracer therefor as a complex with .sup.67 Cu. The latter complex also provides a source of beta radiation for selective destruction of lung malignancies as well as gamma radiation useful for image analysis of the situs thereof by single photon emission computed tomography, as an example, both in vivo. Copper-64 may be substituted for the .sup.67 Cu if only radiotracer characteristics are of interest. This lighter isotope of copper is a positron emitter, and positron emission tomography techniques cna be used to locate the malignant tissue mass.

Copy number losses define subgroups of dedifferentiated liposarcoma with poor prognosis and genomic instability.

PubMed

Crago, Aimee M; Socci, Nicholas D; DeCarolis, Penelope; O'Connor, Rachael; Taylor, Barry S; Qin, Li-Xuan; Antonescu, Cristina R; Singer, Samuel

2012-03-01

Molecular events underlying progression of well-differentiated liposarcoma (WDLS) to dedifferentiated liposarcoma (DDLS) are poorly defined. This study sought to identify copy number alterations (CNA) associated with dedifferentiation of WDLS, with DDLS morphology, and with patient outcomes. Fifty-five WDLS and 52 DDLS were analyzed using Agilent 244K comparative genomic hybridization and Affymetrix U133A expression arrays. CNAs were identified by RAE analysis. Thirty-nine of the DDLS specimens were categorized morphologically by a single pathologist. Nine regions of CNA were identified as recurrent in DDLS but not WDLS; 79% of DDLS had at least one of these CNAs. Loss of the chromosome segment 11q23-24, the most common event, was observed only in DDLS that morphologically resembled the genomically complex sarcomas, undifferentiated pleomorphic sarcoma and myxofibrosarcoma. 11q23-24 loss was itself associated with increased genomic complexity in DDLS. Loss of 19q13, but not 11q23-24, was associated with poor prognosis. Median disease-specific survival was shorter for patients with19q13 loss (27 months) than for patients with diploid 19q13 (>90 months; P < 0.0025), and 19q13 loss was associated with local recurrence (HR, 2.86; P = 0.013). Common copy number losses were associated with transcriptional downregulation of potential tumor suppressors and adipogenesis-related genes (e.g., EI24 and CEBPA). Dedifferentiation of WDLS is associated with recurrent CNAs in 79% of tumors. In DDLS, loss of 11q23-24 is associated with genomic complexity and distinct morphology whereas loss of 19q13 predicts poor prognosis. CNAs in liposarcoma improve risk stratification for patients and will help identify potential tumor suppressors driving liposarcoma progression.

Prediction of outcome in newly diagnosed myeloma: a meta-analysis of the molecular profiles of 1905 trial patients

PubMed Central

Shah, V; Sherborne, A L; Walker, B A; Johnson, D C; Boyle, E M; Ellis, S; Begum, D B; Proszek, P Z; Jones, J R; Pawlyn, C; Savola, S; Jenner, M W; Drayson, M T; Owen, R G; Houlston, R S; Cairns, D A; Gregory, W M; Cook, G; Davies, F E; Jackson, G H; Morgan, G J; Kaiser, M F

2018-01-01

Robust establishment of survival in multiple myeloma (MM) and its relationship to recurrent genetic aberrations is required as outcomes are variable despite apparent similar staging. We assayed copy number alterations (CNA) and translocations in 1036 patients from the NCRI Myeloma XI trial and linked these to overall survival (OS) and progression-free survival. Through a meta-anlysis of these data with data from MRC Myeloma IX trial, totalling 1905 newly diagnosed MM patients (NDMM), we confirm the association of t(4;14), t(14;16), t(14;20), del(17p) and gain(1q21) with poor prognosis with hazard ratios (HRs) for OS of 1.60 (P=4.77 × 10−7), 1.74 (P=0.0005), 1.90 (P=0.0089), 2.10 (P=8.86 × 10−14) and 1.68 (P=2.18 × 10−14), respectively. Patients with ‘double-hit’ defined by co-occurrence of at least two adverse lesions have an especially poor prognosis with HRs for OS of 2.67 (P=8.13 × 10−27) for all patients and 3.19 (P=1.23 × 10−18) for intensively treated patients. Using comprehensive CNA and translocation profiling in Myeloma XI we also demonstrate a strong association between t(4;14) and BIRC2/BIRC3 deletion (P=8.7 × 10−15), including homozygous deletion. Finally, we define distinct sub-groups of hyperdiploid MM, with either gain(1q21) and CCND2 overexpression (P<0.0001) or gain(11q25) and CCND1 overexpression (P<0.0001). Profiling multiple genetic lesions can identify MM patients likely to relapse early allowing stratification of treatment. PMID:28584253

Nursing Assistants' Job Commitment: Effect of Nursing Home Organizational Factors and Impact on Resident Well-Being

ERIC Educational Resources Information Center

Bishop, Christine E.; Weinberg, Dana Beth; Leutz, Walter; Dossa, Almas; Pfefferle, Susan G.; Zincavage, Rebekah M.

2008-01-01

Purpose: The purpose of this study was to investigate (a) whether certified nursing assistants (CNAs) are more committed to nursing home jobs when they perceive their jobs as enhanced (greater autonomy, use of knowledge, teamwork), and (b) whether CNA job commitment affects resident satisfaction. Design and Methods: A qualitative exploration of…

CNA Maritime Asia Project. Workshop Two: Naval Developments in Asia

DTIC Science & Technology

2012-08-01

exercises. 3 See for instance, VADM (ret.) Yoji Koda , “A New Carrier Race? Strategy, Force Planning, and JS Hyuga,” Naval War College Review 64, no...power to the country. 5 Yoji Koda , “The Emerging Republic of Korea Navy: A Japanese Perspective,” Naval War College Review 63, no. 2 (Spring 2010

The Classroom "Is" the Newsroom: CNA: A Wire Service Journalism Training Model to Bridge the Theory versus Practice Dichotomy

ERIC Educational Resources Information Center

Tulloch, Christopher David; Mas i Manchon, Lluis

2018-01-01

Although recent journalism education literature has promoted constant innovation, creative curriculum design, and the adaptation of teaching methodologies to the requirements of a fiercely competitive media marketplace, the permanent face-off between the academy and the profession has often led to theoretical models distanced from real newsroom…

Consequences of Empowered CNA Teams in Nursing Home Settings: A Longitudinal Assessment

ERIC Educational Resources Information Center

Yeatts, Dale E.; Cready, Cynthia M.

2007-01-01

Purpose: Recent studies have concluded that there is a lack of "patient-centered" care in nursing homes and subsequently a need for nursing home culture change. As a result, a variety of new, promising initiatives have been introduced, with most of these incorporating the use of "empowered" employees. The purpose of this study…

Death and Dying Attitudes, Anxieties, and Fears of Certified Nursing Assistants: A Descriptive Study

ERIC Educational Resources Information Center

Hamilton, Josephine A.

2010-01-01

The critical role of Certified Nursing Assistants (CNAs) to help elderly nursing home residents' move through declining conditions or diseases to death is salient. It is important for CNAs and nursing home leaders to understand CNAs' attitudes, fears, and anxieties toward death and dying. The quantitative study investigated CNA's…

Joint Interagency Coordination Group - Cyber: Empowering the Combatant Commanders against the no-borders threat

DTIC Science & Technology

2009-05-04

inconvenience and denial of Internet service, CNAs pose a threat to national security, if the right computer is hacked , to every day operations, if baking...expert J3: Current Operations Rep Private Sector/Civilian: cyber/CNA SME J5 Future Operations Rep Private Sector/Civilian: cyber/CND SME Table 2

Ground System Survivability Overview

DTIC Science & Technology

2012-03-27

Avoidance Blast Mitigation Optimization Customer ILIR RDT&E Funding 5.0 % 0.5% GSS has a proven, technically proficient workforce that meets...Evaluation of Defensive-Aid Suites (ARMED) Common Automatic Fire Extinguishing System ( CAFES ) Transparent Armor Development Ground Combat Vehicle...Survey TRADOC (WFO, CNA, etc) Voice of the Customer Sy st em s En gi ne er in g Publish overarching MIL-STD, design guidelines, technical

CNA Maritime Asia Project. Workshop One: The Yellow and East China Seas

DTIC Science & Technology

2012-05-01

TEU) were all in the world’s top 25 ports.2 Shanghai, positioned at the crossroads of the Yellow Sea, East China Sea, and Yangtze River, is the...Sea, and Yangtze River, is the largest port in the world, shipping over 29 million TEU in 2011.4 Nearly 57% of China’s total trade volume emanates

The Perception of "Training Availability" among Certified Nurse Aides: Relationship to CNA Performance, Turnover, Attitudes, Burnout, and Empowerment

ERIC Educational Resources Information Center

Yeatts, Dale E.; Cready, Cynthia; Swan, James; Shen, Yuying

2010-01-01

The purpose of this study was to examine the relationship between the certified nurse aides' (CNAs) perception that "training is always available when needed" and the CNAs' performance, turnover, attitudes, burnout, and empowerment. The data came from a larger study where a self-administered survey instrument was completed by 359 CNAs…

Improving the U.S. Navy Riverine Capability: Lessons from the Colombian Experience

DTIC Science & Technology

2007-12-01

29 A. EVOLUTIONARY RESPONSE TO THREATS .................................. 30 1. La Violencia ...and joint familiarity of terms within coordinating units.38 As defined in the CNA report, logistics might be affected by the type of medical...riverine transformation associated with each. Four specific events will be addressed: the period of La Violencia that took place from 1948 to 1957

Spectrum of mutations in leiomyosarcomas identified by clinical targeted next-generation sequencing.

PubMed

Lee, Paul J; Yoo, Naomi S; Hagemann, Ian S; Pfeifer, John D; Cottrell, Catherine E; Abel, Haley J; Duncavage, Eric J

2017-02-01

Recurrent genomic mutations in uterine and non-uterine leiomyosarcomas have not been well established. Using a next generation sequencing (NGS) panel of common cancer-associated genes, 25 leiomyosarcomas arising from multiple sites were examined to explore genetic alterations, including single nucleotide variants (SNV), small insertions/deletions (indels), and copy number alterations (CNA). Sequencing showed 86 non-synonymous, coding region somatic variants within 151 gene targets in 21 cases, with a mean of 4.1 variants per case; 4 cases had no putative mutations in the panel of genes assayed. The most frequently altered genes were TP53 (36%), ATM and ATRX (16%), and EGFR and RB1 (12%). CNA were identified in 85% of cases, with the most frequent copy number losses observed in chromosomes 10 and 13 including PTEN and RB1; the most frequent gains were seen in chromosomes 7 and 17. Our data show that deletions in canonical cancer-related genes are common in leiomyosarcomas. Further, the spectrum of gene mutations observed shows that defects in DNA repair and chromosomal maintenance are central to the biology of leiomyosarcomas, and that activating mutations observed in other common cancer types are rare in leiomyosarcomas. Copyright © 2017 Elsevier Inc. All rights reserved.

Do Medicaid Wage Pass-through Payments Increase Nursing Home Staffing?

PubMed Central

Feng, Zhanlian; Lee, Yong Suk; Kuo, Sylvia; Intrator, Orna; Foster, Andrew; Mor, Vincent

2010-01-01

Objective To assess the impact of state Medicaid wage pass-through policy on direct-care staffing levels in U.S. nursing homes. Data Sources Online Survey Certification and Reporting (OSCAR) data, and state Medicaid nursing home reimbursement policies over the period 1996–2004. Study Design A fixed-effects panel model with two-step feasible-generalized least squares estimates is used to examine the effect of pass-through adoption on direct-care staff hours per resident day (HPRD) in nursing homes. Data Collection/Extraction Methods A panel data file tracking annual OSCAR surveys per facility over the study period is linked with annual information on state Medicaid wage pass-through and related policies. Principal Findings Among the states introducing wage pass-through over the study period, the policy is associated with between 3.0 and 4.0 percent net increases in certified nurse aide (CNA) HPRD in the years following adoption. No discernable pass-through effect is observed on either registered nurse or licensed practical nurse HPRD. Conclusions State Medicaid wage pass-through programs offer a potentially effective policy tool to boost direct-care CNA staffing in nursing homes, at least in the short term. PMID:20403054

Methicillin-susceptible Staphylococcus aureus endocarditis isolates are associated with clonal complex 30 genotype and a distinct repertoire of enterotoxins and adhesins.

PubMed

Nienaber, Juhsien J C; Sharma Kuinkel, Batu K; Clarke-Pearson, Michael; Lamlertthon, Supaporn; Park, Lawrence; Rude, Thomas H; Barriere, Steve; Woods, Christopher W; Chu, Vivian H; Marín, Mercedes; Bukovski, Suzana; Garcia, Patricia; Corey, G Ralph; Korman, Tony; Doco-Lecompte, Thanh; Murdoch, David R; Reller, L Barth; Fowler, Vance G

2011-09-01

Using multinational collections of methicillin-susceptible Staphylococcus aureus (MSSA) isolates from infective endocarditis (IE) and soft tissue infections (STIs), we sought to (1) validate the finding that S. aureus in clonal complex (CC) 30 is associated with hematogenous complications and (2) test the hypothesis that specific genetic characteristics in S. aureus are associated with infection severity. IE and STI isolates from 2 cohorts were frequency matched by geographic origin. Isolates underwent spa typing to infer CC and multiplex polymerase chain reaction for presence of virulence genes. 114 isolate pairs were genotyped. IE isolates were more likely to be CC30 (19.5% vs 6.2%; P = .005) and to contain 3 adhesins (clfB, cna, map/eap; P < .0001 for all) and 5 enterotoxins (tst, sea, sed, see, and sei; P ≤ .005 for all). CC30 isolates were more likely to contain cna, tst, sea, see, seg, and chp (P < .05 for all). MSSA IE isolates were significantly more likely to be CC30 and to possess a distinct repertoire of virulence genes than MSSA STI isolates from the same region. The genetic basis of this association requires further study.

Netwar

NASA Astrophysics Data System (ADS)

Keen, Arthur A.

2006-04-01

This paper describes technology being developed at 21st Century Technologies to automate Computer Network Operations (CNO). CNO refers to DoD activities related to Attacking and Defending Computer Networks (CNA & CND). Next generation cyber threats are emerging in the form of powerful Internet services and tools that automate intelligence gathering, planning, testing, and surveillance. We will focus on "Search-Engine Hacks", queries that can retrieve lists of router/switch/server passwords, control panels, accessible cameras, software keys, VPN connection files, and vulnerable web applications. Examples include "Titan Rain" attacks against DoD facilities and the Santy worm, which identifies vulnerable sites by searching Google for URLs containing application-specific strings. This trend will result in increasingly sophisticated and automated intelligence-driven cyber attacks coordinated across multiple domains that are difficult to defeat or even understand with current technology. One traditional method of CNO relies on surveillance detection as an attack predictor. Unfortunately, surveillance detection is difficult because attackers can perform search engine-driven surveillance such as with Google Hacks, and avoid touching the target site. Therefore, attack observables represent only about 5% of the attacker's total attack time, and are inadequate to provide warning. In order to predict attacks and defend against them, CNO must also employ more sophisticated techniques and work to understand the attacker's Motives, Means and Opportunities (MMO). CNO must use automated reconnaissance tools, such as Google, to identify information vulnerabilities, and then utilize Internet tools to observe the intelligence gathering, planning, testing, and collaboration activities that represent 95% of the attacker's effort.

Artificial Intelligence and Autonomy: Opportunities and Challenges

DTIC Science & Technology

2017-10-01

Cleared for Public Release Artificial Intelligence & Autonomy Opportunities and Challenges Andrew Ilachinski October 2017 Copyright © 2017 CNA... Artificial Intelligence & Autonomy Opportunities and 5a. CONTRACT NUMBER N00014-16-D-5003 Challenges 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 0605154N...conducted by unmanned and increasingly autonomous weapon systems. This exploratory study considers the state-of-the-art of artificial intelligence (AI

The U.S. India Defense Relationship: Putting the Foundational Agreements in Perspective

DTIC Science & Technology

2017-02-01

forces, and the benefits outweigh any incremental costs in providing the data feed. 65 For example, Siddharth Varadarajan argued in The Hindu that...Cleared for Public Release DISTRIBUTION STATEMENT A. Approved for public release: distribution unlimited. The U.S.-India Defense...opinion of CNA at the time of issue. Distribution DISTRIBUTION STATEMENT A. Approved for public release: distribution unlimited. PUBLIC  RELEASE

CNA Independent Assessment: Air Force Acquisition. Return to Excellence

DTIC Science & Technology

2009-02-01

symptoms that indicate problems with its acquisition system and processes. Some of the most pressing of these symptoms have been: Numerous cost...indicate problems with its acquisition system and proc- esses. Some of the most pressing of these symptoms have been: Frequent cost-schedule performance...Military Deputy MS Milestone NAVAIR Naval Air Systems Command PAR Program Assessment Review PCO Principal Contracting Officer PDR

"¡Puño en Alto!" The Nicaraguan Literacy Campaign and What It Means for Literacy Today

ERIC Educational Resources Information Center

Bender-Slack, Delane

2018-01-01

Modern notions of literacy can be informed by past successes in the field of literacy. One of the most successful national literacy campaigns occurred in Nicaragua in 1980 and was called "Cruzada Nacional de Alfabetización" (CNA). The fight against illiteracy to provide a space for marginalized voices in Nicaragua is a story worth…

The photochemistry of some possible cometary CN parent species

NASA Technical Reports Server (NTRS)

Halpern, Joshua B.

1987-01-01

Laboratory work on the photochemistry of HC3N, C4N2, and CH3CN in relation to their possible role as CN parent molecules in comets is discussed. Photodissociation of HC3N, photolysis of C4N2, and quantum yields of excited CN(B) and CN(A) radicals from the VUV photolysis of CH3CN are considered.

Genome-wide identification of significant aberrations in cancer genome.

PubMed

Yuan, Xiguo; Yu, Guoqiang; Hou, Xuchu; Shih, Ie-Ming; Clarke, Robert; Zhang, Junying; Hoffman, Eric P; Wang, Roger R; Zhang, Zhen; Wang, Yue

2012-07-27

Somatic Copy Number Alterations (CNAs) in human genomes are present in almost all human cancers. Systematic efforts to characterize such structural variants must effectively distinguish significant consensus events from random background aberrations. Here we introduce Significant Aberration in Cancer (SAIC), a new method for characterizing and assessing the statistical significance of recurrent CNA units. Three main features of SAIC include: (1) exploiting the intrinsic correlation among consecutive probes to assign a score to each CNA unit instead of single probes; (2) performing permutations on CNA units that preserve correlations inherent in the copy number data; and (3) iteratively detecting Significant Copy Number Aberrations (SCAs) and estimating an unbiased null distribution by applying an SCA-exclusive permutation scheme. We test and compare the performance of SAIC against four peer methods (GISTIC, STAC, KC-SMART, CMDS) on a large number of simulation datasets. Experimental results show that SAIC outperforms peer methods in terms of larger area under the Receiver Operating Characteristics curve and increased detection power. We then apply SAIC to analyze structural genomic aberrations acquired in four real cancer genome-wide copy number data sets (ovarian cancer, metastatic prostate cancer, lung adenocarcinoma, glioblastoma). When compared with previously reported results, SAIC successfully identifies most SCAs known to be of biological significance and associated with oncogenes (e.g., KRAS, CCNE1, and MYC) or tumor suppressor genes (e.g., CDKN2A/B). Furthermore, SAIC identifies a number of novel SCAs in these copy number data that encompass tumor related genes and may warrant further studies. Supported by a well-grounded theoretical framework, SAIC has been developed and used to identify SCAs in various cancer copy number data sets, providing useful information to study the landscape of cancer genomes. Open-source and platform-independent SAIC software is implemented using C++, together with R scripts for data formatting and Perl scripts for user interfacing, and it is easy to install and efficient to use. The source code and documentation are freely available at http://www.cbil.ece.vt.edu/software.htm.

Preparation of Optically Transparent Films of Poly(methyl methacrylate) (PMMA) and Montmorillonite

DTIC Science & Technology

2001-11-01

methacrylate] [PMMA] and Montmorillonite DISTRIBUTION: Approved for public release, distribution unlimited This paper is part of the following report...Society V6.4 Preparation of Optically Transparent Films of Poly(methyl methacrylate) (PMMA) and Montmorillonite Elena Vasiliul, Chyi-Shan Wang"’ 2...exchanged with 1.40 meq/g of dimethyl dehydrogenated tallow ammonium from a sodium montmorillonite , Cloisite Na+ (CNa). Since the cation-exchange

PRISM. Volume 2, Number 3, June 2011

DTIC Science & Technology

2011-06-01

Institute (SIPRI) Background Paper (Stockholm: SIPRI, April 2009), 3, available at <http://books.sipri.org/files/misc/ SIPRIBP0904a.pdf>. 41 Martin ...Conflict (Washington, DC: CNA, 2010), 28. 46 Nenad Dimitrijevic and Petra Kovacs, “Managing Hatred and Distrust: Changes from the Bottom and the Top...Dimitrijevic and Petra Kovacs (Hungary: Open Society Institute, 2004), xxiv. 47 Simonsen, “Addressing Ethnic Divisions in Post-Conflict Institution-Building

The U.S.-India Defense Relationship: Putting the Foundational Agreements in Perspective

DTIC Science & Technology

2017-02-01

data feeds to other militaries to be interoperable with U.S. forces, and the benefits outweigh any incremental costs in providing the data feed. 65...Cleared for Public Release DISTRIBUTION STATEMENT A. Approved for public release: distribution unlimited. The U.S.-India Defense...opinion of CNA at the time of issue. Distribution DISTRIBUTION STATEMENT A. Approved for public release: distribution unlimited. PUBLIC  RELEASE

Stayers, Leavers, and Switchers among Certified Nursing Assistants in Nursing Homes: A Longitudinal Investigation of Turnover Intent, Staff Retention, and Turnover

ERIC Educational Resources Information Center

Rosen, Jules; Stiehl, Emily M.; Mittal, Vikas; Leana, Carrie R.

2011-01-01

Purpose: Studies of certified nursing assistant (CNA) turnover in nursing homes are typically cross-sectional and include full-time and part-time workers. We conducted a longitudinal study to evaluate the job factors and work attitudes associated with just full-time staying or leaving. For those who did not stay, we assessed reasons for leaving…

Synergistic Effect of Fluconazole and Calcium Channel Blockers against Resistant Candida albicans

PubMed Central

Liu, Shuyuan; Yue, Longtao; Gu, Wenrui; Li, Xiuyun; Zhang, Liuping; Sun, Shujuan

2016-01-01

Candidiasis has increased significantly recently that threatens patients with low immunity. However, the number of antifungal drugs on the market is limited in comparison to the number of available antibacterial drugs. This fact, coupled with the increased frequency of fungal resistance, makes it necessary to develop new therapeutic strategies. Combination drug therapy is one of the most widely used and effective strategy to alleviate this problem. In this paper, we were aimed to evaluate the combined antifungal effects of four CCBs (calcium channel blockers), amlodipine (AML), nifedipine (NIF), benidipine (BEN) and flunarizine (FNZ) with fluconazole against C. albicans by checkerboard and time-killing method. In addition, we determined gene (CCH1, MID1, CNA1, CNB1, YVC1, CDR1, CDR2 and MDR1) expression by quantitative PCR and investigated the efflux pump activity of resistant candida albicans by rhodamine 6G assay to reveal the potential mechanisms. Finally, we concluded that there was a synergy when fluconazole combined with the four tested CCBs against resistant strains, with fractional inhibitory concentration index (FICI) <0.5, but no interaction against sensitive strains (FICI = 0.56 ~ 2). The mechanism studies revealed that fluconazole plus amlodipine caused down-regulating of CNA1, CNB1 (encoding calcineurin) and YVC1 (encoding calcium channel protein in vacuole membrane). PMID:26986478

TAGCNA: A Method to Identify Significant Consensus Events of Copy Number Alterations in Cancer

PubMed Central

Yuan, Xiguo; Zhang, Junying; Yang, Liying; Zhang, Shengli; Chen, Baodi; Geng, Yaojun; Wang, Yue

2012-01-01

Somatic copy number alteration (CNA) is a common phenomenon in cancer genome. Distinguishing significant consensus events (SCEs) from random background CNAs in a set of subjects has been proven to be a valuable tool to study cancer. In order to identify SCEs with an acceptable type I error rate, better computational approaches should be developed based on reasonable statistics and null distributions. In this article, we propose a new approach named TAGCNA for identifying SCEs in somatic CNAs that may encompass cancer driver genes. TAGCNA employs a peel-off permutation scheme to generate a reasonable null distribution based on a prior step of selecting tag CNA markers from the genome being considered. We demonstrate the statistical power of TAGCNA on simulated ground truth data, and validate its applicability using two publicly available cancer datasets: lung and prostate adenocarcinoma. TAGCNA identifies SCEs that are known to be involved with proto-oncogenes (e.g. EGFR, CDK4) and tumor suppressor genes (e.g. CDKN2A, CDKN2B), and provides many additional SCEs with potential biological relevance in these data. TAGCNA can be used to analyze the significance of CNAs in various cancers. It is implemented in R and is freely available at http://tagcna.sourceforge.net/. PMID:22815924

Synergistic Effect of Fluconazole and Calcium Channel Blockers against Resistant Candida albicans.

PubMed

Liu, Shuyuan; Yue, Longtao; Gu, Wenrui; Li, Xiuyun; Zhang, Liuping; Sun, Shujuan

2016-01-01

Candidiasis has increased significantly recently that threatens patients with low immunity. However, the number of antifungal drugs on the market is limited in comparison to the number of available antibacterial drugs. This fact, coupled with the increased frequency of fungal resistance, makes it necessary to develop new therapeutic strategies. Combination drug therapy is one of the most widely used and effective strategy to alleviate this problem. In this paper, we were aimed to evaluate the combined antifungal effects of four CCBs (calcium channel blockers), amlodipine (AML), nifedipine (NIF), benidipine (BEN) and flunarizine (FNZ) with fluconazole against C. albicans by checkerboard and time-killing method. In addition, we determined gene (CCH1, MID1, CNA1, CNB1, YVC1, CDR1, CDR2 and MDR1) expression by quantitative PCR and investigated the efflux pump activity of resistant candida albicans by rhodamine 6G assay to reveal the potential mechanisms. Finally, we concluded that there was a synergy when fluconazole combined with the four tested CCBs against resistant strains, with fractional inhibitory concentration index (FICI) <0.5, but no interaction against sensitive strains (FICI = 0.56 ~ 2). The mechanism studies revealed that fluconazole plus amlodipine caused down-regulating of CNA1, CNB1 (encoding calcineurin) and YVC1 (encoding calcium channel protein in vacuole membrane).

Methicillin-Susceptible Staphylococcus aureus Endocarditis Isolates Are Associated With Clonal Complex 30 Genotype and a Distinct Repertoire of Enterotoxins and Adhesins

PubMed Central

Nienaber, Juhsien J.C.; Sharma Kuinkel, Batu K.; Clarke-Pearson, Michael; Lamlertthon, Supaporn; Park, Lawrence; Rude, Thomas H.; Barriere, Steve; Woods, Christopher W.; Chu, Vivian H.; Marín, Mercedes; Bukovski, Suzana; Garcia, Patricia; Corey, G.Ralph; Korman, Tony; Doco-Lecompte, Thanh; Murdoch, David R.; Reller, L. Barth

2011-01-01

Background. Using multinational collections of methicillin-susceptible Staphylococcus aureus (MSSA) isolates from infective endocarditis (IE) and soft tissue infections (STIs), we sought to (1) validate the finding that S. aureus in clonal complex (CC) 30 is associated with hematogenous complications and (2) test the hypothesis that specific genetic characteristics in S. aureus are associated with infection severity. Methods. IE and STI isolates from 2 cohorts were frequency matched by geographic origin. Isolates underwent spa typing to infer CC and multiplex polymerase chain reaction for presence of virulence genes. Results. 114 isolate pairs were genotyped. IE isolates were more likely to be CC30 (19.5% vs 6.2%; P = .005) and to contain 3 adhesins (clfB, cna, map/eap; P < .0001 for all) and 5 enterotoxins (tst, sea, sed, see, and sei; P ≤ .005 for all). CC30 isolates were more likely to contain cna, tst, sea, see, seg, and chp (P < .05 for all). Conclusions. MSSA IE isolates were significantly more likely to be CC30 and to possess a distinct repertoire of virulence genes than MSSA STI isolates from the same region. The genetic basis of this association requires further study. PMID:21844296

The roles of CYP6AY1 and CYP6ER1 in imidacloprid resistance in the brown planthopper: Expression levels and detoxification efficiency.

PubMed

Bao, Haibo; Gao, Hongli; Zhang, Yixi; Fan, Dongzhe; Fang, Jichao; Liu, Zewen

2016-05-01

Two P450 monooxygenase genes, CYP6AY1 and CYP6ER1, were reported to contribute importantly to imidacloprid resistance in the brown planthopper, Nilaparvata lugens. Although recombinant CYP6AY1 could metabolize imidacloprid efficiently, the expression levels of CYP6ER1 gene were higher in most resistant populations. In the present study, three field populations were collected from different countries, and the bioassay, RNAi and imidacloprid metabolism were performed to evaluate the importance of two P450s in imidacloprid resistance. All three populations, DOT (Dongtai) from China, CNA (Chainat) from Thailand and HCM (Ho Chi Minh) from Vietnam, showed high resistance to imidacloprid (57.0-, 102.9- and 89.0-fold). CYP6AY1 and CYP6ER1 were both over expressed in three populations, with highest ratio of 13.2-fold for CYP6ER1 in HCM population. Synergism test and RNAi analysis confirmed the roles of both P450 genes in imidacloprid resistance. However, CYP6AY1 was indicated more important in CNA population, and CYP6AY1 and CYP6ER1 were equal in HCM population, although the expression level of CYP6ER1 (13.2-fold) was much higher than that of CYP6AY1 (4.11-fold) in HCM population. Although the recombinant proteins of both P450 genes could metabolize imidacloprid efficiently, the catalytic activity of CYP6AY1 (Kcat=3.627 pmol/min/pmol P450) was significantly higher than that of CYP6ER1 (Kcat=2.785 pmol/min/pmol P450). It was supposed that both P450 proteins were important for imidacloprid resistance, in which CYP6AY1 metabolized imidacloprid more efficiently and CYP6ER1 gene could be regulated by imidacloprid to a higher level. Copyright © 2015 Elsevier B.V. All rights reserved.

AACSD: An atomistic analyzer for crystal structure and defects

NASA Astrophysics Data System (ADS)

Liu, Z. R.; Zhang, R. F.

2018-01-01

We have developed an efficient command-line program named AACSD (Atomistic Analyzer for Crystal Structure and Defects) for the post-analysis of atomic configurations generated by various atomistic simulation codes. The program has implemented not only the traditional filter methods like the excess potential energy (EPE), the centrosymmetry parameter (CSP), the common neighbor analysis (CNA), the common neighborhood parameter (CNP), the bond angle analysis (BAA), and the neighbor distance analysis (NDA), but also the newly developed ones including the modified centrosymmetry parameter (m-CSP), the orientation imaging map (OIM) and the local crystallographic orientation (LCO). The newly proposed OIM and LCO methods have been extended for all three crystal structures including face centered cubic, body centered cubic and hexagonal close packed. More specially, AACSD can be easily used for the atomistic analysis of metallic nanocomposite with each phase to be analyzed independently, which provides a unique pathway to capture their dynamic evolution of various defects on the fly. In this paper, we provide not only a throughout overview on various theoretical methods and their implementation into AACSD program, but some critical evaluations, specific testing and applications, demonstrating the capability of the program on each functionality.

Documentation and Testing of the WEAP Model for the Rio Grande/Bravo Basin

DTIC Science & Technology

2006-08-01

border between Texas and the Mexican states of Coahuila, Nuevo Leon and Tamaulipas (Appendix B, Figure 32). There are four reservoirs of interest in this...Camargo - Ciudad Acuna - Ciudad Anhuac - Ciudad Juarez - Matamoros - Metropolitan Monterrey - Nuevo Laredo - Reynosa - Piedras Negras...Rivera, and Jorge A. Hidalgo. (2001). “Sistema de apoyo a la toma de decisions para el manejo integral del agua en cuencas.” IMTA/CNA, Proyecto

Al Qaeda in the Indian Subcontinent (AQIS): An Al Qaeda Affiliate Case Study

DTIC Science & Technology

2017-10-01

conduct this assessment, CNA used a comparative methodology that included eight case studies on groups affiliated or associated with Al-Qaeda. These case...Case Study Pamela G. Faber and Alexander Powell October 2017 This work was performed under Federal Government Contract No. N00014-16-D-5003. Copyright...Director Center for Stability and Development Center for Strategic Studies REPORT DOCUMENTATION PAGE Form ApprovedOMB No. 0704-0188 Public reporting burden

Japan’s Territorial Disputes: CNA Maritime Asia Project: Workshop Three

DTIC Science & Technology

2013-06-01

strengthen, their exercise programs with the Japan Self -Defense Forces (JSDF). These exercises prepare both militaries to deter the use of force and, if...around the islands should be noted. After Lee’s visit, Korea mobilized its air defenses when it claimed a Japanese Self -Defense Force helicopter...lock incidents reported by Japan’s Maritime Self -Defense Force, the first against a destroyer-based helicopter and the second against the frigate

Toward Efficient Military Retirement Accrual Charges

DTIC Science & Technology

2017-01-01

benefited from reviews provided by Al Robbert of RAND and David Rodney of the CNA Corporation. 1 CHAPTER ONE Introduction Primary elements of the costs ...leaving the military. This report focuses on retirement benefits . Public Law (PL) 98–94, enacted in 1984 and implemented in fiscal year (FY) 1985...in the current budget the cost of future retirement benefits asso- ciated with current manning decisions. Under PL 98–94, DoD includes an accrual

Water Scarcity: A Selected Bibliography

DTIC Science & Technology

2011-06-01

2008-2009: The Biennial Report on Freshwater Resources. Washington, DC: Island Press, 2009. 402pp. (TD345 .G633 2009) Grosskruger, Paul L...www.securityandclimate.cna.org/report/ National%20Security%20and%20the%20Threat%20of%20Climate%20Change.pdf Sullivan, Paul J., and Natalie Nasrallah. Improving Natural...2010): 9-14. ProQuest Chen, Linus . "Deja Vu: ESA [Endangered Species Act] Water Clashes in Klamath & Southeast." Natural Resources & Environment 24

Current Effects of Army Materiel Command Operation Order 16 189 at TACOM LCMC

DTIC Science & Technology

2017-05-25

Alexandria, VA: CNA Corporation. 78 Creswell, J. W. (2015). Educational Research: Planning, Conducting, and Evaluating Quantitative and Qualitative...research and development that relate to military requirements and test and evaluation . (d)(3) The Secretary shall establish or designate a single office or...for research. 4. Collect data. 5. Analyze and interpret the data. 42 6. Report and evaluate the research. Step 4 of the research process is

Life Cycle Cost Model for Very High Speed Integrated Circuits.

DTIC Science & Technology

1984-09-01

Intermediate CDFD =Cost to Ship $3.13 (CONUS) N/A All L/Global Tml. XXIX from Factory to $6.00 (Europe) Depot. Dollars/ $6.00 (Asia) * Pound/Trip CDID =Cost... ANALISIS -10%) 179360. 28. 634. 180021. 209 i. , . . - TITL EN~WURfG P1U1’V E PRM CNa TOAL 00g SIGAL P- M ’ASIC C2UP-BIKAR LMLI =MI~D MT2MSIS-10

Evaluation of the Navys Sea/Shore Flow Policy

DTIC Science & Technology

2016-06-01

CNA developed an independent Discrete -Event Simulation model to evaluate and assess the effect of alternative sea/shore flow policies. In this study...remains, even if the system is optimized. In building a Discrete -Event Simulation model, we discovered key factors that should be included in the... Discrete -Event Simulation model to evaluate the impact of sea/shore flow policy (the DES-SSF model) and compared the results with the SSFM for one

Optimizing Adversary Training and the Structure of the Navy Adversary Fleet

DTIC Science & Technology

2013-09-01

ORGANIZATION REPORT NUMBER 9. SPONSORING /MONITORING AGENCY NAME(S) AND ADDRESS(ES) OPNAV N98 2000 Navy Pentagon , Room 5C469 Washington DC, 20350...an overhaul of existing computers and encryption in the range operations centers (CDR R. Van Diepen, OPNAV Simulator Requirements Officer, personal...1.0. Using a simulated annealing heuristic algorithm in conjunction with the utility assignments, CNA found, in order of priority, that the following

Application of a Uniform Price Quality Adjusted Discount Auction for Assigning Voluntary Separation Pay

DTIC Science & Technology

2011-03-01

consistent with economic theory which suggested that younger individuals should discount income at a higher rate than older individuals ( Mankiw , 2004...http://www.cna.org Henderson, D. R. (2007). The concise encyclopedia of economics . Indianapolis, IN: Liberty Fund. Mankiw , N. G. (2004...survey data was used to estimate the effects of personal, professional and economic factors on a Marine officer’s decision to participate in a voluntary

Work autonomy of certified nursing assistants in long-term care facilities: discrepant perceptions between nursing supervisors and certified nursing assistants.

PubMed

Liu, Li-Fan; Liu, Wei-Pei; Wang, Jong-Yi

2011-09-01

Despite increasing demand of certified nursing assistants (CNAs) in long-term care (LTC) facilities, their work autonomy delegated by nursing supervisors remains ambiguous and varied. This study investigates the CNAs' role in LTC facilities by examining the degrees of work autonomy of CNAs from the perspectives of nursing supervisors and CNAs. Whether the characteristics of institutions including ownership of facilities, bed size, staffing levels, and the occupancy rate affected the CNAs' work autonomy and delegations was also examined. A stratified random sampling method was used to sample LTC facilities in Taiwan. A self-administered structured questionnaire was answered by a senior nursing supervisor and CNA in each sampled institution for their perception of work autonomy in the 5 main aspects of CNAs' job contents: personal care, affiliated nursing care, auxiliary medical service, social care, and administration services. Student t test and general linear models (GLM) were used to test the mean differences of CNAs' work autonomy and their relationship with the institutions' characteristics. Nursing supervisors and CNAs both rated the highest scores of work autonomy in the aspect of personal care, and the lowest scores in the aspect of affiliated nursing care. However, the nursing supervisors expected higher work autonomy of CNAs on the work items particularly in affiliated nursing care and auxiliary medical services than did the CNAs (P < .05). The institutional-level factors were significantly associated with perceptions of nursing supervisors toward CNAs' work autonomy. The ownership (hospital-based or freestanding homes), sizes (capacity), occupancy rates, CNA staff numbers of the long-term care facilities, and resident numbers were related to the CNAs' work autonomy as perceived by their nursing supervisors. No difference between the aspects of administration activities and social care was seen. There are discordance views towards CNAs' work autonomy both in nursing supervisors and CNAs across different settings in LTC institutions. The characteristics of institutions influence perceptions of CNAs' work autonomy as perceived by nursing supervisors. Clear and mandated regulation of CNA job contents is needed for their work identity and autonomy to improve the quality of care in LTC facilities. Copyright © 2011 American Medical Directors Association. Published by Elsevier Inc. All rights reserved.

Impact of conventional or intensive milk replacer programs on Holstein heifer performance through six months of age and during first lactation.

PubMed

Raeth-Knight, M; Chester-Jones, H; Hayes, S; Linn, J; Larson, R; Ziegler, D; Ziegler, B; Broadwater, N

2009-02-01

The objectives were to evaluate the impact of conventional or intensive milk replacer (MR) feeding programs on heifer calf performance through 6 mo of age, age at first calving, and first lactation performance. At 3 (+/-1 d) d of age, 133 Holstein heifer calves from 3 commercial dairy farms were randomly assigned, within calf source, to a conventional [20% crude protein (CP), 20% fat] or intensive MR (28% CP, 18% fat). Milk replacer treatments and percent solids were 1) conventional nonacidified (CNA), 13.9%; 2) conventional acidified (CA), 13.9%; 3) modified intensive high solids (IHS), 16.7%; 4) modified intensive low solids (ILS), 12.5%; and 5) intensive high solids, high feeding (IHSHF), 16.7%. Calves were individually housed and remained on trial for 56 d. At 2 mo of age, heifers were grouped in pens by treatment with 6 heifers per pen (4 pens per treatment). An 18.1% CP grower concentrate mix (dry matter basis) was fed to heifers that received a conventional MR and a 21.2% CP grower concentrate mix was fed to heifers that received the intensive MR preweaning. Heifers were offered 2.45 kg/d (dry matter basis) of their respective grower concentrate mix for 112 d plus free access to hay and water. At approximately 24 wk of age, heifers were transported to a second-stage grower before returning to their respective farms approximately 1 mo before calving. First-lactation performance was determined using Dairy Herd Improvement Association records. The IHSHF treatment resulted in increased calf body weight and hip height during the preweaning and early postweaning (PEP) period and the postweaning heifer grower (PHG) period as compared with the conventional (CNA and CA) or modified intensive MR treatments (IHS and ILS). Calves receiving the IHS treatment were heavier at d 56 of the PEP period compared with the conventional or ILS treatments; however, this growth advantage was not maintained in the PHG period. Feed cost per kilogram of gain during the PEP period was lowest for CNA and CA, intermediate for IHS and ILS, and highest for the IHSHF treatment. There was no effect of MR feeding program on first-lactation performance; however, heifers that received the IHSHF MR preweaning calved 27.5 d earlier than those fed a conventional MR.

Determination of denudation rates by the measurement of meteoric 10Be in Guadiana river sediment samples (Spain) by low-energy AMS.

PubMed

Padilla, S; López-Gutiérrez, J M; Sampath, D M R; Boski, T; Nieto, J M; García-León, M

2018-09-01

The concentration of meteoric 10 Be in estuarine sediment samples has been measured by Spanish Accelerator for Radionuclides Analysis (SARA) at CNA and subsequently used to assess the denudation rate in Guadiana river basin together with the sediment budget method, on both sides of the frontier between Spain and Portugal. The two methods yielded coincident results. The estimation by the 10 Be method gave the denudation rate of (0.76 ± 0.10) × 10 -2  cm/y. After correcting for an approximate 80% attenuation of the sediment discharge into the ocean, caused by the river dams, the sediment budget method yielded the rate of (0.77 ± 0.17) × 10 -2  cm/y. Copyright © 2018 Elsevier Ltd. All rights reserved.

Close Vicinity of PrP Expressing Cells (FDC) with Noradrenergic Fibers in Healthy Sheep Spleen

PubMed Central

Lezmi, S.; Hunsmann, G.; Baron, T.

2001-01-01

In naturally and experimentally occurring scrapie in sheep, prions invade the immune system and replicate in lymphoid organs. Here we analysed immunohistochemically, in seven spleens of 6-month-old healthy sheep, the nature of the cells expressing prion protein (PrP) potentially supporting prion replication, as well as their relationship with autonomic innervation. PrP was identified using either RB1 rabbit antiserum or 4F2 monoclonal antibody directed against AA 108–123 portion of the bovine and AA 79–92 of human prion protein respectively. Using double labelling analysis, we demonstrated that PrPc is expressed by follicular dendritic cells using a specific monoclonal antibody (CNA42). We also showed the close vicinity of these PrP expressing cells with noradrenergic fibers, using a polyclonal tyrosine hydroxylase antibody. Our results may help the study of the cellular requirements for the possible neuroinvasion from the spleen. PMID:11785673

The Tuareg: A Nation Without Borders? A CNA Strategic Studies Conference Report

DTIC Science & Technology

2013-05-01

claim to “ethnic specificity.” An ethnic branch of the Berbers , the Tuareg are culturally and linguistically unique. Despite strong tribal and caste...The Tuareg are an ethnic branch of the Berbers but also have mem- bers of Arab and black African ancestry. Often referred to as the “Kurds of the...cluster of closely related dia- lects of a southern Berber language group (Tamasheq, Tamajeq, Tamahaq), which, while different, are mutually

American Grand Strategy and Seapower. Conference Report

DTIC Science & Technology

2011-11-01

Senior Fellow, Watson  Institute for International Studies, Brown University  10 Speakers  The Honorable  Seth  Cropsey, Senior Advisor, CNA; Senior...and the anticipation of future security challenges based on past experiences. Connections between seapower and prosperity Dr. Seth Cropsey noted...Force, is a second-rate Air Force. 91 Participant biographies Seth Cropsey Dr. Seth Cropsey served as Deputy Under Secretary of the Navy for

Assessing the Impact of and Needs for Navy Language, Regional Expertise, and Culture Training

DTIC Science & Technology

2012-10-01

Assessing the Impact of and Needs for Navy Language, Regional Expertise, and Culture Training Neil B. Carey • Edward J. Schmitz • Zachary T...Francisco, CA, gives medication to a child during a medical & dental community assistance project (MEDCAP/DENCAP). Petty Officer Barker is stationed aboard...concerns about this questionnaire, please refer them to Neil Carey , Ph.D., at 703-824-2356 or careyn@cna.org. 77 78 Appendix D Appendix D

CNA/The Institute for Statecraft Meeting on Evaluating and Countering the Threat from the Islamic State

DTIC Science & Technology

2015-08-10

Charlie Hebdo.  Mastery of social media enables IS to exist as a virtual global caliphate. Islamic State: From Jihadi Movement to Potential Global...military skills but also in classic terror methods , in propaganda techniques, and in deception. As a conventional military, IS has demonstrated...Salafism, a strict constructionist , originalist interpretation of the core texts of Islam. Their intention is to reform Islam and return to what they

78 FR 9529 - National School Lunch Program and School Breakfast Program: Nutrition Standards for All Foods...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-02-08

...This rule proposes to amend the National School Lunch Program and School Breakfast Program regulations consistent with amendments made in the Healthy, Hunger-Free Kids Act of 2010 (HHFKA). The HHFKA requires that the Secretary promulgate proposed regulations to establish nutrition standards for foods sold in schools other than those foods provided under the Child Nutrition Act of 1966 (CNA) and the Richard B. Russell National School Lunch Act (NSLA). The HHFKA amends the CNA, requiring that such standards shall be consistent with the most recent Dietary Guidelines for Americans and that the Secretary shall consider authoritative scientific recommendations for nutrition standards; existing school nutrition standards, including voluntary standards for beverages and snack foods; current State and local standards; the practical application of the nutrition standards; and special exemptions for infrequent school-sponsored fundraisers (other than fundraising through vending machines, school stores, snack bars, a la carte sales and any other exclusions determined by the Secretary). The HHFKA also amended the NSLA to require that schools participating in the National School Lunch Program make potable water available to children at no charge in the place where lunches are served during the meal service. These proposed changes are intended to improve the health and well-being of the Nation's children, increase consumption of healthful foods during the school day and create an environment that reinforces the development of healthy eating habits.

Fast Decomposition of Three-Component Spectra of Fluorescence Quenching by White and Grey Methods of Data Modeling.

PubMed

Kałka, Andrzej J; Turek, Andrzej M

2018-04-03

'White' and 'grey' methods of data modeling have been employed to resolve the heterogeneous fluorescence from a fluorophore mixture of 9-cyanoanthracene (CNA), 10-chloro-9-cyanoanthracene (ClCNA) and 9,10-dicyanoanthracene (DCNA) into component individual fluorescence spectra. The three-component spectra of fluorescence quenching in methanol were recorded for increasing amounts of lithium bromide used as a quencher. The associated intensity decay profiles of differentially quenched fluorescence of single components were modeled on the basis of a linear Stern-Volmer plot. These profiles are necessary to initiate the fitting procedure in both 'white' and 'grey' modeling of the original data matrices. 'White' methods of data modeling, called also 'hard' methods, are based on chemical/physical laws expressed in terms of some well-known or generally accepted mathematical equations. The parameters of these models are not known and they are estimated by least squares curve fitting. 'Grey' approaches to data modeling, also known as hard-soft modeling techniques, make use of both hard-model and soft-model parts. In practice, the difference between 'white' and 'grey' methods lies in the way in which the 'crude' fluorescence intensity decays of the mixture components are estimated. In the former case they are given in a functional form while in the latter as digitized curves which, in general, can only be obtained by using dedicated techniques of factor analysis. In the paper, the initial values of the Stern-Volmer constants of pure components were evaluated by both 'point-by-point' and 'matrix' versions of the method making use of the concept of wavelength dependent intensity fractions as well as by the rank annihilation factor analysis applied to the data matrices of the difference fluorescence spectra constructed in two ways: from the spectra recorded for a few excitation lines at the same concentration of a fluorescence quencher or classically from a series of the spectra measured for one selected excitation line but for increasing concentration of the quencher. The results of multiple curve resolution obtained by all types of the applied methods have been scrutinized and compared. In addition, the effect of inadequacy of sample preparation and increasing instrumental noise on the shape of the resolved spectral profiles has been studied on several datasets mimicking the measured data matrices. Graphical Abstract ᅟ.

Determining the Sensitivity of CAT-ASVAB (Computerized Adaptive Testing- Armed Services Vocational Aptitude Battery) Scores to Changes in Item Response Curves with the Medium of Administration

DTIC Science & Technology

1986-08-01

most examinees. Therefore it appears psychometrically ac - ceptable for the CAT -ASVAB project to proceed without item recalibration based on...MEMORANDUM DETERMINING THE SENSITIVITY OF CAT -ASVAB SCORES TO CHANGES IN ITEM RESPONSE CURVES WITH THE MEDIUM OF ADMINISTRATION D. R. Divgi...Subj: Center for Naval Analyses Research Memorandum 86-189 End: (1) CNA Research Memorandum 86-189, "Determining the Sensitivity of CAT -ASVAB

U.S. Navy Capstone Strategy Policy, Vision and Concept Documents. What to Consider Before You Write One

DTIC Science & Technology

2009-03-01

Richard M. Nixon was President of the United States and Admiral Elmo R. Zumwalt, Jr. was Chief of Naval Operations. The listing above captures only...Moreover, since the 1980s, and largely mandated by the U.S. Congress, a torrent of unclassified U.S. government strategy documents has been released...documents? (IV) CNA • Personalities change • 8 U.S. Presidents • 13 Secretaries of Defense • 11 Chairmen of the Joint Chiefs of Staff • 15

The Chemistry of Nitrogen Compounds in Combustion Processes.

DTIC Science & Technology

1984-03-02

the A levels above v - 5 do contribute to the spectrum. Thus, we tentatively conclude that multiphoton excitation is a major process in this system...populations of these six CN( A ) levels , as shown in Figure 8. There is a strong inversion with more than half of the CN(A) formed being in the v-2 level. It...apparent that the CN( A ) levels shown in Figure 7, all for v ) 3, represent only a few percent of the total excitation. The dynamics of the dissociation

U.S. Naval Strategy in the 1980s: Selected Documents

DTIC Science & Technology

2008-12-01

Linton Brooks, USN (Ret.), Commander Mitch Brown, USN (Ret.), Captain John Byron, USN (Ret.), Hon. Seth Cropsey (CNA), Colonel George M. Dallas (MCCDC...Secretary Lehman, Admiral James Watkins , General P. X. Kelley, and Admiral Carlisle A. H. Trost in the key articles published in Proceedings and that...Admiral Thomas B. Hayward, 1 July 1978–30 June 1982 Admiral James D. Watkins , 30 June 1982–30 June 1986 Admiral Carlisle A. H. Trost, 1 July 1986–29

Deterrence and Influence: The Navy’s Role in Preventing War. Revision 1

DTIC Science & Technology

2009-03-01

are designed to influence actors at the earliest phases of the conflict spectrum. Our objective is to analyze how U.S. non-nuclear capabilities can...34 Foreign Affairs (Fall 1991), pp. 66-82; Paul H. Nitze, "Is It Time to Junk Our Nukes?" Washington Post , 16 January 1994, p. Cl; Charles T. Allan...gain new insights and test our ideas. We consulted with SMEs from CNA, IDA, OPNAV, OSD, USSTRATCOM, academic institutions, and various think tanks

Report of the Defense Science Board Task Force on Trends and Implications of Climate Change on National and International Security

DTIC Science & Technology

2011-10-01

Propulsion Laboratory Dr. Diane Evans Jet Propulsion Laboratory CAPT Tim Gallaudet US Navy Task Force on Climate Change Mr. David Goldwyn State...Ashley Moran Strauss Center, University of Texas, Austin DOD’s (Minerva) Climate Change and African Political Stability Project CAPT Timothy ... Gallaudet Office of the Oceanographer of the Navy Navy’s Climate Change Task Force Dr. Sherri Goodman, Dr. Ralph Espach and Mr. Peter MacKenzie CNA

U.S. Navy Capstone Strategies and Concepts (1991-2000): Strategy, Policy, Concept, and Vision Documents

DTIC Science & Technology

2012-03-01

PROJECT NUMBER 5e. TASK NUMBER 5f. WORK UNIT NUMBER 7. PERFORMING ORGANIZATION NAME(S) AND ADDRESS(ES) CNA Corporation,4825 Mark Center Drive... industry & USMC OMFTS experience  Project Team created BPR “activity model” (Oct-Dec 1995) OPNAV N513, N812; HQMC Plans, PP&O; MCCDC; NDC; SRA...Alexandria,VA,22311 8. PERFORMING ORGANIZATION REPORT NUMBER 9. SPONSORING/MONITORING AGENCY NAME(S) AND ADDRESS(ES) 10. SPONSOR/MONITOR’S ACRONYM(S) 11

A Comparison of Services Utilized by Acupuncture and Non-Acupuncture Patients in the Military Health System

DTIC Science & Technology

2009-06-26

three diagnoses of acupuncture patients within the MHS in FY08 were: (a) Lumbago, (b) Myalgia and Myositis unspecified, and (c) Cervicalgia. Table 1...of Total Diagnosis Description Encounters Lumbago Myalgia and Myositis unspecified Cervical gia Acute or chronic pain in the lumbar or sacral...Lumbago, Myalgia and Myositis unspecified, or Cervicalgia during FY08. This study is based off the CNA study of CAM usage in the MHS conducted by Jaditz

Report of the Eleventh Seminar Conducted by CNA and ISKRAN on Russian-American Relations, December, 1998. Volume 2: Detailed Discussions

DTIC Science & Technology

2000-02-01

Grigory Raporta The View from the Russian Security Council . . . . . . . 95 Meeting with Ambassador Uspensky THIS PAGE INTENTIONALLY LEFT BLANK Eleventh...One can draw the unpleasant analogy that Russia, like Weimar Germany, must pay a kind of reparations for losing the Cold War. In this view , IMF assis...were difficult years for U.S.-Russian relations. Primakov did not always say "yes" like Mr. Kozyrev . But Primakov, while promoting Russia’s national

Occurrence of genes coding for MSCRAMM and biofilm-associated protein Bap in Staphylococcus spp. isolated from bovine subclinical mastitis and relationship with somatic cell counts.

PubMed

Zuniga, Eveline; Melville, Priscilla A; Saidenberg, André B S; Laes, Marco A; Gonsales, Fernanda F; Salaberry, Sandra R S; Gregori, Fabio; Brandão, Paulo E; dos Santos, Franklin G B; Lincopan, Nilton E; Benites, Nilson R

2015-12-01

This study aimed to elucidate aspects of the epidemiology of bovine subclinical mastitis through the assessment of genes encoding MSCRAMM (microbial surface components recognizing adhesive matrix molecules - a group of adhesins) and protein Bap (implicated in biofilm formation), in coagulase-positive (CPS) and coagulase-negative (CNS) Staphylococcus isolated from subclinical mastitis. Milk samples were collected for microbiological exams, somatic cell count (SCC) and a survey of the genes coding for MSCRAMM (cna, eno, ebpS, fnbA, fnbB and fib) and biofilm-associated protein Bap (bap) in 106 Staphylococcus spp. isolates using PCR. The frequencies of occurrence of eno (82.1%), fnbA (72.6%), fib (71.7%) and bap (56.6%) were higher (P < 0.0001) compared with the other assessed genes (cna, ebpS and fnbB). The higher frequency of occurrence (P < 0.005) of the bap gene in CNS compared with CPS suggests that in these species biofilm formation is an important mechanism for the persistence of the infection. The medians of the SCCs in the samples where eno, fnbA, fib and bap genes were detected were higher compared with Staphylococcus without the assessed genes (P < 0.05) and negative samples (P < 0.01), which indicated that the presence of these MSCRAMM may be related to a higher intensity of the inflammatory process. Copyright © 2015 Elsevier Ltd. All rights reserved.

Environmental issues relevant to the preparation of USAID/Mozambique`s country program strategic plan

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

NONE

1994-01-01

The present moment offers a unique opportunity to address Mozambique`s environmental problems, according to this assessment of Mozambique`s natural and environmental resources. Conducted to help USAID/M prepare its Country Program Strategic Plan (CPSP), the assessment covers: (1) the status of Mozambique`s natural resources (soil and land, water, vegetative cover, wildlife/biodiversity and nonrenewable resources), with emphasis on conservation and management of biological diversity and tropical forests; (2) shortcomings in the knowledge and management of these resources; (3) the efforts of other donors and NGOs to address natural resources degradation; and (4) recommendations. According to the report, while all three of themore » CPSP`s focus areas -- income generation, social services, the democratic governance -- can contribute notably to sustainable use of the environment, the income focus will have the most impact, as families who are struggling to survive often turn to destructive patterns of land use. The report cautions USAID/M not to neglect, in its emphasis on NGOs, the state agencies that will be responsible for guaranteeing security in areas such as land rights. In particular, the Mission should promote the policymaking and enforcement role of the National Commission for the Environment (CNA) and should involve the CNA in Mission environmental assessments. Appendices include a summary of donor environmental activities in Mozambique; a tabulated portrait of Mozambique`s forest resources and forestry sector; and a list of state agencies with responsibilities in Mozambique`s coastal zone.« less

Copy number profiling of adult relapsed B-cell precursor acute lymphoblastic leukemia reveals potential leukemia progression mechanisms.

PubMed

Ribera, Jordi; Zamora, Lurdes; Morgades, Mireia; Mallo, Mar; Solanes, Neus; Batlle, Montserrat; Vives, Susana; Granada, Isabel; Juncà, Jordi; Malinverni, Roberto; Genescà, Eulàlia; Guàrdia, Ramon; Mercadal, Santiago; Escoda, Lourdes; Martinez-Lopez, Joaquín; Tormo, Mar; Esteve, Jordi; Pratcorona, Marta; Martinez-Losada, Carmen; Solé, Francesc; Feliu, Evarist; Ribera, Josep-Maria

2017-11-01

The outcome of relapsed adult acute lymphoblastic leukemia (ALL) remains dismal despite new therapeutic approaches. Previous studies analyzing relapse samples have shown a high degree of heterogeneity regarding gene alterations without an evident relapse signature. Bone marrow or peripheral blood samples from 31 adult B-cell precursor ALL patients at first relapse, and 21 paired diagnostic samples were analyzed by multiplex ligation probe-dependent amplification (MLPA). Nineteen paired diagnostic and relapse samples of these 21 patients were also analyzed by SNP arrays. A trend to acquire homozygous CDKN2A/B deletions and a significant increase in the number of copy number alterations (CNA) was observed from diagnosis to first relapse. Evolution from an ancestral clone was the main pattern of clonal evolution. Relapse samples were extremely heterogeneous regarding CNA frequencies. However, CDKN2A/B, PAX5, ETV6, ATM, IKZF1, VPREB1, and TP53 deletions and duplications of 1q, 8q, 17q, 21, X/Y PAR1, and Xp were frequently detected at relapse. Duplications of genes involved in cell proliferation, drug resistance and stem cell homeostasis regulation, as well as deletions of KDM6A and STAG2 genes emerged as specific alterations at relapse. Genomics of relapsed adult B-cell precursor ALL is highly heterogeneous, although some recurrent lesions involved in essential pathways deregulation were frequently observed. Selective and simultaneous targeting of these deregulated pathways may improve the results of current salvage therapies. © 2017 Wiley Periodicals, Inc.

Molecular diagnosis of cryptococcal meningitis in cerebrospinal fluid: comparison of primer sets for Cryptococcus neoformans and Cryptococcus gattii species complex.

PubMed

Martins, Marilena dos Anjos; Brighente, Kate Bastos Santos; Matos, Terezinha Aparecida de; Vidal, Jose Ernesto; Hipólito, Daise Damaris Carnietto de; Pereira-Chioccola, Vera Lucia

2015-01-01

This study evaluated the use of polymerase chain reaction for cryptococcal meningitis diagnosis in clinical samples. The sensitivity and specificity of the methodology were evaluated using eight Cryptococcus neoformans/C. gattii species complex reference strains and 165 cerebrospinal fluid samples from patients with neurological diseases divided into two groups: 96 patients with cryptococcal meningitis and AIDS; and 69 patients with other neurological opportunistic diseases (CRL/AIDS). Two primer sets were tested (CN4-CN5 and the multiplex CNa70S-CNa70A/CNb49S-CNb-49A that amplify a specific product for C. neoformans and another for C. gattii). CN4-CN5 primer set was positive in all Cryptococcus standard strains and in 94.8% in DNA samples from cryptococcal meningitis and AIDS group. With the multiplex, no 448-bp product of C. gattii was observed in the clinical samples of either group. The 695bp products of C. neoformans were observed only in 64.6% of the cryptococcal meningitis and AIDS group. This primer set was negative for two standard strains. The specificity based on the negative samples from the CTL/AIDS group was 98.5% in both primer sets. These data suggest that the CN4/CN5 primer set was highly sensitive for the identification of C. neoformans/C. gattii species complex in cerebrospinal fluid samples from patients with clinical suspicion of cryptococcal meningitis. Copyright © 2014 Elsevier Editora Ltda. All rights reserved.

The Expanding Context of European and Mediterranean Security: A Joint Project Between the Center for Naval Analyses (CNA) and Centro Militare di Studi Strategici (CeMiSS)

DTIC Science & Technology

2007-04-01

has deployed several police-type assistance missions. The UN’s Food and Agriculture Organization (FAO), has, in the broadest of senses, a "security...34 mandate, inasmuch as food shortages in the world ineluctably are a direct cause of insecurity, which, in turn, is likely to require response by...failure of international institutions, like the International Maritime Organization, to address the environmental and safety impacts of shipping on coastal

The Expanding Context of European and Mediterranean Security: A Joint Project Between the Center for Naval Analyses (CNA) and Centro Militare di Studi Strategici (CeMiSS)

DTIC Science & Technology

2007-07-01

deployed several police-type assistance missions. The UN’s Food and Agriculture Organization (FAO), has, in the broadest of senses, a "security" mandate...inasmuch as food shortages in the world ineluctably are a direct cause of insecurity, which, in turn, is likely to require response by "security... safety impacts of shipping on coastal states 5. Yale University Press (1962) 57 6.3 Modern challenges preventing achievement of desired end states * Flag

The Collagen-Binding Adhesin Is a Virulence Factor in Staphylococcus aureus Keratitis

PubMed Central

Rhem, Marcus N.; Lech, Elizabeth M.; Patti, Joseph M.; McDevitt, Damien; Höök, Magnus; Jones, Dan B.; Wilhelmus, Kirk R.

2000-01-01

A collagen-binding strain of Staphylococcus aureus produced suppurative inflammation in a rabbit model of soft contact lens-associated bacterial keratitis more often than its collagen-binding-negative isogenic mutant. Reintroduction of the cna gene on a multicopy plasmid into the mutant helped it regain its corneal adherence and infectivity. The topical application of a collagen-binding peptide before bacterial challenge decreased S. aureus adherence to deepithelialized corneas. These data suggest that the collagen-binding adhesin is involved in the pathogenesis of S. aureus infection of the cornea. PMID:10816547

Origins of the Human Genome Project

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

Cook-Deegan, Robert

1993-07-01

The human genome project was borne of technology, grew into a science bureaucracy in the US and throughout the world, and is now being transformed into a hybrid academic and commercial enterprise. The next phase of the project promises to veer more sharply toward commercial application, harnessing both the technical prowess of molecular biology and the rapidly growing body of knowledge about DNA structure to the pursuit of practical benefits. Faith that the systematic analysis of DNA structure will prove to be a powerful research tool underlies the rationale behind the genome project. The notion that most genetic information ismore » embedded in the sequence of CNA base pairs comprising chromosomes is a central tenet. A rough analogy is to liken an organism's genetic code to computer code. The coal of the genome project, in this parlance, is to identify and catalog 75,000 or more files (genes) in the software that directs construction of a self-modifying and self-replicating system -- a living organism.« less

Origins of the Human Genome Project

DOE R&D Accomplishments Database

Cook-Deegan, Robert (Affiliation: Institute of Medicine, National Academy of Sciences)

1993-07-01

The human genome project was borne of technology, grew into a science bureaucracy in the United States and throughout the world, and is now being transformed into a hybrid academic and commercial enterprise. The next phase of the project promises to veer more sharply toward commercial application, harnessing both the technical prowess of molecular biology and the rapidly growing body of knowledge about DNA structure to the pursuit of practical benefits. Faith that the systematic analysis of DNA structure will prove to be a powerful research tool underlies the rationale behind the genome project. The notion that most genetic information is embedded in the sequence of CNA base pairs comprising chromosomes is a central tenet. A rough analogy is to liken an organism's genetic code to computer code. The coal of the genome project, in this parlance, is to identify and catalog 75,000 or more files (genes) in the software that directs construction of a self-modifying and self-replicating system -- a living organism.

Editorial

NASA Astrophysics Data System (ADS)

Boerma, Dirk O.; Climent-Font, Aurelio; Respaldiza, Miguel Ángel

2006-08-01

The IBA conference has taken place in different countries from all over the world. It started in the United States in 1973, and since then has been held biennially without interruption, becoming the reference meeting on ion beam analysis and related methods and techniques. In its 17th edition, two Spanish laboratories, one from the Universidad de Sevilla and one from the Universidad Autónoma de Madrid had the honour and responsibility of organizing the conference. These two laboratories are, so far, the only ones in the country equipped with accelerators dedicated to ion beam analysis; the Centro Nacional de Aceleradores (CNA) in Seville and the Centro de Micro-Análisis de Materiales (CMAM) in Madrid. We took up this task enthusiastically, conscious that Spain has only very recently been equipped with IBA techniques and that this event would highlight to the scientific community of our country the importance and involvement of IBA techniques in new scientific and technological developments. The conference was held at the Melia Sevilla Hotel in Seville, Spain from 26 June-1 July 2005. This special issue of Nuclear Instruments and Methods in Physics Research B contains the published proceedings of the conference.

DR-Integrator: a new analytic tool for integrating DNA copy number and gene expression data.

PubMed

Salari, Keyan; Tibshirani, Robert; Pollack, Jonathan R

2010-02-01

DNA copy number alterations (CNA) frequently underlie gene expression changes by increasing or decreasing gene dosage. However, only a subset of genes with altered dosage exhibit concordant changes in gene expression. This subset is likely to be enriched for oncogenes and tumor suppressor genes, and can be identified by integrating these two layers of genome-scale data. We introduce DNA/RNA-Integrator (DR-Integrator), a statistical software tool to perform integrative analyses on paired DNA copy number and gene expression data. DR-Integrator identifies genes with significant correlations between DNA copy number and gene expression, and implements a supervised analysis that captures genes with significant alterations in both DNA copy number and gene expression between two sample classes. DR-Integrator is freely available for non-commercial use from the Pollack Lab at http://pollacklab.stanford.edu/ and can be downloaded as a plug-in application to Microsoft Excel and as a package for the R statistical computing environment. The R package is available under the name 'DRI' at http://cran.r-project.org/. An example analysis using DR-Integrator is included as supplemental material. Supplementary data are available at Bioinformatics online.

A critical narrative analysis of shared decision-making in acute inpatient mental health care.

PubMed

Stacey, Gemma; Felton, Anne; Morgan, Alastair; Stickley, Theo; Willis, Martin; Diamond, Bob; Houghton, Philip; Johnson, Beverley; Dumenya, John

2016-01-01

Shared decision-making (SDM) is a high priority in healthcare policy and is complementary to the recovery philosophy in mental health care. This agenda has been operationalised within the Values-Based Practice (VBP) framework, which offers a theoretical and practical model to promote democratic interprofessional approaches to decision-making. However, these are limited by a lack of recognition of the implications of power implicit within the mental health system. This study considers issues of power within the context of decision-making and examines to what extent decisions about patients' care on acute in-patient wards are perceived to be shared. Focus groups were conducted with 46 mental health professionals, service users, and carers. The data were analysed using the framework of critical narrative analysis (CNA). The findings of the study suggested each group constructed different identity positions, which placed them as inside or outside of the decision-making process. This reflected their view of themselves as best placed to influence a decision on behalf of the service user. In conclusion, the discourse of VBP and SDM needs to take account of how differentials of power and the positioning of speakers affect the context in which decisions take place.

Atomic Scale Investigation of Structural Properties and Glass Forming Ability of Ti100-x Al x Metallic Glasses

NASA Astrophysics Data System (ADS)

Tahiri, M.; Hasnaoui, A.; Sbiaai, K.

2018-03-01

In this work, we employed molecular dynamics (MD) simulations to study Ti-Al metallic glasses (MGs) using the embedded atom method (EAM) potential to model the atomic interaction with different compositions. The results showed evidence of the metallic glass formation induced by the split occurring in the second peak of the radial distribution function (RDF) curves implying both Ti and Al atoms. The common neighbor analysis (CNA) method confirmed the presence of the icosahedral clusters with a maximum amount observed for an alloy with 75 pct of Al. Analysis of coordination numbers (CNs) indicated that the total CNs are nearly unchanged in these systems. Finally, Voronoi tessellation analyses (VTA) showed a higher value of the number of icosahedral units at Ti25Al75 composition. This specific composition represents a nearby peritectic point localized at a low melting point in the Ti-Al binary phase diagram. The glass forming ability (GFA) becomes important when the fraction of Al increases by forming and connecting "icosahedral-like" clusters (12-coordinated <0, 0, 12, 0> and 13-coordinated <0, 1, 10, 2>) and by playing a main role in the structure stability of the Ti-Al MGs.

Atomic Scale Investigation of Structural Properties and Glass Forming Ability of Ti100- x Al x Metallic Glasses

NASA Astrophysics Data System (ADS)

Tahiri, M.; Hasnaoui, A.; Sbiaai, K.

2018-06-01

In this work, we employed molecular dynamics (MD) simulations to study Ti-Al metallic glasses (MGs) using the embedded atom method (EAM) potential to model the atomic interaction with different compositions. The results showed evidence of the metallic glass formation induced by the split occurring in the second peak of the radial distribution function (RDF) curves implying both Ti and Al atoms. The common neighbor analysis (CNA) method confirmed the presence of the icosahedral clusters with a maximum amount observed for an alloy with 75 pct of Al. Analysis of coordination numbers (CNs) indicated that the total CNs are nearly unchanged in these systems. Finally, Voronoi tessellation analyses (VTA) showed a higher value of the number of icosahedral units at Ti25Al75 composition. This specific composition represents a nearby peritectic point localized at a low melting point in the Ti-Al binary phase diagram. The glass forming ability (GFA) becomes important when the fraction of Al increases by forming and connecting "icosahedral-like" clusters (12-coordinated <0, 0, 12, 0> and 13-coordinated <0, 1, 10, 2>) and by playing a main role in the structure stability of the Ti-Al MGs.

Genomic profiling reveals extensive heterogeneity in somatic DNA copy number aberrations of canine hemangiosarcoma

PubMed Central

Thomas, Rachael; Borst, Luke; Rotroff, Daniel; Motsinger-Reif, Alison; Lindblad-Toh, Kerstin; Modiano, Jaime F.; Breen, Matthew

2017-01-01

Canine hemangiosarcoma is a highly aggressive vascular neoplasm associated with extensive clinical and anatomical heterogeneity and a grave prognosis. Comprehensive molecular characterization of hemangiosarcoma may identify novel therapeutic targets and advanced clinical management strategies, but there are no published reports of tumor-associated genome instability and disrupted gene dosage in this cancer. We performed genome-wide microarray-based somatic DNA copy number profiling of 75 primary intra-abdominal hemangiosarcomas from five popular dog breeds that are highly predisposed to this disease. The cohort exhibited limited global genomic instability, compared to other canine sarcomas studied to date, and DNA copy number aberrations (CNAs) were predominantly of low amplitude. Recurrent imbalances of several key cancer-associated genes were evident; however the global penetrance of any single CNA was low and no distinct hallmark aberrations were evident. Copy number gains of dog chromosomes 13, 24 and 31, and loss of chromosome 16, were the most recurrent CNAs involving large chromosome regions, but their relative distribution within and between cases suggests they most likely represent passenger aberrations. CNAs involving CDKN2A, VEGFA and the SKI oncogene were identified as potential driver aberrations of hemangiosarcoma development, highlighting potential targets for therapeutic modulation. CNA profiles were broadly conserved between the five breeds, although subregional variation was evident, including a near two-fold lower incidence of VEGFA gain in Golden Retrievers versus other breeds (22% versus 40%). These observations support prior transcriptional studies suggesting that the clinical heterogeneity of this cancer may reflect the existence of multiple, molecularly-distinct subtypes of canine hemangiosarcoma. PMID:24599718

Genomic profiling reveals extensive heterogeneity in somatic DNA copy number aberrations of canine hemangiosarcoma.

PubMed

Thomas, Rachael; Borst, Luke; Rotroff, Daniel; Motsinger-Reif, Alison; Lindblad-Toh, Kerstin; Modiano, Jaime F; Breen, Matthew

2014-09-01

Canine hemangiosarcoma is a highly aggressive vascular neoplasm associated with extensive clinical and anatomical heterogeneity and a grave prognosis. Comprehensive molecular characterization of hemangiosarcoma may identify novel therapeutic targets and advanced clinical management strategies, but there are no published reports of tumor-associated genome instability and disrupted gene dosage in this cancer. We performed genome-wide microarray-based somatic DNA copy number profiling of 75 primary intra-abdominal hemangiosarcomas from five popular dog breeds that are highly predisposed to this disease. The cohort exhibited limited global genomic instability, compared to other canine sarcomas studied to date, and DNA copy number aberrations (CNAs) were predominantly of low amplitude. Recurrent imbalances of several key cancer-associated genes were evident; however, the global penetrance of any single CNA was low and no distinct hallmark aberrations were evident. Copy number gains of dog chromosomes 13, 24, and 31, and loss of chromosome 16, were the most recurrent CNAs involving large chromosome regions, but their relative distribution within and between cases suggests they most likely represent passenger aberrations. CNAs involving CDKN2A, VEGFA, and the SKI oncogene were identified as potential driver aberrations of hemangiosarcoma development, highlighting potential targets for therapeutic modulation. CNA profiles were broadly conserved between the five breeds, although subregional variation was evident, including a near twofold lower incidence of VEGFA gain in Golden Retrievers versus other breeds (22 versus 40 %). These observations support prior transcriptional studies suggesting that the clinical heterogeneity of this cancer may reflect the existence of multiple, molecularly distinct subtypes of canine hemangiosarcoma.

Stayers, leavers, and switchers among certified nursing assistants in nursing homes: a longitudinal investigation of turnover intent, staff retention, and turnover.

PubMed

Rosen, Jules; Stiehl, Emily M; Mittal, Vikas; Leana, Carrie R

2011-10-01

Studies of certified nursing assistant (CNA) turnover in nursing homes are typically cross-sectional and include full-time and part-time workers. We conducted a longitudinal study to evaluate the job factors and work attitudes associated with just full-time staying or leaving. For those who did not stay, we assessed reasons for leaving and satisfaction following job transition. A random sample of CNAs identified through the Pennsylvania Department of Health's CNA registry, working ≥ 30 hr weekly in a nursing facility was surveyed by telephone at baseline and 1 year later. Of the 620 responding to both surveys, 532 (85.8%) remained (stayers), 52 (8.4%) switched to another facility (switchers), and 36 (5.8%) left the industry (leavers). At baseline, switchers reported higher turnover intentions and fewer benefits compared with stayers and left for new opportunities. Leavers had lower job satisfaction and emotional well-being and left for health reasons. Turnover intentions were predicted by low job satisfaction and low emotional well-being. Actual turnover was predicted only by turnover intentions and by the absence of health insurance. Pay was not a predictor of turnover intent or turnover. There are two distinct groups of CNAs contributing to turnover. Attitudinal factors, such as job satisfaction and emotional well-being, are mediated via turnover intentions to effect actual turnover. Even accounting for methodological differences, this turnover rate is lower than previous studies, which use alternative methods and include part-time workers. This study should help nursing home administrators better understand the work-related factors associated with staff turnover.

Renal and cardiovascular responses to water immersion in trained runners and swimmers

NASA Technical Reports Server (NTRS)

Convertino, V. A.; Tatro, D. L.; Rogan, R. B.

1993-01-01

The purpose of this study was to determine if fluid-electrolyte, renal, hormonal, and cardiovascular responses during and after multi-hour water immersion were associated with aerobic training. Additionally, we compared these responses in those who trained in a hypogravic versus a 1-g environment. Seventeen men comprised three similarly aged groups: six long-distance runners, five competitive swimmers, and six untrained control subjects. Each subject underwent 5 h of immersion in water [mean (SE)] 36.0 (0.5) degrees C to the neck. Immediately before and at each hour of immersion, blood and urine samples were collected and analyzed for sodium (Na), potassium, osmolality, and creatinine (Cr). Plasma antidiuretic hormone and aldosterone were also measured. Hematocrits were used to calculate relative changes in plasma volume (% delta Vpl). Heart rate response to submaximal cycle ergometer exercise (35% peak oxygen uptake) was measured before and after water immersion. Water immersion induced significant increases in urine flow, Na clearance (CNa), and a 3-5% decrease in Vpl. Urine flow during immersion was greater (P < 0.05) in runners [2.4 (0.4) ml.min-1] compared to controls [1.3 (0.1) ml.min-1]. However, % delta Vpl, CCr, CNa and CH2O during immersion were not different (P > 0.05) between runners, swimmers, and controls. After 5 h of immersion, there was an increase (P < 0.05) in submaximal exercise heart rate of 9 (3) and 10 (3) beats.min-1 in both runners and controls, respectively, but no change (P > 0.05) was observed in swimmers.(ABSTRACT TRUNCATED AT 250 WORDS).

Report on the Second KIMS-CNA Conference: The PLA Navys Build-Up and ROK-USN Cooperation

DTIC Science & Technology

2009-02-01

known as the “Military Combat Preparations” (junshi douzheng zhunbei; 军事斗 争 准备) 4) Strategic missions and objectives (zhanlue renwu he mubiao; 战 略任务和目标...junshi douzheng zhunbei; 军事斗 争 准备) 2) “Net-centric warfare” (wangluo zhongxin zhan; 网络中心 战 ), rather than combat platforms (zuozhan pingtai; 作 战 平台...Military Science Warfare Theory and Strategic Studies Department (zhanzheng lilun he zhanlue yanjiu bu; 战 争 理论和 战 略研究部). 20 security and MOOTW.66 The

Report on the KIMS-CNA Conference (2nd): The PLA Navy’s Build-Up and ROK-USN Cooperation, Held in Seoul, Korea on 20 November 2008

DTIC Science & Technology

2009-02-01

Kegan Paul International and The AEI Press, 1996), p. 274. See also his "China’s Push Through the South China Sea: The Interaction of Bureaucratic and...to " green /blue water" navy enable to secure its vast maritime territorial claims with modern combat capability. For long time, the Chinese navy...operational capability placed somewhat between "coastal defense" and "full ocean-going green water fleet." It is conceivable that the Chinese navy’s

Using a Tandem Pelletron accelerator to produce a thermal neutron beam for detector testing purposes.

PubMed

Irazola, L; Praena, J; Fernández, B; Macías, M; Bedogni, R; Terrón, J A; Sánchez-Nieto, B; Arias de Saavedra, F; Porras, I; Sánchez-Doblado, F

2016-01-01

Active thermal neutron detectors are used in a wide range of measuring devices in medicine, industry and research. For many applications, the long-term stability of these devices is crucial, so that very well controlled neutron fields are needed to perform calibrations and repeatability tests. A way to achieve such reference neutron fields, relying on a 3 MV Tandem Pelletron accelerator available at the CNA (Seville, Spain), is reported here. This paper shows thermal neutron field production and reproducibility characteristics over few days. Copyright © 2015 Elsevier Ltd. All rights reserved.

3 GeV Booster Synchrotron Conceptual Design Report

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

Wiedemann, Helmut

2009-06-02

Synchrotron light cna be produced from a relativistic particle beam circulating in a storage ring at extremely high intensity and brilliance over a large spectral region reaching from the far infrared regime to hard x-rays. The particles, either electrons or positrons, radiate as they are deflected in the fields of the storage ring bending magnets or of magnets specially optimized for the production of synchrotron light. The synchrotron light being very intense and well collimated in the forward direction has become a major tool in a large variety of research fields in physics, chemistry, material science, biology, and medicine.

Handbook of Ballistic and Engineering Data for Ammunition. Volume 2. 76-1-42 to 105-1-314 Included

DTIC Science & Technology

1950-07-01

PLaragraphs I General ------------------------------ 1 ITT Description ------------------------- 2- 4 Hm Interior balli3tic data --------------- 6 - 6 IV...Shot T33 be classified as limited standard; by item 30181 , it was made limited procurement type. a. Form factor (Proj Type 7). i, = 0.97. b. Ballistic...01 .90 7- 7 %PU .65 -4- 4w .80 go, PAN.,. II.W CNA PIS 4 ELEVATION MILS t I i f 1 1 1 1 1 1 ; i t 0 200 400 600 Goo 1000 1200 KOO 12 FOR SHELL. HM

IDSA update from the city of brotherly love.

PubMed

Ghandi, R

2000-01-01

Data from a major new trial called START II (Selection of Thymidine Analog Therapy), was presented at this year's Infectious Diseases Society of America (IDSA) conference. One trial compared d4T/ddI/IDV combination therapy with AZT/3TC/IDV in treatment-naive individuals. A second trial, CNA 3003, compared triple NRTI therapy with AZT/3TC/abacavir to dual therapy with AZT/3TC; patients who added abacavir to the treatment showed decreased viral loads. Additional clinical trials using 3TC are detailed. Drug resistance, investigational agents, HIV diagnostic testing, and opportunistic infections are also discussed.

Genomic structures of dysplastic nodule and concurrent hepatocellular carcinoma.

PubMed

Lee, Minho; Kim, Kyung; Kim, Shinn Young; Jung, Seung-Hyun; Yoon, Jonghwan; Kim, Min Sung; Park, Hyeon-Chun; Jung, Eun Sun; Chung, Yeun-Jun; Lee, Sug Hyung

2018-06-24

Although high-grade dysplastic nodule (HGDN) is a preneoplastic lesion that precedes hepatocellular carcinoma (HCC), the genomic structures of HGDN in conjunction with HCC remain elusive. The objective of this study was to identify genomic alterations of HGDN and its difference from HCC that may drive HGDN progression to HCC. We analyzed 16 regions of paired HGDN and HCC from 6 patients using whole-exome sequencing to find somatic mutation and copy number alteration (CNA) profiles of HGDN and HCC. The number of mutations, driver mutations, and CNAs of HGDNs were not significantly different from those of HCCs. We identified that the CNA gain of 1q25.3-1q42.13 was predominant in the HCCs compared to that in the HGDNs. Two cases (one nodule-in-nodule case and another case with closely attached HCC and HGDN) showed several overlapped driver mutations (CTNNB1 and CEBPA) and CNAs (losses of CDKN2A, RB1 and TP53) between HGDNs and HCCs, suggesting their roles in the early HCC development. The other 4 cases with spatially separated HCCs and HGDNs showed few overlapped alterations between the paired HCCs and HGDNs. Mutations in ERBB2 and CCND1, and CNAs (gains of CTNNB1, MET and SMO and losses of PTEN, TP53 and SETD2) were identified as 'HCC-predominant', suggesting their roles in the progression of HGDN to HCC. Our data show that HCCs are direct descendants of HGDNs in some cases, but there is no direct evidence of such relationship in spatially separated cases. Genomic features of HGDN identified in this study provide a useful resource for dissecting clues for the genetic diagnosis of HGDN and HCC. Copyright © 2018. Published by Elsevier Inc.

The role of radiotherapy in the treatment of childhood intracranial germinoma: long-term survival and late effects.

PubMed

Strojan, Primoz; Zadravec, Lorna Zaletel; Anzic, Jozica; Korenjak, Roman; Jereb, Berta

2006-07-01

The aim of the present report was to evaluate the role of radiotherapy in the treatment of childhood intracranial germinoma in view of long-term survival and functional outcome. Nine children with histologically verified intracranial germinomas treated in Slovenia between 1983 and 1995 were reviewed. The four boys and five girls were 8.8-16.9 years old (median, 11.3 years). Five tumors were suprasellar, three were in the pineal region, and one patient had bifocal disease. Two patients had disseminated tumor. All patients received radiotherapy: six to the tumor bed, one to the whole brain, and two to the whole central nervous axis (CNA). The doses to the tumor bed ranged from 30 to 46 Gy (median, 44 Gy) and to the CNA were 24 and 34.5 Gy. Five patients received neoadjuvant cyclophosphamide and three patients, all with beta-human chorionic gonadotropin secreting tumors, received neoadjuvant cisplatin-based chemotherapy. Six patients are alive 12.8-21.8 years (median, 19 years) from diagnosis. The causes of death in three patients were disseminated disease, toxicity of salvage chemotherapy, and secondary etoposide-induced leukemia. All patients with suprasellar tumors presented with overt endocrinopathy. Results of psychological evaluation were subnormal in one out of five patients tested. Estimate of mental deterioration due to therapy ranged from 0% to 30% (median, 15%). Emotional disorder was registered in four patients and psycho-organic syndrome in three. Our results on long-term survival and functional outcome confirm the efficacy and relative safety of limited-field and reduced-dose radiotherapy for childhood intracranial germinoma when supplemented with chemotherapy. Copyright 2006 Wiley-Liss, Inc.

Stayers, Leavers, and Switchers Among Certified Nursing Assistants in Nursing Homes: A Longitudinal Investigation of Turnover Intent, Staff Retention, and Turnover

PubMed Central

Rosen, Jules

2011-01-01

Purpose: Studies of certified nursing assistant (CNA) turnover in nursing homes are typically cross-sectional and include full-time and part-time workers. We conducted a longitudinal study to evaluate the job factors and work attitudes associated with just full-time staying or leaving. For those who did not stay, we assessed reasons for leaving and satisfaction following job transition. Design and Methods: A random sample of CNAs identified through the Pennsylvania Department of Health's CNA registry, working≥30 hr weekly in a nursing facility was surveyed by telephone at baseline and 1 year later. Results: Of the 620 responding to both surveys, 532 (85.8%) remained (stayers), 52 (8.4%) switched to another facility (switchers), and 36 (5.8%) left the industry (leavers). At baseline, switchers reported higher turnover intentions and fewer benefits compared with stayers and left for new opportunities. Leavers had lower job satisfaction and emotional well-being and left for health reasons. Turnover intentions were predicted by low job satisfaction and low emotional well-being. Actual turnover was predicted only by turnover intentions and by the absence of health insurance. Pay was not a predictor of turnover intent or turnover. Implications: There are two distinct groups of CNAs contributing to turnover. Attitudinal factors, such as job satisfaction and emotional well-being, are mediated via turnover intentions to effect actual turnover. Even accounting for methodological differences, this turnover rate is lower than previous studies, which use alternative methods and include part-time workers. This study should help nursing home administrators better understand the work-related factors associated with staff turnover. PMID:21498629

Genome-scale strain designs based on regulatory minimal cut sets.

PubMed

Mahadevan, Radhakrishnan; von Kamp, Axel; Klamt, Steffen

2015-09-01

Stoichiometric and constraint-based methods of computational strain design have become an important tool for rational metabolic engineering. One of those relies on the concept of constrained minimal cut sets (cMCSs). However, as most other techniques, cMCSs may consider only reaction (or gene) knockouts to achieve a desired phenotype. We generalize the cMCSs approach to constrained regulatory MCSs (cRegMCSs), where up/downregulation of reaction rates can be combined along with reaction deletions. We show that flux up/downregulations can virtually be treated as cuts allowing their direct integration into the algorithmic framework of cMCSs. Because of vastly enlarged search spaces in genome-scale networks, we developed strategies to (optionally) preselect suitable candidates for flux regulation and novel algorithmic techniques to further enhance efficiency and speed of cMCSs calculation. We illustrate the cRegMCSs approach by a simple example network and apply it then by identifying strain designs for ethanol production in a genome-scale metabolic model of Escherichia coli. The results clearly show that cRegMCSs combining reaction deletions and flux regulations provide a much larger number of suitable strain designs, many of which are significantly smaller relative to cMCSs involving only knockouts. Furthermore, with cRegMCSs, one may also enable the fine tuning of desired behaviours in a narrower range. The new cRegMCSs approach may thus accelerate the implementation of model-based strain designs for the bio-based production of fuels and chemicals. MATLAB code and the examples can be downloaded at http://www.mpi-magdeburg.mpg.de/projects/cna/etcdownloads.html. krishna.mahadevan@utoronto.ca or klamt@mpi-magdeburg.mpg.de Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Nuclear micro-probe analysis of Arabidopsis thaliana leaves

NASA Astrophysics Data System (ADS)

Ager, F. J.; Ynsa, M. D.; Domínguez-Solís, J. R.; López-Martín, M. C.; Gotor, C.; Romero, L. C.

2003-09-01

Phytoremediation is a cost-effective plant-based approach for remediation of soils and waters which takes advantage of the remarkable ability of some plants to concentrate elements and compounds from the environment and to metabolize various molecules in their tissues, such as toxic heavy metals and organic pollutants. Nowadays, phytoremediation technology is becoming of paramount importance when environmental decontamination is concerned, due to the emerging knowledge of its physiological and molecular mechanisms and the new biological and engineering strategies designed to optimize and improve it. In addition, the feasibility of using plants for environmental cleanup has been confirmed by many different trials around the world. Arabidopsis thaliana plants can be used for basic studies to improve the technology on phytoremediation. Making use of nuclear microscopy techniques, in this paper we study leaves of wild type and transgenic A. thaliana plants grown in a cadmium-rich environment under different conditions. Micro-PIXE, RBS and SEM analyses, performed on the scanning proton micro-probe at the CNA in Seville (Spain), prove that cadmium is preferentially sequestered in the central region of epidermal trichome and allow comparing the effects of genetic modifications.

Single nucleotide polymorphism array karyotyping: a diagnostic and prognostic tool in myelodysplastic syndromes with unsuccessful conventional cytogenetic testing.

PubMed

Arenillas, Leonor; Mallo, Mar; Ramos, Fernando; Guinta, Kathryn; Barragán, Eva; Lumbreras, Eva; Larráyoz, María-José; De Paz, Raquel; Tormo, Mar; Abáigar, María; Pedro, Carme; Cervera, José; Such, Esperanza; José Calasanz, María; Díez-Campelo, María; Sanz, Guillermo F; Hernández, Jesús María; Luño, Elisa; Saumell, Sílvia; Maciejewski, Jaroslaw; Florensa, Lourdes; Solé, Francesc

2013-12-01

Cytogenetic aberrations identified by metaphase cytogenetics (MC) have diagnostic, prognostic, and therapeutic implications in myelodysplastic syndromes (MDS). However, in some MDS patients MC study is unsuccesful. Single nucleotide polymorphism array (SNP-A) based karyotyping could be helpful in these cases. We performed SNP-A in 62 samples from bone marrow or peripheral blood of primary MDS with an unsuccessful MC study. SNP-A analysis enabled the detection of aberrations in 31 (50%) patients. We used the copy number alteration information to apply the International Prognostic Scoring System (IPSS) and we observed differences in survival between the low/intermediate-1 and intermediate-2/high risk patients. We also saw differences in survival between very low/low/intermediate and the high/very high patients when we applied the revised IPSS (IPSS-R). In conclusion, SNP-A can be used successfully in PB samples and the identification of CNA by SNP-A improve the diagnostic and prognostic evaluation of this group of MDS patients. Copyright © 2013 Wiley Periodicals, Inc.

Gold and electrum jewellery in the strategic area of Gadir in Phoenician period

NASA Astrophysics Data System (ADS)

Ortega-Feliu, I.; Gómez-Tubío, B.; Ontalba Salamanca, M. Á.; Respaldiza, M. Á.; de la Bandera, M. L.; Ovejero Zappino, G.

2007-07-01

A set of ancient gold jewellery was found in Cádiz (formerly Gadir, south Spain) in tombs dated in Phoenician-Archaic period (VII-VI century BC), and nowadays is exhibited in the local Museum. The production of this strategic area is of great interest for the knowledge of the commercial routes along the Mediterranean Sea at that time. Part of this production has already been analyzed by the authors, finding compositional differences and identifying soldering procedures, thanks to the use of the external microbeam. Absolutely non destructive analysis was performed. For this work we have again employed PIXE spectrometry with 2.2 MeV protons from the 3 MV Pelletron accelerator at the CNA to characterize the metallic alloys and the manufacturing techniques. We have found an unusual composition characterized by around 50 wt.% gold, 50 wt.% silver and some copper, which can be identified as ELECTRUM. Few analytical data of this particular kind of alloy are reported in the bibliography. The study of these objects can help to follow the trade of metals in the Phoenician-colonial period.

Effects of Hafnium Additions on the Solidification Behavior of Directionally Solidified Superalloys.

DTIC Science & Technology

1981-10-01

h t (3-1) : where R is the instantaneous rate and h is the transient height. This transient was computed ahead of time on an IBM 370 interactive...form of thermocouple EMF output vs. time, taken at various positions serve as input parameters for the TCTEMP deck for the IBM 370. In its present...iuDv oWIiCNA u 41 S~Q 0 01 0, 0 0 0 % 00 .0 C) 1 0o u- I 0 o0 N 0N Itp 0 0 oitoain3 iuOOJ~d aflOA oian WUOied awnlOA S 1241 - 5 .A - _ A A - S

Crystal growth of organics for nonlinear optical applications

NASA Technical Reports Server (NTRS)

Singh, N. B.; Mazelsky, R.

1993-01-01

The crystal growth and characterization of organic and inorganic nonlinear optical materials were extensively studied. For example, inorganic crystals such as thallium arsenic selenide were studied in our laboratory for several years and crystals in sizes over 2.5 cm in diameter are available. Organic crystals are suitable for the ultraviolet and near infrared region, but are relatively less developed than their inorganic counterparts. Very high values of the second harmonic conversion efficiency and the electro-optic coefficient were reported for organic compounds. Single crystals of a binary organic alloy based on m.NA and CNA were grown and higher second harmonic conversion efficiency than the values reported for m.NA were observed.

Integration of copy number and transcriptomics provides risk stratification in prostate cancer: A discovery and validation cohort study

PubMed Central

Ross-Adams, H.; Lamb, A.D.; Dunning, M.J.; Halim, S.; Lindberg, J.; Massie, C.M.; Egevad, L.A.; Russell, R.; Ramos-Montoya, A.; Vowler, S.L.; Sharma, N.L.; Kay, J.; Whitaker, H.; Clark, J.; Hurst, R.; Gnanapragasam, V.J.; Shah, N.C.; Warren, A.Y.; Cooper, C.S.; Lynch, A.G.; Stark, R.; Mills, I.G.; Grönberg, H.; Neal, D.E.

2015-01-01

Background Understanding the heterogeneous genotypes and phenotypes of prostate cancer is fundamental to improving the way we treat this disease. As yet, there are no validated descriptions of prostate cancer subgroups derived from integrated genomics linked with clinical outcome. Methods In a study of 482 tumour, benign and germline samples from 259 men with primary prostate cancer, we used integrative analysis of copy number alterations (CNA) and array transcriptomics to identify genomic loci that affect expression levels of mRNA in an expression quantitative trait loci (eQTL) approach, to stratify patients into subgroups that we then associated with future clinical behaviour, and compared with either CNA or transcriptomics alone. Findings We identified five separate patient subgroups with distinct genomic alterations and expression profiles based on 100 discriminating genes in our separate discovery and validation sets of 125 and 103 men. These subgroups were able to consistently predict biochemical relapse (p = 0.0017 and p = 0.016 respectively) and were further validated in a third cohort with long-term follow-up (p = 0.027). We show the relative contributions of gene expression and copy number data on phenotype, and demonstrate the improved power gained from integrative analyses. We confirm alterations in six genes previously associated with prostate cancer (MAP3K7, MELK, RCBTB2, ELAC2, TPD52, ZBTB4), and also identify 94 genes not previously linked to prostate cancer progression that would not have been detected using either transcript or copy number data alone. We confirm a number of previously published molecular changes associated with high risk disease, including MYC amplification, and NKX3-1, RB1 and PTEN deletions, as well as over-expression of PCA3 and AMACR, and loss of MSMB in tumour tissue. A subset of the 100 genes outperforms established clinical predictors of poor prognosis (PSA, Gleason score), as well as previously published gene signatures (p = 0.0001). We further show how our molecular profiles can be used for the early detection of aggressive cases in a clinical setting, and inform treatment decisions. Interpretation For the first time in prostate cancer this study demonstrates the importance of integrated genomic analyses incorporating both benign and tumour tissue data in identifying molecular alterations leading to the generation of robust gene sets that are predictive of clinical outcome in independent patient cohorts. PMID:26501111

Validated spectrofluorimetric method for the determination of clonazepam in pharmaceutical preparations.

PubMed

Ibrahim, Fawzia; El-Enany, Nahed; Shalan, Shereen; Elsharawy, Rasha

2016-05-01

A simple, highly sensitive and validated spectrofluorimetric method was applied in the determination of clonazepam (CLZ). The method is based on reduction of the nitro group of clonazepam with zinc/CaCl2, and the product is then reacted with 2-cyanoacetamide (2-CNA) in the presence of ammonia (25%) yielding a highly fluorescent product. The produced fluorophore exhibits strong fluorescence intensity at ʎ(em) = 383 nm after excitation at ʎ(ex) = 333 nm. The method was rectilinear over a concentration range of 0.1-0.5 ng/mL with a limit of detection (LOD) of 0.0057 ng/mL and a limit of quantification (LOQ) of 0.017 ng/mL. The method was fully validated and successfully applied to the determination of CLZ in its tablets with a mean percentage recovery of 100.10 ± 0.75%. Method validation according to ICH Guidelines was evaluated. Statistical analysis of the results obtained using the proposed method was successfully compared with those obtained using a reference method, and there was no significance difference between the two methods in terms of accuracy and precision. Copyright © 2015 John Wiley & Sons, Ltd.

Intense uniform precipitation of low-energy electrons over the polar cap

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

Meng, C.; Kroehl, H.W.

1977-06-01

Analysis of precipitating electron data from the Defense Meteorological Satellite Program (DMSP) revealed significant enhancements (as large as two orders of magnitude) over the quiet time level of the low-energy electron flux over the polar cap during magnetic storms in September and October 1974. Strong asymmetry between the two polar caps was observed, and it may indicate that these electrons are of interplanetary (i.e., solar) origin and that their entry is influenced by the interplanetary magnetic field as illustrated by Yeager and Frank (1976) and Fennell et al., (1975). Energy spectra showing the spatial and temporal variations of the phenomenamore » are presented. There also is a region between the equatorward edge of the polar cap enhancement and the poleward edge of the evening auroral precipitation in which the electron flux drops down to the background level. If the observed intense polar cap precipitation is indeed of interplanetary origin, this void region implies that the poleward boundary of the auroral precipitation does not coincide with the equatorward boundary of the open field lines and that their separation cna be as wide as a few degrees in latitude.« less

Chromosomal Minimal Critical Regions in Therapy-Related Leukemia Appear Different from Those of De Novo Leukemia by High-Resolution aCGH

PubMed Central

Itzhar, Nathalie; Dessen, Philippe; Toujani, Saloua; Auger, Nathalie; Preudhomme, Claude; Richon, Catherine; Lazar, Vladimir; Saada, Véronique; Bennaceur, Anelyse; Bourhis, Jean Henri; de Botton, Stéphane; Bernheim, Alain

2011-01-01

Therapy-related acute leukemia (t-AML), is a severe complication of cytotoxic therapy used for primary cancer treatment. The outcome of these patients is poor, compared to people who develop de novo acute leukemia (p-AML). Cytogenetic abnormalities in t-AML are similar to those found in p-AML but present more frequent unfavorable karyotypes depending on the inducting agent. Losses of chromosome 5 or 7 are observed after alkylating agents while balanced translocations are found after topoisomerase II inhibitors. This study compared t-AML to p-AML using high resolution array CGH in order to find copy number abnormalities (CNA) at a higher resolution than conventional cytogenetics. More CNAs were observed in 30 t-AML than in 36 p-AML: 104 CNAs were observed with 63 losses and 41 gains (mean number 3.46 per case) in t-AML, while in p-AML, 69 CNAs were observed with 32 losses and 37 gains (mean number of 1.9 per case). In primary leukemia with a previously “normal” karyotype, 18% exhibited a previously undetected CNA, whereas in the (few) t-AML with a normal karyotype, the rate was 50%. Several minimal critical regions (MCRs) were found in t-AML and p-AML. No common MCRs were found in the two groups. In t-AML a 40kb deleted MCR pointed to RUNX1 on 21q22, a gene coding for a transcription factor implicated in frequent rearrangements in leukemia and in familial thrombocytopenia. In de novo AML, a 1Mb MCR harboring ERG and ETS2 was observed from patients with complex aCGH profiles. High resolution cytogenomics obtained by aCGH and similar techniques already published allowed us to characterize numerous non random chromosome abnormalities. This work supports the hypothesis that they can be classified into several categories: abnormalities common to all AML; those more frequently found in t-AML and those specifically found in p-AML. PMID:21339820

Chromosomal minimal critical regions in therapy-related leukemia appear different from those of de novo leukemia by high-resolution aCGH.

PubMed

Itzhar, Nathalie; Dessen, Philippe; Toujani, Saloua; Auger, Nathalie; Preudhomme, Claude; Richon, Catherine; Lazar, Vladimir; Saada, Véronique; Bennaceur, Anelyse; Bourhis, Jean Henri; de Botton, Stéphane; Bernheim, Alain

2011-02-14

Therapy-related acute leukemia (t-AML), is a severe complication of cytotoxic therapy used for primary cancer treatment. The outcome of these patients is poor, compared to people who develop de novo acute leukemia (p-AML). Cytogenetic abnormalities in t-AML are similar to those found in p-AML but present more frequent unfavorable karyotypes depending on the inducting agent. Losses of chromosome 5 or 7 are observed after alkylating agents while balanced translocations are found after topoisomerase II inhibitors. This study compared t-AML to p-AML using high resolution array CGH in order to find copy number abnormalities (CNA) at a higher resolution than conventional cytogenetics. More CNAs were observed in 30 t-AML than in 36 p-AML: 104 CNAs were observed with 63 losses and 41 gains (mean number 3.46 per case) in t-AML, while in p-AML, 69 CNAs were observed with 32 losses and 37 gains (mean number of 1.9 per case). In primary leukemia with a previously "normal" karyotype, 18% exhibited a previously undetected CNA, whereas in the (few) t-AML with a normal karyotype, the rate was 50%. Several minimal critical regions (MCRs) were found in t-AML and p-AML. No common MCRs were found in the two groups. In t-AML a 40 kb deleted MCR pointed to RUNX1 on 21q22, a gene coding for a transcription factor implicated in frequent rearrangements in leukemia and in familial thrombocytopenia. In de novo AML, a 1 Mb MCR harboring ERG and ETS2 was observed from patients with complex aCGH profiles. High resolution cytogenomics obtained by aCGH and similar techniques already published allowed us to characterize numerous non random chromosome abnormalities. This work supports the hypothesis that they can be classified into several categories: abnormalities common to all AML; those more frequently found in t-AML and those specifically found in p-AML.

Trench-shaped binding sites promote multiple classes of interactions between collagen and the adherence receptors, alpha(1)beta(1) integrin and Staphylococcus aureus cna MSCRAMM.

PubMed

Rich, R L; Deivanayagam, C C; Owens, R T; Carson, M; Höök, A; Moore, D; Symersky, J; Yang, V W; Narayana, S V; Höök, M

1999-08-27

Most mammalian cells and some pathogenic bacteria are capable of adhering to collagenous substrates in processes mediated by specific cell surface adherence molecules. Crystal structures of collagen-binding regions of the human integrin alpha(2)beta(1) and a Staphylococcus aureus adhesin reveal a "trench" on the surface of both of these proteins. This trench can accommodate a collagen triple-helical structure and presumably represents the ligand-binding site (Emsley, J., King, S. L., Bergelson, J. M., and Liddington, R. C. (1997) J. Biol. Chem. 272, 28512-28517; Symersky, J., Patti, J. M., Carson, M., House-Pompeo, K., Teale, M., Moore, D., Jin, L., Schneider, A., DeLucas, L. J., Höök, M., and Narayana, S. V. L. (1997) Nat. Struct. Biol. 4, 833-838). We report here the crystal structure of the alpha subunit I domain from the alpha(1)beta(1) integrin. This collagen-binding protein also contains a trench on one face in which the collagen triple helix may be docked. Furthermore, we compare the collagen-binding mechanisms of the human alpha(1) integrin I domain and the A domain from the S. aureus collagen adhesin, Cna. Although the S. aureus and human proteins have unrelated amino acid sequences, secondary structure composition, and cation requirements for effective ligand binding, both proteins bind at multiple sites within one collagen molecule, with the sites in collagen varying in their affinity for the adherence molecule. We propose that (i) these evolutionarily dissimilar adherence proteins recognize collagen via similar mechanisms, (ii) the multisite, multiclass protein/ligand interactions observed in these two systems result from a binding-site trench, and (iii) this unusual binding mechanism may be thematic for proteins binding extended, rigid ligands that contain repeating structural motifs.

The C2 Domain Protein Cts1 Functions in the Calcineurin Signaling Circuit during High-Temperature Stress Responses in Cryptococcus neoformans ▿ †

PubMed Central

Aboobakar, Eanas F.; Wang, Xuying; Heitman, Joseph; Kozubowski, Lukasz

2011-01-01

Calcineurin is a conserved calcium/calmodulin-dependent serine/threonine-specific protein phosphatase that acts in cell stress responses. Calcineurin is essential for growth at 37°C and for virulence of the human fungal pathogen Cryptococcus neoformans, but its substrates remain unknown. The C2 domain-containing, phospholipid-binding protein Cts1 was previously identified as a multicopy suppressor of a calcineurin mutation in C. neoformans. Here we further characterize the function of Cts1 and the links between Cts1 and calcineurin. GFP-Cts1 localizes to cytoplasmic puncta and colocalizes with the endosomal marker FM4-64. The cts1Δ mutant shows a distinct FM4-64 staining pattern, suggesting involvement of Cts1 in endocytic trafficking. In large budded cells, GFP-Cts1 localizes transiently at the mother bud neck, as a single ring that undergoes contraction. mCherry-Cts1 colocalizes with the GFP-tagged calcineurin catalytic subunit Cna1 at sites of mRNA processing at 37°C, suggesting that Cts1 and calcineurin function coordinately during thermal stress. GFP-Cts1 exhibits slower electrophoretic mobility for cells grown at 37°C than for cells grown at 24°C, and the shift to a higher molecular weight is more pronounced in the presence of the calcineurin inhibitor FK506. In vitro treatment with calf intestinal alkaline phosphatase (CIP) restores faster electrophoretic mobility to GFP-Cts1, suggesting that Cts1 is phosphorylated at 37°C and may be dephosphorylated in a calcineurin-dependent manner. mCherry-Cts1 also coimmunoprecipitates with GFP-Cna1, with greater complex formation at 37°C than at 24°C. Taken together, these findings support potential roles for Cts1 in endocytic trafficking, mRNA processing, and cytokinesis and suggest that Cts1 is a substrate of calcineurin during high-temperature stress responses. PMID:22002655

Global epigenetic profiling identifies methylation subgroups associated with recurrence-free survival in meningioma

PubMed Central

Olar, Adriana; Wani, Khalida M; Wilson, Charmaine D; Zadeh, Gelareh; DeMonte, Franco; Jones, David TW; Pfister, Stefan M; Sulman, Erik P; Aldape, Kenneth D

2017-01-01

Meningioma is the most common primary brain tumor and carries a substantial risk of local recurrence. Methylation profiles of meningioma and their clinical implications are not well understood. We hypothesized that aggressive meningiomas have unique DNA methylation patterns that could be used to better stratify patient management. Samples (n=140) were profiled using the Illumina HumanMethylation450 BeadChip. Unsupervised modeling on a training set (n=89) identified 2 molecular methylation subgroups of meningioma (MM) with significantly different recurrence free survival (RFS) times between the groups: a prognostically unfavorable subgroup (MM-UNFAV) and a prognostically favorable subgroup (MM-FAV). This finding was validated in the remaining 51 samples and led to a baseline meningioma methylation classifier (bMMC) defined by 283 CpG loci (283-bMMC). To further optimize a recurrence predictor, probes subsumed within the baseline classifier were subject to additional modeling using a similar training/validation approach, leading to a 64-CpG loci meningioma methylation predictor (64-MMP). After adjustment for relevant clinical variables [WHO grade, mitotic index, Simpson grade, sex, location, and copy number aberrations (CNA)] multivariable analyses for RFS showed that the baseline methylation classifier was not significant (p=0.0793). The methylation predictor however was significantly associated with tumor recurrence (p<0.0001). CNA were extracted from the 450k intensity profiles. Tumor samples in the MM-UNFAV subgroup showed an overall higher proportion of CNAs compared to the MM-FAV subgroup tumors and the CNAs were complex in nature. CNAs in the MM-UNFAV subgroup included recurrent losses of 1p, 6q, 14q and 18q, and gain of 1q, all of which were previously identified as indicators of poor outcome. In conclusion, our analyses demonstrate robust DNA methylation signatures in meningioma that correlate with CNAs and stratify patients by recurrence risk. PMID:28130639

Winery vermicomposts to control the leaching of diuron, imidacloprid and their metabolites: role of dissolved organic carbon content.

PubMed

Fernández-Bayo, Jesús D; Nogales, Rogelio; Romero, Esperanza

2015-01-01

Soil organic amendment addition is an effective practice in Mediterranean areas due to its associated high agricultural benefits and its potential to reduce the pesticide impact on water resources. However, their metabolites have received scarce attention, even when they may pose more risk than their parent compounds. Two winery vermicomposts obtained from spent grape marc (V1) and the mixture vine shoot-biosolid vinasses (V2) have been investigated as low cost organic amendments to minimize the leaching of diuron, imidacloprid and their metabolites in columns packed with a sandy loam (S1) and a silty-clay loam soil (S2) under steady state flow conditions. In the unamended soil columns, leached amounts of diuron were 75% and 53% in S1 and S2, respectively. Its metabolites (3-(3,4-dichlorophenyl)-1-methylurea, DPMU; and 3,4-dichlorophenylurea, DPU) percolated less than 35% of the total applied amount. The amount of the metabolite 3,4-dichloroaniline (DCA) was 2% and 30% for S1 and S2, respectively. Leaching of imidacloprid was 79% and 96% for S1 and S2, respectively, while its metabolite 6-chloronicotinic acid (CNA) was entirely leached. In the vermicompost-amended columns, the leaching of diuron was reduced 2 to 3-fold. DPMU and DPU were also significantly reduced (more than 6-fold). DCA did not appear in any of the leachates of the amended soil columns. Imidacloprid leaching was reduced 1 to 2-folds in the amended columns. The amendments did not affect the transport of CNA. The dissolved organic carbon (DOC) from the vermicomposts did not enhance pesticide transport throughout the soil in any case. This qualitative study presents these vermicomposts as an effective potential low-cost tool in reducing pesticide and metabolite leaching. The next step would be to test them under more realistic conditions.

Growth inhibition and ultrastructural alterations induced by Delta24(25)-sterol methyltransferase inhibitors in Candida spp. isolates, including non-albicans organisms.

PubMed

Ishida, Kelly; Rodrigues, Juliany Cola Fernandes; Ribeiro, Marcos Dornelas; Vila, Taíssa Vieira Machado; de Souza, Wanderley; Urbina, Julio A; Nakamura, Celso Vataru; Rozental, Sonia

2009-04-20

Although Candida species are commensal microorganisms, they can cause many invasive fungal infections. In addition, antifungal resistance can contribute to failure of treatment.The purpose of this study was to evaluate the antifungal activity of inhibitors of Delta24(25)-sterol methyltransferase (24-SMTI), 20-piperidin-2-yl-5alpha-pregnan-3beta-20(R)-diol (AZA), and 24(R,S),25-epiminolanosterol (EIL), against clinical isolates of Candida spp., analysing the ultrastructural changes. AZA and EIL were found to be potent growth inhibitors of Candida spp. isolates. The median MIC50 was 0.5 microg.ml-1 for AZA and 2 microg.ml-1 for EIL, and the MIC90 was 2 microg.ml-1 for both compounds. All strains used in this study were susceptible to amphotericin B; however, some isolates were fluconazole- and itraconazole-resistant. Most of the azole-resistant isolates were Candida non-albicans (CNA) species, but several of them, such as C. guilliermondii, C. zeylanoides, and C. lipolytica, were susceptible to 24-SMTI, indicating a lack of cross-resistance. Reference strain C. krusei (ATCC 6258, FLC-resistant) was consistently susceptible to AZA, although not to EIL. The fungicidal activity of 24-SMTI was particularly high against CNA isolates. Treatment with sub-inhibitory concentrations of AZA and EIL induced several ultrastructural alterations, including changes in the cell-wall shape and thickness, a pronounced disconnection between the cell wall and cytoplasm with an electron-lucent zone between them, mitochondrial swelling, and the presence of electron-dense vacuoles. Fluorescence microscopy analyses indicated an accumulation of lipid bodies and alterations in the cell cycle of the yeasts. The selectivity of 24-SMTI for fungal cells versus mammalian cells was assessed by the sulforhodamine B viability assay. Taken together, these results suggest that inhibition of 24-SMT may be a novel approach to control Candida spp. infections, including those caused by azole-resistant strains.

Growth inhibition and ultrastructural alterations induced by Δ24(25)-sterol methyltransferase inhibitors in Candida spp. isolates, including non-albicans organisms

PubMed Central

2009-01-01

Background Although Candida species are commensal microorganisms, they can cause many invasive fungal infections. In addition, antifungal resistance can contribute to failure of treatment. The purpose of this study was to evaluate the antifungal activity of inhibitors of Δ24(25)-sterol methyltransferase (24-SMTI), 20-piperidin-2-yl-5α-pregnan-3β-20(R)-diol (AZA), and 24(R,S),25-epiminolanosterol (EIL), against clinical isolates of Candida spp., analysing the ultrastructural changes. Results AZA and EIL were found to be potent growth inhibitors of Candida spp. isolates. The median MIC50 was 0.5 μg.ml-1 for AZA and 2 μg.ml-1 for EIL, and the MIC90 was 2 μg.ml-1 for both compounds. All strains used in this study were susceptible to amphotericin B; however, some isolates were fluconazole- and itraconazole-resistant. Most of the azole-resistant isolates were Candida non-albicans (CNA) species, but several of them, such as C. guilliermondii, C. zeylanoides, and C. lipolytica, were susceptible to 24-SMTI, indicating a lack of cross-resistance. Reference strain C. krusei (ATCC 6258, FLC-resistant) was consistently susceptible to AZA, although not to EIL. The fungicidal activity of 24-SMTI was particularly high against CNA isolates. Treatment with sub-inhibitory concentrations of AZA and EIL induced several ultrastructural alterations, including changes in the cell-wall shape and thickness, a pronounced disconnection between the cell wall and cytoplasm with an electron-lucent zone between them, mitochondrial swelling, and the presence of electron-dense vacuoles. Fluorescence microscopy analyses indicated an accumulation of lipid bodies and alterations in the cell cycle of the yeasts. The selectivity of 24-SMTI for fungal cells versus mammalian cells was assessed by the sulforhodamine B viability assay. Conclusion Taken together, these results suggest that inhibition of 24-SMT may be a novel approach to control Candida spp. infections, including those caused by azole-resistant strains. PMID:19379501

Genome-wide comparison of paired fresh frozen and formalin-fixed paraffin-embedded gliomas by custom BAC and oligonucleotide array comparative genomic hybridization: facilitating analysis of archival gliomas

PubMed Central

Mohapatra, Gayatry; Engler, David A.; Starbuck, Kristen D.; Kim, James C.; Bernay, Derek C.; Scangas, George A.; Rousseau, Audrey; Batchelor, Tracy T.; Betensky, Rebecca A.; Louis, David N.

2010-01-01

Molecular genetic analysis of cancer is rapidly evolving as a result of improvement in genomic technologies and the growing applicability of such analyses to clinical oncology. Array based comparative genomic hybridization (aCGH) is a powerful tool for detecting DNA copy number alterations (CNA), particularly in solid tumors, and has been applied to the study of malignant gliomas. In the clinical setting, however, gliomas are often sampled by small biopsies and thus formalin-fixed paraffin-embedded (FFPE) blocks are often the only tissue available for genetic analysis, especially for rare types of gliomas. Moreover, the biological basis for the marked intratumoral heterogeneity in gliomas is most readily addressed in FFPE material. Therefore, for gliomas, the ability to use DNA from FFPE tissue is essential for both clinical and research applications. In this study, we have constructed a custom bacterial artificial chromosome (BAC) array and show excellent sensitivity and specificity for detecting CNAs in a panel of paired frozen and FFPE glioma samples. Our study demonstrates a high concordance rate between CNAs detected in FFPE compared to frozen DNA. We have also developed a method of labeling DNA from FFPE tissue that allows efficient hybridization to oligonucleotide arrays. This labeling technique was applied to a panel of biphasic anaplastic oligoastrocytomas (AOA) to identify genetic changes unique to each component. Together, results from these studies suggest that BAC and oligonucleotide aCGH are sensitive tools for detecting CNAs in FFPE DNA, and can enable genome-wide analysis of rare, small and/or histologically heterogeneous gliomas. PMID:21080181

Hydrometeorological hazards basin "El Salado", with detailed analysis of the micro "El Zarco" and "Tamarindos" in the municipality of Puerto Vallarta, Jalisco

NASA Astrophysics Data System (ADS)

Núñez Gutiérrez, M.

2013-05-01

In recent years, there has been a change in regard to the hazard of flooding in the basin environment "Salting" specifically in watersheds of streams "El Zarco" and "Tamarind", located in the area of Township north of Puerto Vallara, Jalisco, lately it has become precipitation, of a cyclonic convective having with it, but short-lived intensive storms, and coupled with the growth of the metropolitan area of Puerto Vallarta, which has clogged up the drainage outlet sea water stored on site until it disappears evapotranspiration. Hydrometeorological analysis is performed based on the triangulation method where hydrometric records are used, by the weather station of "The Desembocada" of Puerto Vallarta, which is the only one authorized by the CNA, however the main source that handles official values of the weather stations in the Mexican Republic, is the database ERIC III (Rapid Information Extractor climatological version III), and in their weather stations precipitation data and temperature average, minimum and maximum monthly are available. This is combined with probabilistic methods, based on the exploration of the probability distribution function (FDP) with the method of small distributions where methods are used Pearson's chi-square, Student t, Fisher F, for smaller data less than 30 years and the functions of discrete or continuous probability to estimate rainfall intensity also used digital terrain models with sufficient mapping for elevations, precipitation, temperature (SIG).;

Genomic analysis of adult B-ALL identifies potential markers of shorter survival.

PubMed

Patel, Shiven; Mason, Clinton C; Glenn, Martha J; Paxton, Christian N; South, Sara T; Cessna, Melissa H; Asch, Julie; Cobain, Erin F; Bixby, Dale L; Smith, Lauren B; Reshmi, Shalini; Gastier-Foster, Julie M; Schiffman, Joshua D; Miles, Rodney R

2017-05-01

B lymphoblastic leukemia (B-ALL) in adults has a higher risk of relapse and lower long-term survival than pediatric B-ALL, but data regarding genetic prognostic biomarkers are much more limited for adult patients. We identified 70 adult B-ALL patients from three institutions and performed genome-wide analysis via single nucleotide polymorphism (SNP) arrays on DNA isolated from their initial diagnostic sample and, when available, relapse bone marrow specimens to identify recurring copy number alterations (CNA). As B-cell developmental genes play a crucial role in this leukemia, we assessed such for recurrent deletions in diagnostic and relapse samples. We confirmed previous findings that the most prevalent deletions of these genes occur in CDKN2A, IKZF1, and PAX5, with several others at lower frequencies. Of the 16 samples having paired diagnostic and relapse samples, 5 showed new deletions in these recurrent B-cell related genes and 8 showed abolishment. Deletion of EBF1 heralded a significant negative prognostic impact on relapse free survival in univariate and multivariate analyses. The combination of both a CDKN2A/B deletion and an IKZF1 alteration (26% of cases) also showed a trend toward predicting worse overall survival compared to having only one or neither of these deletions. These findings add to the understanding of genomic influences on this comparably understudied disease cohort that upon further validation may help identify patients who would benefit from upfront treatment intensification. Copyright © 2017 Elsevier Ltd. All rights reserved.

Pseudo-Outbreak of Actinomyces graevenitzii Associated with Bronchoscopy

PubMed Central

Peaper, David R.; Havill, Nancy L.; Aniskiewicz, Michael; Callan, Deborah; Pop, Olivia; Towle, Dana

2014-01-01

Outbreaks and pseudo-outbreaks of infection related to bronchoscopy typically involve Gram-negative bacteria, Mycobacterium species or Legionella species. We report an unusual bronchoscopy-related pseudo-outbreak due to Actinomyces graevenitzii. Extensive epidemiological and microbiological investigation failed to identify a common source. Strain typing revealed that the cluster was comprised of heterogeneous strains of A. graevenitzii. A change in laboratory procedures for Actinomyces cultures was coincident with the emergence of the pseudo-outbreak, and we determined that A. graevenitzii isolates more readily adopted a white, dry, molar tooth appearance on anaerobic colistin nalidixic acid (CNA) agar which likely facilitated its detection and identification in bronchoscopic specimens. This unusual pseudo-outbreak was related to frequent requests of bronchoscopists for Actinomyces cultures combined with a change in microbiology laboratory practices. PMID:25355767

Radioactivity impacts of the Fukushima Nuclear Accident on the atmosphere

NASA Astrophysics Data System (ADS)

Lin, W.; Chen, L.; Yu, W.; Ma, H.; Zeng, Z.; Lin, J.; Zeng, S.

2015-02-01

The Fukushima Nuclear Accident (FNA) resulted in a large amount of radionuclides released into the atmosphere and dispersed globally, which has greatly raised public concerns. The state of the art for source terms of 19 kinds of radionuclides derived from the FNA was comprehensively collected and compared with levels of the global fallout and the Chernobyl Nuclear Accident (CNA). The atmospheric impacts of the FNA were evaluated from three aspects including radioactive baseline of the atmosphere, the concentration limits in standards and radiological protection. The FNA should not impose significant radiological risk on the public members in the countries excluding Japan. A conceptual scheme of Fukushima-derived radionuclides with physical and physicochemical insights on different temporal-spatial timescales was discussed and illustrated to understand their fates in the atmosphere.

A Robust Protocol for Using Multiplexed Droplet Digital PCR to Quantify Somatic Copy Number Alterations in Clinical Tissue Specimens.

PubMed

Hughesman, Curtis B; Lu, X J David; Liu, Kelly Y P; Zhu, Yuqi; Poh, Catherine F; Haynes, Charles

2016-01-01

The ability of droplet digital PCR (ddPCR) to accurately determine the concentrations of amplifiable targets makes it a promising platform for measuring copy number alterations (CNAs) in genomic biomarkers. However, its application to clinical samples, particularly formalin-fixed paraffin-embedded specimens, will require strategies to reliably determine CNAs in DNA of limited quantity and quality. When applied to cancerous tissue, those methods must also account for global genetic instability and the associated probability that the abundance(s) of one or more chosen reference loci do not represent the average ploidy of cells comprising the specimen. Here we present an experimental design strategy and associated data analysis tool that enables accurate determination of CNAs in a panel of biomarkers using multiplexed ddPCR. The method includes strategies to optimize primer and probes design to cleanly segregate droplets in the data output from reaction wells amplifying multiple independent templates, and to correct for bias from artifacts such as DNA fragmentation. We demonstrate how a panel of reference loci can be used to determine a stable CNA-neutral benchmark. These innovations, when taken together, provide a comprehensive strategy that can be used to reliably detect biomarker CNAs in DNA extracted from either frozen or FFPE tissue biopsies.

Developing the green house nursing care team: variations on development and implementation.

PubMed

Bowers, Barbara J; Nolet, Kimberly

2014-02-01

A core component of the Green House nursing home model is an altered supervisory relationship between the nurse and direct care workers. Some have expressed concern that the Green House model might weaken professional nursing oversight, threatening the quality of clinical care. This qualitative research study explores the role of the nurse as implemented in the Green House model, focusing on how variations in the nursing team influence clinical care practices. Dimensional analysis, a "second generation" grounded theory methodology, was used to conduct this study. Data were collected through observations and interviews with 37 nurses, 68 CNAs, and 11 Guides working at 11 Green House sites. Implementation of the nursing role within the Green House model varied both within and across sites. Four nursing model types were identified: Traditional, Visitor, Parallel, and Integrated. Care processes, CNA/Shahbaz skill development, and worker stress varied with each nursing model. Government policies have been enacted to support culture change. However, there is currently little guidance for regulators, providers, or consumers regarding variability in how culture change practices are implemented and consequences of these variations. This article outlines the importance of understanding these practices at a level of detail that distinguishes and supports those that are most promising.

Developing the Green House Nursing Care Team: Variations on Development and Implementation

PubMed Central

Bowers, Barbara J.

2014-01-01

Purpose of the Study: A core component of the Green House nursing home model is an altered supervisory relationship between the nurse and direct care workers. Some have expressed concern that the Green House model might weaken professional nursing oversight, threatening the quality of clinical care. This qualitative research study explores the role of the nurse as implemented in the Green House model, focusing on how variations in the nursing team influence clinical care practices. Design and Methods: Dimensional analysis, a “second generation” grounded theory methodology, was used to conduct this study. Data were collected through observations and interviews with 37 nurses, 68 CNAs, and 11 Guides working at 11 Green House sites. Results: Implementation of the nursing role within the Green House model varied both within and across sites. Four nursing model types were identified: Traditional, Visitor, Parallel, and Integrated. Care processes, CNA/Shahbaz skill development, and worker stress varied with each nursing model. Implications: Government policies have been enacted to support culture change. However, there is currently little guidance for regulators, providers, or consumers regarding variability in how culture change practices are implemented and consequences of these variations. This article outlines the importance of understanding these practices at a level of detail that distinguishes and supports those that are most promising. PMID:24443606

Comparative analysis of agr groups and virulence genes among subclinical and clinical mastitis Staphylococcus aureus isolates from sheep flocks of the Northeast of Brazil.

PubMed

de Almeida, Lara M; de Almeida, Mayra Zilta P R B; de Mendonça, Carla L; Mamizuka, Elsa M

2013-01-01

Staphylococcus aureus is one of the most frequent mastitis causative agents in small ruminants. The expression of most virulence genes of S. aureus is controlled by an accessory gene regulator (agr) locus. This study aimed to ascertain the prevalence of the different agr groups and to evaluate the occurrence of encoding genes for cytotoxin, adhesins and toxins with superantigen activity in S. aureus isolates from milk of ewes with clinical and subclinical mastitis in sheep flocks raised for meat production The agr groups I and II were identified in both cases of clinical and subclinical mastitis. Neither the arg groups III and IV nor negative agr were found. The presence of cflA gene was identified in 100% of the isolates. The frequency of hla and lukE-D genes was high - 77.3 and 82.8%, respectively and all isolates from clinical mastitis presented these genes. The sec gene, either associated to tst gene or not, was identified only in isolates from subclinical mastitis. None of the following genes were identified: bbp, ebpS, cna, fnbB, icaA, icaD, bap, hlg, lukM-lukF-PV and se-a-b-d-e.

Clonal selection in xenografted TAM recapitulates the evolutionary process of myeloid leukemia in Down syndrome.

PubMed

Saida, Satoshi; Watanabe, Ken-ichiro; Sato-Otsubo, Aiko; Terui, Kiminori; Yoshida, Kenichi; Okuno, Yusuke; Toki, Tsutomu; Wang, RuNan; Shiraishi, Yuichi; Miyano, Satoru; Kato, Itaru; Morishima, Tatsuya; Fujino, Hisanori; Umeda, Katsutsugu; Hiramatsu, Hidefumi; Adachi, Souichi; Ito, Etsuro; Ogawa, Seishi; Ito, Mamoru; Nakahata, Tatsutoshi; Heike, Toshio

2013-05-23

Transient abnormal myelopoiesis (TAM) is a clonal preleukemic disorder that progresses to myeloid leukemia of Down syndrome (ML-DS) through the accumulation of genetic alterations. To investigate the mechanism of leukemogenesis in this disorder, a xenograft model of TAM was established using NOD/Shi-scid, interleukin (IL)-2Rγ(null) mice. Serial engraftment after transplantation of cells from a TAM patient who developed ML-DS a year later demonstrated their self-renewal capacity. A GATA1 mutation and no copy number alterations (CNAs) were detected in the primary patient sample by conventional genomic sequencing and CNA profiling. However, in serial transplantations, engrafted TAM-derived cells showed the emergence of divergent subclones with another GATA1 mutation and various CNAs, including a 16q deletion and 1q gain, which are clinically associated with ML-DS. Detailed genomic analysis identified minor subclones with a 16q deletion or this distinct GATA1 mutation in the primary patient sample. These results suggest that genetically heterogeneous subclones with varying leukemia-initiating potential already exist in the neonatal TAM phase, and ML-DS may develop from a pool of such minor clones through clonal selection. Our xenograft model of TAM may provide unique insight into the evolutionary process of leukemia.

Evaluation of chromogenic medium and direct latex agglutination test for detection of group B streptococcus in vaginal specimens from pregnant women in Lebanon and Kuwait.

PubMed

Ghaddar, Nahed; Alfouzan, Wadha; Anastasiadis, Elie; Al Jiser, Tamima; Itani, Saad Eddine; Dernaika, Racha; Eid, Toufic; Ghaddar, Ali; Charafeddine, Adib; Dhar, Rita; El Hajj, Hiba

2014-10-01

This study was undertaken to evaluate chromogenic medium and a direct latex agglutination test (DLA) for detection of Group B Streptococcus (GBS) in the vaginal specimens of pregnant women, and to ascertain the prevalence of GBS in this population in Kuwait and Lebanon. Vaginal swabs, collected from women at 35-37 weeks of gestation, were cultured on 5 % sheep blood agar (SBA), colistin nalidixic acid agar (CNA), Strept B Select chromogenic agar (SBS) as well as Lim enrichment broth in 168 cases in Lebanon while only SBA was used for 1391 samples in Kuwait. In addition, vaginal samples from 102 GBS-positive and 20 GBS-negative women near the time of delivery were collected in Kuwait for evaluation of the DLA test. During the study period, the prevalence of GBS colonization was determined to be 20.7 % (288/1391) in Kuwait while 18.4 % (31) of 168 pregnant women in Lebanon had vaginal cultures positive for GBS. By direct plating of vaginal swabs on the three media used, the isolation rates of GBS were 51.6, 64.5 and 77.4 % on SBA, CNA and SBS, respectively, which increased to 90.35, 93.1 and 96.8 %, respectively, following subculture in Lim broth after 18 h of incubation. The sensitivity of the DLA test was found to be dependent on the density of GBS colonization, resulting in 100 % sensitivity and 100 % specificity for heavy (>10(2) c.f.u. per swab) and moderately heavy (50-100 c.f.u. per swab) growth of GBS. However, for vaginal specimens yielding <50 c.f.u. per swab, the sensitivity, specificity, positive and negative predictive values of the DLA test were 100, 55.5, 63.6 and 100 %, respectively. In conclusion, a chromogenic agar, such as SBS, and a DLA test can be used for rapid detection of GBS in pregnant women. The DLA test, in particular, could prove to be a useful tool for immediate detection of GBS in women near delivery so that intrapartum antibiotic prophylaxis can be initiated. © 2014 The Authors.

Pseudo-outbreak of Actinomyces graevenitzii associated with bronchoscopy.

PubMed

Peaper, David R; Havill, Nancy L; Aniskiewicz, Michael; Callan, Deborah; Pop, Olivia; Towle, Dana; Boyce, John M

2015-01-01

Outbreaks and pseudo-outbreaks of infection related to bronchoscopy typically involve Gram-negative bacteria, Mycobacterium species or Legionella species. We report an unusual bronchoscopy-related pseudo-outbreak due to Actinomyces graevenitzii. Extensive epidemiological and microbiological investigation failed to identify a common source. Strain typing revealed that the cluster was comprised of heterogeneous strains of A. graevenitzii. A change in laboratory procedures for Actinomyces cultures was coincident with the emergence of the pseudo-outbreak, and we determined that A. graevenitzii isolates more readily adopted a white, dry, molar tooth appearance on anaerobic colistin nalidixic acid (CNA) agar which likely facilitated its detection and identification in bronchoscopic specimens. This unusual pseudo-outbreak was related to frequent requests of bronchoscopists for Actinomyces cultures combined with a change in microbiology laboratory practices. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

From healing to witchcraft: on ritual speech and roboticization in the hospital.

PubMed

Pine, Adrienne

2011-06-01

Healthcare Information Technology (HIT), touted as a panacea by U.S. political actors ranging from Newt Gingrich to Barack Obama, is central to emerging forms of healthcare governance which Holmes et al.-in their critique of the institutionalization of magical thinking brought about by Orwellian techno-Newspeak-have provocatively labeled fascistic. Drawing from data collected over 3 years of working with and teaching continuing education (CE) courses for thousands of registered nurses as lead political educator for the California Nurses Association/National Nurses Organizing Committee (CNA/NNOC), I argue that HIT is an integral component of a broader technological restructuring of healthcare and thus society, both of which are part of a social discourse that is tied to a transformative system of ritual speech, with profound implications for healthcare work, patient health, and democracy.

Dim Networks: The Utility of Social Network Analysis for Illuminating Partner Security Force Networks

DTIC Science & Technology

2015-12-01

use of social network analysis (SNA) has allowed the military to map dark networks of terrorist organizations and selectively target key elements...data to improve SC. 14. SUBJECT TERMS social network analysis, dark networks, light networks, dim networks, security cooperation, Southeast Asia...task may already exist. Recently, the use of social network analysis (SNA) has allowed the military to map dark networks of terrorist organizations

Inter- and intra-patient clonal and subclonal heterogeneity of chronic lymphocytic leukaemia: evidence from circulating and lymph nodal compartments

PubMed Central

Bonina, Silvia; Messina, Monica; Chiaretti, Sabina; Ilari, Caterina; Cafforio, Luciana; Raponi, Sara; Mauro, Francesca Romana; Di Maio, Valeria; De Propris, Maria Stefania; Nanni, Mauro; Ciardullo, Carmela; Rossi, Davide; Gaidano, Gianluca; Guarini, Anna; Rabadan, Raul; Foà, Robin

2015-01-01

Summary Whole exome sequencing and copy number aberration (CNA) analysis was performed on cells taken from peripheral blood (PB) and lymph nodes (LN) of patients with chronic lymphocytic leukaemia (CLL). Of 64 non-silent somatic mutations, 54 (84.4%) were clonal in both compartments, 3 (4.7%) were PB-specific and 7 (10.9%) were LN-specific. Most of the LN- or PB-specific mutations were subclonal in the other corresponding compartment (variant frequency 0.5-5.3%). Of 41 CNAs, 27 (65.8%) were shared by both compartments and 7 (17.1%) were LN- or PB-specific. Overall, 6 of 9 cases (66.7%) showed genomic differences between the compartments. At subsequent relapse, Case 10, with 6 LN-specific lesions, and Case 100, with 6 LN-specific and 8 PB-specific lesions, showed, in the PB, the clonal expansion of LN-derived lesions with an adverse impact: SF3B1 mutation, BIRC3 deletion, del8(p23.3-p11.1), del9(p24.3-p13.1) and gain 2(p25.3-p14). CLL shows an intra-patient clonal heterogeneity according to the disease compartment, with both LN and PB-specific mutations/CNAs. The LN microenvironment might contribute to the clonal selection of unfavourable lesions, as LN-derived mutations/CNAs can appear in the PB at relapse. PMID:26597680

The presence of both bone sialoprotein-binding protein gene and collagen adhesin gene as a typical virulence trait of the major epidemic cluster in isolates from orthopedic implant infections.

PubMed

Campoccia, Davide; Speziale, Pietro; Ravaioli, Stefano; Cangini, Ilaria; Rindi, Simonetta; Pirini, Valter; Montanaro, Lucio; Arciola, Carla Renata

2009-12-01

Staphylococcus aureus is a major, highly clonal, pathogen causing implant infections. This study aimed at investigating the diverse distribution of bacterial adhesins in most prevalent S. aureus strain types causing orthopaedic implant infections. 200 S. aureus isolates, categorized into ribogroups by automated ribotyping, i.e. rDNA restriction fragment length polymorphism analysis, were screened for the presence of a panel of adhesins genes. Within the collection of isolates, automated ribotyping detected 98 distinct ribogroups. For many ribogroups, characteristic tandem genes arrangements could be identified. In the predominant S. aureus cluster, enlisting 27 isolates, the bbp gene encoding bone sialoprotein-binding protein appeared a typical virulence trait, found in 93% of the isolates. Conversely, the bbp gene was identified in just 10% of the remaining isolates of the collection. In this cluster, co-presence of bbp with the cna gene encoding collagen adhesin was a pattern consistently observed. These findings indicate a crucial role of both these adhesins, able to bind the most abundant bone proteins, in the pathogenesis of orthopaedic implant infections, there where biomaterials interface bone tissues. This study suggests that specific adhesins may synergistically act in the onset of implant infections and that anti-adhesin strategies should be targeted to adhesins conjointly present.

Isolation of 236U and 239,240Pu from seawater samples and its determination by Accelerator Mass Spectrometry.

PubMed

López-Lora, Mercedes; Chamizo, Elena; Villa-Alfageme, María; Hurtado-Bermúdez, Santiago; Casacuberta, Núria; García-León, Manuel

2018-02-01

In this work we present and evaluate a radiochemical procedure optimised for the analysis of 236 U and 239,240 Pu in seawater samples by Accelerator Mass Spectrometry (AMS). The method is based on Fe(OH) 3 co-precipitation of actinides and uses TEVA® and UTEVA® extraction chromatography resins in a simplified way for the final U and Pu purification. In order to improve the performance of the method, the radiochemical yields are analysed in 1 to 10L seawater volumes using alpha spectrometry (AS) and Inductively Coupled Plasma Mass Spectrometry (ICP-MS). Robust 80% plutonium recoveries are obtained; however, it is found that Fe(III) concentration in the precipitation solution and sample volume are the two critical and correlated parameters influencing the initial uranium extraction through Fe(OH) 3 co-precipitation. Therefore, we propose an expression that optimises the sample volume and Fe(III) amounts according to both the 236 U and 239,240 Pu concentrations in the samples and the performance parameters of the AMS facility. The method is validated for the current setup of the 1MV AMS system (CNA, Sevilla, Spain), where He gas is used as a stripper, by analysing a set of intercomparison seawater samples, together with the Laboratory of Ion Beam Physics (ETH, Zürich, Switzerland). Copyright © 2017 Elsevier B.V. All rights reserved.

Outsourcing veterans for long-term care: comparison of community and state veterans' nursing homes.

PubMed

Laberge, Alexandre; Weech-Maldonado, Robert; Johnson, Christopher E; Jia, Huanguang; Dewald, Lloyd

2008-01-01

This study compares the characteristics of state veterans' nursing homes and community nursing homes with VA per-diem residentes between 1999 - 2002. A structure, process, and outcome model was used to examine whether there was any difference in the multi-dimensional quality measures among the three types of community nursing homes (for profit, not-for-profit, and government) and state veterans' nursing homes. For profit community nursing homes were less likely to achieve nurse staffing standards while government facilities were more likely to achieve CNA staffing standards when compared to the state veterans' homes. All community nursing homes had a lower prevelance of tube feeds and catheterization when compared to state veterans' nursing homes. Only government community nursing homes had significantly lower quality of life deficiencies and pressure sore prevelance when compared to state veterans' nursing homes. Vigilant monitoring of all long-term care facilities utilized by veterans is needed.

Conscientious objection: a call to nursing leadership.

PubMed

Ford, Natalie J; Fraser, Kimberly D; Marck, Patricia B

2010-09-01

In this paper we argue that nurse leaders need to work actively to create morally supportive environments for nurses in Canada that provide adequate room to exercise conscientious objection. Morally supportive environments engender a safe atmosphere to engage in open dialogue and action regarding conflict of conscience. The CNA's 2008 Code of Ethics for Registered Nurses has recognized the importance of conscientious objection in nursing and has created key guidelines for the registered nurse to follow when a conflict in conscience is being considered or declared. Nurse leaders need to further develop the understanding of conflicts of conscience through education, well-written guidelines for conscientious objection in workplaces and engagement in research to uncover underlying barriers to the enactment of conscientious objections. With advancements in technology, changing healthcare policies and increasing scope of practice, both reflection and dialogue on conscientious objection are critical for the continuing moral development of nurses in Canada.

Nurse assistant mental models, sensemaking, care actions, and consequences for nursing home residents.

PubMed

Anderson, Ruth A; Ammarell, Natalie; Bailey, Donald; Colón-Emeric, Cathleen; Corazzini, Kirsten N; Lillie, Melissa; Piven, Mary Lynn Scotton; Utley-Smith, Queen; McDaniel, Reuben R

2005-10-01

In a nursing home case study using observation and interview data, the authors described two mental models that guided certified nurse assistants (CNAs) in resident care. The Golden Rule guided CNAs to respond to residents as they would want someone to do for them. Mother wit guided CNAs to treat residents as they would treat their own children. These mental models engendered self-control and affection but also led to actions such as infantilization and misinterpretations about potentially undiagnosed conditions such as depression or pain. Furthermore, the authors found that CNAs were isolated from clinicians; little resident information was exchanged. They suggest ways to alter CNA mental models to give them a better basis for action and strategies for connecting CNAs and clinical professionals to improve information flow about residents. Study results highlight a critical need for registered nurses (RNs) to be involved in frontline care.

PyPathway: Python Package for Biological Network Analysis and Visualization.

PubMed

Xu, Yang; Luo, Xiao-Chun

2018-05-01

Life science studies represent one of the biggest generators of large data sets, mainly because of rapid sequencing technological advances. Biological networks including interactive networks and human curated pathways are essential to understand these high-throughput data sets. Biological network analysis offers a method to explore systematically not only the molecular complexity of a particular disease but also the molecular relationships among apparently distinct phenotypes. Currently, several packages for Python community have been developed, such as BioPython and Goatools. However, tools to perform comprehensive network analysis and visualization are still needed. Here, we have developed PyPathway, an extensible free and open source Python package for functional enrichment analysis, network modeling, and network visualization. The network process module supports various interaction network and pathway databases such as Reactome, WikiPathway, STRING, and BioGRID. The network analysis module implements overrepresentation analysis, gene set enrichment analysis, network-based enrichment, and de novo network modeling. Finally, the visualization and data publishing modules enable users to share their analysis by using an easy web application. For package availability, see the first Reference.

Social network analysis: Presenting an underused method for nursing research.

PubMed

Parnell, James Michael; Robinson, Jennifer C

2018-06-01

This paper introduces social network analysis as a versatile method with many applications in nursing research. Social networks have been studied for years in many social science fields. The methods continue to advance but remain unknown to most nursing scholars. Discussion paper. English language and interpreted literature was searched from Ovid Healthstar, CINAHL, PubMed Central, Scopus and hard copy texts from 1965 - 2017. Social network analysis first emerged in nursing literature in 1995 and appears minimally through present day. To convey the versatility and applicability of social network analysis in nursing, hypothetical scenarios are presented. The scenarios are illustrative of three approaches to social network analysis and include key elements of social network research design. The methods of social network analysis are underused in nursing research, primarily because they are unknown to most scholars. However, there is methodological flexibility and epistemological versatility capable of supporting quantitative and qualitative research. The analytic techniques of social network analysis can add new insight into many areas of nursing inquiry, especially those influenced by cultural norms. Furthermore, visualization techniques associated with social network analysis can be used to generate new hypotheses. Social network analysis can potentially uncover findings not accessible through methods commonly used in nursing research. Social networks can be analysed based on individual-level attributes, whole networks and subgroups within networks. Computations derived from social network analysis may stand alone to answer a research question or incorporated as variables into robust statistical models. © 2018 John Wiley & Sons Ltd.

Contemporary Network Proteomics and Its Requirements

PubMed Central

Goh, Wilson Wen Bin; Wong, Limsoon; Sng, Judy Chia Ghee

2013-01-01

The integration of networks with genomics (network genomics) is a familiar field. Conventional network analysis takes advantage of the larger coverage and relative stability of gene expression measurements. Network proteomics on the other hand has to develop further on two critical factors: (1) expanded data coverage and consistency, and (2) suitable reference network libraries, and data mining from them. Concerning (1) we discuss several contemporary themes that can improve data quality, which in turn will boost the outcome of downstream network analysis. For (2), we focus on network analysis developments, specifically, the need for context-specific networks and essential considerations for localized network analysis. PMID:24833333

Network meta-analysis: an introduction for clinicians.

PubMed

Rouse, Benjamin; Chaimani, Anna; Li, Tianjing

2017-02-01

Network meta-analysis is a technique for comparing multiple treatments simultaneously in a single analysis by combining direct and indirect evidence within a network of randomized controlled trials. Network meta-analysis may assist assessing the comparative effectiveness of different treatments regularly used in clinical practice and, therefore, has become attractive among clinicians. However, if proper caution is not taken in conducting and interpreting network meta-analysis, inferences might be biased. The aim of this paper is to illustrate the process of network meta-analysis with the aid of a working example on first-line medical treatment for primary open-angle glaucoma. We discuss the key assumption of network meta-analysis, as well as the unique considerations for developing appropriate research questions, conducting the literature search, abstracting data, performing qualitative and quantitative synthesis, presenting results, drawing conclusions, and reporting the findings in a network meta-analysis.

A comprehensive probabilistic analysis model of oil pipelines network based on Bayesian network

NASA Astrophysics Data System (ADS)

Zhang, C.; Qin, T. X.; Jiang, B.; Huang, C.

2018-02-01

Oil pipelines network is one of the most important facilities of energy transportation. But oil pipelines network accident may result in serious disasters. Some analysis models for these accidents have been established mainly based on three methods, including event-tree, accident simulation and Bayesian network. Among these methods, Bayesian network is suitable for probabilistic analysis. But not all the important influencing factors are considered and the deployment rule of the factors has not been established. This paper proposed a probabilistic analysis model of oil pipelines network based on Bayesian network. Most of the important influencing factors, including the key environment condition and emergency response are considered in this model. Moreover, the paper also introduces a deployment rule for these factors. The model can be used in probabilistic analysis and sensitive analysis of oil pipelines network accident.

Exploration of the integration of care for persons with a traumatic brain injury using social network analysis methodology.

PubMed

Lamontagne, Marie-Eve

2013-01-01

Integration is a popular strategy to increase the quality of care within systems of care. However, there is no common language, approach or tool allowing for a valid description, comparison and evaluation of integrated care. Social network analysis could be a viable methodology to provide an objective picture of integrated networks. To illustrate social network analysis use in the context of systems of care for traumatic brain injury. We surveyed members of a network using a validated questionnaire to determine the links between them. We determined the density, centrality, multiplexity, and quality of the links reported. The network was described as moderately dense (0.6), the most prevalent link was knowledge, and four organisation members of a consortium were central to the network. Social network analysis allowed us to create a graphic representation of the network. Social network analysis is a useful methodology to objectively characterise integrated networks.

Network Analysis Tools: from biological networks to clusters and pathways.

PubMed

Brohée, Sylvain; Faust, Karoline; Lima-Mendez, Gipsi; Vanderstocken, Gilles; van Helden, Jacques

2008-01-01

Network Analysis Tools (NeAT) is a suite of computer tools that integrate various algorithms for the analysis of biological networks: comparison between graphs, between clusters, or between graphs and clusters; network randomization; analysis of degree distribution; network-based clustering and path finding. The tools are interconnected to enable a stepwise analysis of the network through a complete analytical workflow. In this protocol, we present a typical case of utilization, where the tasks above are combined to decipher a protein-protein interaction network retrieved from the STRING database. The results returned by NeAT are typically subnetworks, networks enriched with additional information (i.e., clusters or paths) or tables displaying statistics. Typical networks comprising several thousands of nodes and arcs can be analyzed within a few minutes. The complete protocol can be read and executed in approximately 1 h.

Understanding complex interactions using social network analysis.

PubMed

Pow, Janette; Gayen, Kaberi; Elliott, Lawrie; Raeside, Robert

2012-10-01

The aim of this paper is to raise the awareness of social network analysis as a method to facilitate research in nursing research. The application of social network analysis in assessing network properties has allowed greater insight to be gained in many areas including sociology, politics, business organisation and health care. However, the use of social networks in nursing has not received sufficient attention. Review of literature and illustration of the application of the method of social network analysis using research examples. First, the value of social networks will be discussed. Then by using illustrative examples, the value of social network analysis to nursing will be demonstrated. The method of social network analysis is found to give greater insights into social situations involving interactions between individuals and has particular application to the study of interactions between nurses and between nurses and patients and other actors. Social networks are systems in which people interact. Two quantitative techniques help our understanding of these networks. The first is visualisation of the network. The second is centrality. Individuals with high centrality are key communicators in a network. Applying social network analysis to nursing provides a simple method that helps gain an understanding of human interaction and how this might influence various health outcomes. It allows influential individuals (actors) to be identified. Their influence on the formation of social norms and communication can determine the extent to which new interventions or ways of thinking are accepted by a group. Thus, working with key individuals in a network could be critical to the success and sustainability of an intervention. Social network analysis can also help to assess the effectiveness of such interventions for the recipient and the service provider. © 2012 Blackwell Publishing Ltd.

Identifying changes in the support networks of end-of-life carers using social network analysis

PubMed Central

Leonard, Rosemary; Horsfall, Debbie; Noonan, Kerrie

2015-01-01

End-of-life caring is often associated with reduced social networks for both the dying person and for the carer. However, those adopting a community participation and development approach, see the potential for the expansion and strengthening of networks. This paper uses Knox, Savage and Harvey's definitions of three generations social network analysis to analyse the caring networks of people with a terminal illness who are being cared for at home and identifies changes in these caring networks that occurred over the period of caring. Participatory network mapping of initial and current networks was used in nine focus groups. The analysis used key concepts from social network analysis (size, density, transitivity, betweenness and local clustering) together with qualitative analyses of the group's reflections on the maps. The results showed an increase in the size of the networks and that ties between the original members of the network strengthened. The qualitative data revealed the importance between core and peripheral network members and the diverse contributions of the network members. The research supports the value of third generation social network analysis and the potential for end-of-life caring to build social capital. PMID:24644162

Spectrum-Based and Collaborative Network Topology Analysis and Visualization

ERIC Educational Resources Information Center

Hu, Xianlin

2013-01-01

Networks are of significant importance in many application domains, such as World Wide Web and social networks, which often embed rich topological information. Since network topology captures the organization of network nodes and links, studying network topology is very important to network analysis. In this dissertation, we study networks by…

Exploration of the integration of care for persons with a traumatic brain injury using social network analysis methodology

PubMed Central

Lamontagne, Marie-Eve

2013-01-01

Introduction Integration is a popular strategy to increase the quality of care within systems of care. However, there is no common language, approach or tool allowing for a valid description, comparison and evaluation of integrated care. Social network analysis could be a viable methodology to provide an objective picture of integrated networks. Goal of the article To illustrate social network analysis use in the context of systems of care for traumatic brain injury. Method We surveyed members of a network using a validated questionnaire to determine the links between them. We determined the density, centrality, multiplexity, and quality of the links reported. Results The network was described as moderately dense (0.6), the most prevalent link was knowledge, and four organisation members of a consortium were central to the network. Social network analysis allowed us to create a graphic representation of the network. Conclusion Social network analysis is a useful methodology to objectively characterise integrated networks. PMID:24250281

Amplicons on chromosome 3 contain oncogenes induced by recurrent exposure to 12-O-tetradecanoylphorbol-13-acetate and sodium n-butyrate and Epstein-Barr virus reactivation in a nasopharyngeal carcinoma cell line.

PubMed

Lee, Chia-Huei; Fang, Chih-Yeu; Sheu, Jim Jinn-Chyuan; Chang, Yao; Takada, Kenzo; Chen, Jen-Yang

2008-08-01

Nasopharyngeal carcinoma (NPC) is closely associated with Epstein-Barr virus (EBV) infection and exposure to environmental carcinogens. In this study, an inducible Epstein-Barr virus (EBV) reactivation NPC cell line, NA, was used to investigate the impact of recurrent 12-O-tetradecanoylphorbol-13-acetate-sodium n-butyrate (TPA/SB) treatment and EBV reactivation on chromosomal abnormalities utilizing array-based comparative genomic hybridization (CGH). It was observed that most copy-number aberrations (CNA) were progressively nonrandomly clustered on chromosomes 3, 8, and 9, as the frequency of TPA/SB treatment and EBV reactivation increased. All of the prominent amplicons detected (including 3p14.1, 3p13, 3p12.3, 3p12.2, 3q26.2, 3q26.31, and 3q26.32) were located on chromosome 3, with multiple oncogenes assigned to these sites. The amplification patterns of 3p12.3 and 3q26.2 were validated using fluorescence in situ hybridization (FISH) analysis. Subsequent quantitative real-time polymerase chain reaction detected increasing expression of ROBO1 and SKIL oncogenes in NA cells harboring higher frequency of TPA/SB treatment and EBV reactivation, consistent with copy-number amplification of these loci. These findings demonstrate that a high incidence of TPA/SB induced-EBV reactivation has a profound influence on the carcinogenesis of NPC through altered DNA copy number.

Inhibition of colorectal cancer genomic copy number alterations and chromosomal fragile site tumor suppressor FHIT and WWOX deletions by DNA mismatch repair

PubMed Central

Gelincik, Ozkan; Blecua, Pedro; Edelmann, Winfried; Kucherlapati, Raju; Zhou, Kathy; Jasin, Maria; Gümüş, Zeynep H.; Lipkin, Steven M.

2017-01-01

Homologous recombination (HR) enables precise DNA repair after DNA double strand breaks (DSBs) using identical sequence templates, whereas homeologous recombination (HeR) uses only partially homologous sequences. Homeologous recombination introduces mutations through gene conversion and genomic deletions through single-strand annealing (SSA). DNA mismatch repair (MMR) inhibits HeR, but the roles of mammalian MMR MutL homologues (MLH1, PMS2 and MLH3) proteins in HeR suppression are poorly characterized. Here, we demonstrate that mouse embryonic fibroblasts (MEFs) carrying Mlh1, Pms2, and Mlh3 mutations have higher HeR rates, by using 7,863 uniquely mapping paired direct repeat sequences (DRs) in the mouse genome as endogenous gene conversion and SSA reporters. Additionally, when DSBs are induced by gamma-radiation, Mlh1, Pms2 and Mlh3 mutant MEFs have higher DR copy number alterations (CNAs), including DR CNA hotspots previously identified in mouse MMR-deficient colorectal cancer (dMMR CRC). Analysis of The Cancer Genome Atlas CRC data revealed that dMMR CRCs have higher genome-wide DR HeR rates than MMR proficient CRCs, and that dMMR CRCs have deletion hotspots in tumor suppressors FHIT/WWOX at chromosomal fragile sites FRA3B and FRA16D (which have elevated DSB rates) flanked by paired homologous DRs and inverted repeats (IR). Overall, these data provide novel insights into the MMR-dependent HeR inhibition mechanism and its role in tumor suppression. PMID:29069730

The Application of Social Network Analysis to Team Sports

ERIC Educational Resources Information Center

Lusher, Dean; Robins, Garry; Kremer, Peter

2010-01-01

This article reviews how current social network analysis might be used to investigate individual and group behavior in sporting teams. Social network analysis methods permit researchers to explore social relations between team members and their individual-level qualities simultaneously. As such, social network analysis can be seen as augmenting…

Unified functional network and nonlinear time series analysis for complex systems science: The pyunicorn package

NASA Astrophysics Data System (ADS)

Donges, Jonathan F.; Heitzig, Jobst; Beronov, Boyan; Wiedermann, Marc; Runge, Jakob; Feng, Qing Yi; Tupikina, Liubov; Stolbova, Veronika; Donner, Reik V.; Marwan, Norbert; Dijkstra, Henk A.; Kurths, Jürgen

2015-11-01

We introduce the pyunicorn (Pythonic unified complex network and recurrence analysis toolbox) open source software package for applying and combining modern methods of data analysis and modeling from complex network theory and nonlinear time series analysis. pyunicorn is a fully object-oriented and easily parallelizable package written in the language Python. It allows for the construction of functional networks such as climate networks in climatology or functional brain networks in neuroscience representing the structure of statistical interrelationships in large data sets of time series and, subsequently, investigating this structure using advanced methods of complex network theory such as measures and models for spatial networks, networks of interacting networks, node-weighted statistics, or network surrogates. Additionally, pyunicorn provides insights into the nonlinear dynamics of complex systems as recorded in uni- and multivariate time series from a non-traditional perspective by means of recurrence quantification analysis, recurrence networks, visibility graphs, and construction of surrogate time series. The range of possible applications of the library is outlined, drawing on several examples mainly from the field of climatology.

Detailed genome-wide SNP analysis of major salivary carcinomas localizes subtype-specific chromosome sites and oncogenes of potential clinical significance.

PubMed

Zhang, Li; Mitani, Yoshitsugu; Caulin, Carlos; Rao, Pulivarthi H; Kies, Merrill S; Saintigny, Pierre; Zhang, Nianxiang; Weber, Randal S; Lippman, Scott M; El-Naggar, Adel K

2013-06-01

The molecular genetic alterations underlying the development and diversity of salivary gland carcinomas are largely unknown. To characterize these events, comparative genomic hybridization analysis was performed, using a single-nucleotide polymorphism microarray platform, of 60 fresh-frozen specimens that represent the main salivary carcinoma types: mucoepidermoid carcinoma (MEC), adenoid cystic carcinoma (ACC), and salivary duct carcinoma (SDC). The results were correlated with the clinicopathologic features and translocation statuses to characterize the genetic alterations. The most commonly shared copy number abnormalities (CNAs) in all types were losses at chromosomes 6q23-26 and the 9p21 region. Subtype-specific CNAs included a loss at 12q11-12 in ACC and a gain at 17q11-12 in SDC. Focal copy number losses included 1p36.33-p36-22 in ACC, 9p13.2 in MEC, and 3p12.3-q11-2, 6q21-22.1, 12q14.1, and 12q15 in SDC. Tumor-specific amplicons were identified at 11q23.3 (PVRL1) in ACC, 11q13.3 (NUMA1) in MEC, and 6p21.1 (CCND3), 9p13.2 (PAX5), 12q15 (CNOT2/RAB3IP), 12q21.1 (GLIPR1L1), and 17q12 (ERBB2/CCL4) in SDC. A comparative CNA analysis of fusion-positive and fusion-negative ACCs and MECs revealed relatively lower CNAs in fusion-positive tumors than in fusion-negative tumors in both tumor types. An association between CNAs and high grade and advanced stage was observed in MECs only. These findings support the pathogenetic segregation of these entities and define novel chromosomal sites for future identification of biomarkers and therapeutic targets. Copyright © 2013 American Society for Investigative Pathology. Published by Elsevier Inc. All rights reserved.

On the topological structure of multinationals network

NASA Astrophysics Data System (ADS)

Joyez, Charlie

2017-05-01

This paper uses a weighted network analysis to examine the structure of multinationals' implantation countries network. Based on French firm-level dataset of multinational enterprises (MNEs) the network analysis provides information on each country position in the network and in internationalization strategies of French MNEs through connectivity preferences among the nodes. The paper also details network-wide features and their recent evolution toward a more decentralized structure. While much has been said on international trade network, this paper shows that multinational firms' studies would also benefit from network analysis, notably by investigating the sensitivity of the network construction to firm heterogeneity.

MONGKIE: an integrated tool for network analysis and visualization for multi-omics data.

PubMed

Jang, Yeongjun; Yu, Namhee; Seo, Jihae; Kim, Sun; Lee, Sanghyuk

2016-03-18

Network-based integrative analysis is a powerful technique for extracting biological insights from multilayered omics data such as somatic mutations, copy number variations, and gene expression data. However, integrated analysis of multi-omics data is quite complicated and can hardly be done in an automated way. Thus, a powerful interactive visual mining tool supporting diverse analysis algorithms for identification of driver genes and regulatory modules is much needed. Here, we present a software platform that integrates network visualization with omics data analysis tools seamlessly. The visualization unit supports various options for displaying multi-omics data as well as unique network models for describing sophisticated biological networks such as complex biomolecular reactions. In addition, we implemented diverse in-house algorithms for network analysis including network clustering and over-representation analysis. Novel functions include facile definition and optimized visualization of subgroups, comparison of a series of data sets in an identical network by data-to-visual mapping and subsequent overlaying function, and management of custom interaction networks. Utility of MONGKIE for network-based visual data mining of multi-omics data was demonstrated by analysis of the TCGA glioblastoma data. MONGKIE was developed in Java based on the NetBeans plugin architecture, thus being OS-independent with intrinsic support of module extension by third-party developers. We believe that MONGKIE would be a valuable addition to network analysis software by supporting many unique features and visualization options, especially for analysing multi-omics data sets in cancer and other diseases. .

Multidimensional Analysis of Linguistic Networks

NASA Astrophysics Data System (ADS)

Araújo, Tanya; Banisch, Sven

Network-based approaches play an increasingly important role in the analysis of data even in systems in which a network representation is not immediately apparent. This is particularly true for linguistic networks, which use to be induced from a linguistic data set for which a network perspective is only one out of several options for representation. Here we introduce a multidimensional framework for network construction and analysis with special focus on linguistic networks. Such a framework is used to show that the higher is the abstraction level of network induction, the harder is the interpretation of the topological indicators used in network analysis. Several examples are provided allowing for the comparison of different linguistic networks as well as to networks in other fields of application of network theory. The computation and the intelligibility of some statistical indicators frequently used in linguistic networks are discussed. It suggests that the field of linguistic networks, by applying statistical tools inspired by network studies in other domains, may, in its current state, have only a limited contribution to the development of linguistic theory.

Social Network Analysis as a Methodological Approach to Explore Health Systems: A Case Study Exploring Support among Senior Managers/Executives in a Hospital Network.

PubMed

De Brún, Aoife; McAuliffe, Eilish

2018-03-13

Health systems research recognizes the complexity of healthcare, and the interacting and interdependent nature of components of a health system. To better understand such systems, innovative methods are required to depict and analyze their structures. This paper describes social network analysis as a methodology to depict, diagnose, and evaluate health systems and networks therein. Social network analysis is a set of techniques to map, measure, and analyze social relationships between people, teams, and organizations. Through use of a case study exploring support relationships among senior managers in a newly established hospital group, this paper illustrates some of the commonly used network- and node-level metrics in social network analysis, and demonstrates the value of these maps and metrics to understand systems. Network analysis offers a valuable approach to health systems and services researchers as it offers a means to depict activity relevant to network questions of interest, to identify opinion leaders, influencers, clusters in the network, and those individuals serving as bridgers across clusters. The strengths and limitations inherent in the method are discussed, and the applications of social network analysis in health services research are explored.

The relative efficiency of modular and non-modular networks of different size

PubMed Central

Tosh, Colin R.; McNally, Luke

2015-01-01

Most biological networks are modular but previous work with small model networks has indicated that modularity does not necessarily lead to increased functional efficiency. Most biological networks are large, however, and here we examine the relative functional efficiency of modular and non-modular neural networks at a range of sizes. We conduct a detailed analysis of efficiency in networks of two size classes: ‘small’ and ‘large’, and a less detailed analysis across a range of network sizes. The former analysis reveals that while the modular network is less efficient than one of the two non-modular networks considered when networks are small, it is usually equally or more efficient than both non-modular networks when networks are large. The latter analysis shows that in networks of small to intermediate size, modular networks are much more efficient that non-modular networks of the same (low) connective density. If connective density must be kept low to reduce energy needs for example, this could promote modularity. We have shown how relative functionality/performance scales with network size, but the precise nature of evolutionary relationship between network size and prevalence of modularity will depend on the costs of connectivity. PMID:25631996

Network Analysis in Community Psychology: Looking Back, Looking Forward.

PubMed

Neal, Zachary P; Neal, Jennifer Watling

2017-09-01

Network analysis holds promise for community psychology given the field's aim to understand the interplay between individuals and their social contexts. Indeed, because network analysis focuses explicitly on patterns of relationships between actors, its theories and methods are inherently extra-individual in nature and particularly well suited to characterizing social contexts. But, to what extent has community psychology taken advantage of this network analysis as a tool for capturing context? To answer these questions, this study provides a review of the use network analysis in articles published in American Journal of Community Psychology. Looking back, we describe and summarize the ways that network analysis has been employed in community psychology research to understand the range of ways community psychologists have found the technique helpful. Looking forward and paying particular attention to analytic issues identified in past applications, we provide some recommendations drawn from the network analysis literature to facilitate future applications of network analysis in community psychology. © 2017 The Authors. American Journal of Community Psychology published by Wiley Periodicals, Inc. on behalf of Society for Community Research and Action.

GAT: a graph-theoretical analysis toolbox for analyzing between-group differences in large-scale structural and functional brain networks.

PubMed

Hosseini, S M Hadi; Hoeft, Fumiko; Kesler, Shelli R

2012-01-01

In recent years, graph theoretical analyses of neuroimaging data have increased our understanding of the organization of large-scale structural and functional brain networks. However, tools for pipeline application of graph theory for analyzing topology of brain networks is still lacking. In this report, we describe the development of a graph-analysis toolbox (GAT) that facilitates analysis and comparison of structural and functional network brain networks. GAT provides a graphical user interface (GUI) that facilitates construction and analysis of brain networks, comparison of regional and global topological properties between networks, analysis of network hub and modules, and analysis of resilience of the networks to random failure and targeted attacks. Area under a curve (AUC) and functional data analyses (FDA), in conjunction with permutation testing, is employed for testing the differences in network topologies; analyses that are less sensitive to the thresholding process. We demonstrated the capabilities of GAT by investigating the differences in the organization of regional gray-matter correlation networks in survivors of acute lymphoblastic leukemia (ALL) and healthy matched Controls (CON). The results revealed an alteration in small-world characteristics of the brain networks in the ALL survivors; an observation that confirm our hypothesis suggesting widespread neurobiological injury in ALL survivors. Along with demonstration of the capabilities of the GAT, this is the first report of altered large-scale structural brain networks in ALL survivors.

Sample size and power considerations in network meta-analysis

PubMed Central

2012-01-01

Background Network meta-analysis is becoming increasingly popular for establishing comparative effectiveness among multiple interventions for the same disease. Network meta-analysis inherits all methodological challenges of standard pairwise meta-analysis, but with increased complexity due to the multitude of intervention comparisons. One issue that is now widely recognized in pairwise meta-analysis is the issue of sample size and statistical power. This issue, however, has so far only received little attention in network meta-analysis. To date, no approaches have been proposed for evaluating the adequacy of the sample size, and thus power, in a treatment network. Findings In this article, we develop easy-to-use flexible methods for estimating the ‘effective sample size’ in indirect comparison meta-analysis and network meta-analysis. The effective sample size for a particular treatment comparison can be interpreted as the number of patients in a pairwise meta-analysis that would provide the same degree and strength of evidence as that which is provided in the indirect comparison or network meta-analysis. We further develop methods for retrospectively estimating the statistical power for each comparison in a network meta-analysis. We illustrate the performance of the proposed methods for estimating effective sample size and statistical power using data from a network meta-analysis on interventions for smoking cessation including over 100 trials. Conclusion The proposed methods are easy to use and will be of high value to regulatory agencies and decision makers who must assess the strength of the evidence supporting comparative effectiveness estimates. PMID:22992327

An Application of Social Network Analysis on Military Strategy, System Networks and the Phases of War

DTIC Science & Technology

2015-03-26

1977. [29] J. D. Guzman, R. F. Deckro, M. J. Robbins, J. F. Morris and N. A. Ballester, “An Analytical Comparison of Social Network Measures,” IEEE...AN APPLICATION OF SOCIAL NETWORK ANALYSIS ON MILITARY STRATEGY, SYSTEM NETWORKS AND THE PHASES OF...subject to copyright protection in the United States. AFIT-ENS-MS-15-M-117 AN APPLICATION OF SOCIAL NETWORK ANALYSIS ON MILITARY STRATEGY

Co-authorship network analysis in health research: method and potential use.

PubMed

Fonseca, Bruna de Paula Fonseca E; Sampaio, Ricardo Barros; Fonseca, Marcus Vinicius de Araújo; Zicker, Fabio

2016-04-30

Scientific collaboration networks are a hallmark of contemporary academic research. Researchers are no longer independent players, but members of teams that bring together complementary skills and multidisciplinary approaches around common goals. Social network analysis and co-authorship networks are increasingly used as powerful tools to assess collaboration trends and to identify leading scientists and organizations. The analysis reveals the social structure of the networks by identifying actors and their connections. This article reviews the method and potential applications of co-authorship network analysis in health. The basic steps for conducting co-authorship studies in health research are described and common network metrics are presented. The application of the method is exemplified by an overview of the global research network for Chikungunya virus vaccines.

Network Visualization Project (NVP)

DTIC Science & Technology

2016-07-01

network visualization, network traffic analysis, network forensics 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF ABSTRACT UU 18. NUMBER OF...shell, is a command-line framework used for network forensic analysis. Dshell processes existing pcap files and filters output information based on

Integrated network capacity analysis for freight railroads.

DOT National Transportation Integrated Search

2016-02-23

Rail network capacity analysis should consider all network infrastructures in an integrated way, with the challenges of the nonlinear relationships at each network element, a link or a node, and complexity of the interaction between various network e...

Social network type and morale in old age.

PubMed

Litwin, H

2001-08-01

The aim of this research was to derive network types among an elderly population and to examine the relationship of network type to morale. Secondary analysis of data compiled by the Israeli Central Bureau of Statistics (n = 2,079) was employed, and network types were derived through K-means cluster analysis. Respondents' morale scores were regressed on network types, controlling for background and health variables. Five network types were derived. Respondents in diverse or friends networks reported the highest morale; those in exclusively family or restricted networks had the lowest. Multivariate regression analysis underscored that certain network types were second among the study variables in predicting respondents' morale, preceded only by disability level (Adjusted R(2) =.41). Classification of network types allows consideration of the interpersonal environments of older people in relation to outcomes of interest. The relative effects on morale of elective versus obligated social ties, evident in the current analysis, is a case in point.

Noninvasive Electromagnetic Source Imaging and Granger Causality Analysis: An Electrophysiological Connectome (eConnectome) Approach

PubMed Central

Sohrabpour, Abbas; Ye, Shuai; Worrell, Gregory A.; Zhang, Wenbo

2016-01-01

Objective Combined source imaging techniques and directional connectivity analysis can provide useful information about the underlying brain networks in a non-invasive fashion. Source imaging techniques have been used successfully to either determine the source of activity or to extract source time-courses for Granger causality analysis, previously. In this work, we utilize source imaging algorithms to both find the network nodes (regions of interest) and then extract the activation time series for further Granger causality analysis. The aim of this work is to find network nodes objectively from noninvasive electromagnetic signals, extract activation time-courses and apply Granger analysis on the extracted series to study brain networks under realistic conditions. Methods Source imaging methods are used to identify network nodes and extract time-courses and then Granger causality analysis is applied to delineate the directional functional connectivity of underlying brain networks. Computer simulations studies where the underlying network (nodes and connectivity pattern) is known were performed; additionally, this approach has been evaluated in partial epilepsy patients to study epilepsy networks from inter-ictal and ictal signals recorded by EEG and/or MEG. Results Localization errors of network nodes are less than 5 mm and normalized connectivity errors of ~20% in estimating underlying brain networks in simulation studies. Additionally, two focal epilepsy patients were studied and the identified nodes driving the epileptic network were concordant with clinical findings from intracranial recordings or surgical resection. Conclusion Our study indicates that combined source imaging algorithms with Granger causality analysis can identify underlying networks precisely (both in terms of network nodes location and internodal connectivity). Significance The combined source imaging and Granger analysis technique is an effective tool for studying normal or pathological brain conditions. PMID:27740473

Noninvasive Electromagnetic Source Imaging and Granger Causality Analysis: An Electrophysiological Connectome (eConnectome) Approach.

PubMed

Sohrabpour, Abbas; Ye, Shuai; Worrell, Gregory A; Zhang, Wenbo; He, Bin

2016-12-01

Combined source-imaging techniques and directional connectivity analysis can provide useful information about the underlying brain networks in a noninvasive fashion. Source-imaging techniques have been used successfully to either determine the source of activity or to extract source time-courses for Granger causality analysis, previously. In this work, we utilize source-imaging algorithms to both find the network nodes [regions of interest (ROI)] and then extract the activation time series for further Granger causality analysis. The aim of this work is to find network nodes objectively from noninvasive electromagnetic signals, extract activation time-courses, and apply Granger analysis on the extracted series to study brain networks under realistic conditions. Source-imaging methods are used to identify network nodes and extract time-courses and then Granger causality analysis is applied to delineate the directional functional connectivity of underlying brain networks. Computer simulations studies where the underlying network (nodes and connectivity pattern) is known were performed; additionally, this approach has been evaluated in partial epilepsy patients to study epilepsy networks from interictal and ictal signals recorded by EEG and/or Magnetoencephalography (MEG). Localization errors of network nodes are less than 5 mm and normalized connectivity errors of ∼20% in estimating underlying brain networks in simulation studies. Additionally, two focal epilepsy patients were studied and the identified nodes driving the epileptic network were concordant with clinical findings from intracranial recordings or surgical resection. Our study indicates that combined source-imaging algorithms with Granger causality analysis can identify underlying networks precisely (both in terms of network nodes location and internodal connectivity). The combined source imaging and Granger analysis technique is an effective tool for studying normal or pathological brain conditions.

Network meta-analysis: an introduction for pharmacists.

PubMed

Xu, Yina; Amiche, Mohamed Amine; Tadrous, Mina

2018-05-21

Network meta-analysis is a new tool used to summarize and compare studies for multiple interventions, irrespective of whether these interventions have been directly evaluated against each other. Network meta-analysis is quickly becoming the standard in conducting therapeutic reviews and clinical guideline development. However, little guidance is available to help pharmacists review network meta-analysis studies in their practice. Major institutions such as the Cochrane Collaboration, Agency for Healthcare Research and Quality, Canadian Agency for Drugs and Technologies in Health, and National Institute for Health and Care Excellence Decision Support Unit have endorsed utilizing network meta-analysis to establish therapeutic evidence and inform decision making. Our objective is to introduce this novel technique to pharmacy practitioners, and highlight key assumptions behind network meta-analysis studies.

Fighting Dark Networks: Using Social Network Analysis to Implement the Special Operations Targeting Process for Direct and Indirect Approaches

DTIC Science & Technology

2013-03-01

Wouter De Nooy, Andrej Mrvar and Vladimir Batagelj , Exploratory Social Network Analysis with Pajek, (New York: Cambridge University Press, 2005), 5...Granovetter, “The Strength of Weak Ties,” 1350–1368. 151 de Nooy, Mrvar , and Batagelj , Exploratory Social Network Analysis with Pajek, 151. 152...Spacetime Wrinkles Exhibit (1995). de Nooy, Wouter, Andrej Mrvar , and Vladimir Batagelj . Exploratory Social Network Analysis with Pajek. Cambridge

Impact of lysozyme on stability mechanism of nanozirconia aqueous suspension

NASA Astrophysics Data System (ADS)

Szewczuk-Karpisz, Katarzyna; Wiśniewska, Małgorzata

2016-08-01

The effect of lysozyme (LSZ) presence on the zirconium(IV) oxide (ZrO2) aqueous suspension stability was examined. The applied zirconia contains mesopores (with a diameter about 30 nm) and its mean particle size is about 100 nm. To determine the stability mechanism of ZrO2 suspension in the biopolymer presence, the adsorption and electrokinetic (surface charge density and zeta potential) measurements were performed in the pH range 3-10. The lysozyme adsorption on the nanozirconia surface proceeds mainly through electrostatic forces. Under solid-polymer repulsion conditions, there is no adsorption of lysozyme (pH < 6, CNaCl 0.01 mol/dm3). The increase of solution ionic strength to 0.2 mol/dm3 causes screening of unfavourable forces and biopolymer adsorption becomes possible. The LSZ addition to the ZrO2 suspension influences its stability. At pH 3, 4.6 and 7.6, slight improvement of the system stability was obtained. In turn, at pH 9 considerable destabilization of nanozirconia particles covered by polymeric layers occurs.

Cadmium localization and quantification in the plant Arabidopsis thaliana using micro-PIXE

NASA Astrophysics Data System (ADS)

Ager, F. J.; Ynsa, M. D.; Domínguez-Solís, J. R.; Gotor, C.; Respaldiza, M. A.; Romero, L. C.

2002-04-01

Remediation of metal-contaminated soils and waters poses a challenging problem due to its implications in the environment and the human health. The use of metal-accumulating plants to remove toxic metals, including Cd, from soil and aqueous streams has been proposed as a possible solution to this problem. The process of using plants for environmental restoration is termed phytoremediation. Cd is a particularly favourable target metal for this technology because it is readily transported and accumulated in the shoots of several plant species. This paper investigates the sites of metal localization within Arabidopsis thaliana leaves, when plants are grown in a cadmium-rich environment, by making use of nuclear microscopy techniques. Micro-PIXE, RBS and SEM analyses were performed on the scanning proton microprobe at the CNA in Seville (Spain), showing that cadmium is sequestered within the trichomes on the leaf surface. Additionally, regular PIXE analyses were performed on samples prepared by an acid digestion method in order to assess the metal accumulation of such plants.

Copy Number Alterations and Methylation in Ewing's Sarcoma

PubMed Central

Jahromi, Mona S.; Jones, Kevin B.; Schiffman, Joshua D.

2011-01-01

Ewing's sarcoma is the second most common bone malignancy affecting children and young adults. The prognosis is especially poor in metastatic or relapsed disease. The cell of origin remains elusive, but the EWS-FLI1 fusion oncoprotein is present in the majority of cases. The understanding of the molecular basis of Ewing's sarcoma continues to progress slowly. EWS-FLI1 affects gene expression, but other factors must also be at work such as mutations, gene copy number alterations, and promoter methylation. This paper explores in depth two molecular aspects of Ewing's sarcoma: copy number alterations (CNAs) and methylation. While CNAs consistently have been reported in Ewing's sarcoma, their clinical significance has been variable, most likely due to small sample size and tumor heterogeneity. Methylation is thought to be important in oncogenesis and balanced karyotype cancers such as Ewing's, yet it has received only minimal attention in prior studies. Future CNA and methylation studies will help to understand the molecular basis of this disease. PMID:21437220

Geriatric Training Academy: innovative education for certified nurse aides and charge nurses.

PubMed

Cherry, Barbara; Marshall-Gray, Paula; Laurence, Ann; Green, Alexia; Valadez, Ana; Scott-Tilley, Donna; Merritt, Pearl

2007-03-01

Quality care for the rapidly growing number of older Americans is a major challenge facing the health care industry today. With the baby-boom generation "coming of age"--older age-the need for quality long-term care workers is on the rise. It is estimated that the number of persons needing assisted or alternative living arrangements will increase from 15 million in 2000 to 27 million in 2050 (U.S. Department of Health and Human Services [HHS], 2003). In response to the rising demand for quality long-term care workers, the Geriatric Education and Training Academy (the Academy) was created at Texas Tech University Health Sciences Center (TTUHSC) to provide advanced geriatric education and training for certified nurse aides (CNA), licensed vocational nurses (LVN) and registered nurses (RN) who work in long-term care facilities. This article describes how the Academy is addressing the need for the recruitment, education, and retention of long-term care workers for the expanding geriatric population in West Texas.

In Vitro Antifungal Activity and Mode of Action of 2',4'-Dihydroxychalcone against Aspergillus fumigatus

PubMed Central

Seo, Young Ho; Kim, Sung-Su

2015-01-01

2',4'-Dihydroxychalcone (2',4'-DHC) was identified from a heat shock protein 90 (Hsp90)-targeting library as a compound with Hsp90 inhibitory and antifungal effects. In the presence of 2',4'-DHC (8 µg/mL), radial growth of Aspergillus fumigatus was inhibited 20% compared to the control, and green pigmentation was completely blocked. The expression of the conidiation-associated genes abaA, brlA, and wetA was significantly decreased (approximately 3- to 5-fold) by treatment with 2',4'-DHC. The expression of calcineurin signaling components, cnaA and crzA, was also significantly reduced. The inhibitory effects of 2',4'-DHC on metabolic activity and mycelial growth were significantly enhanced by combination treatment with itraconazole and caspofungin. Docking studies indicated that 2',4'-DHC bind to the ATPase domain of Hsp90. These results suggest that 2',4'-DHC act as an Hsp90-calcinurin pathway inhibitor. PMID:26190922

In Vitro Antifungal Activity and Mode of Action of 2',4'-Dihydroxychalcone against Aspergillus fumigatus.

PubMed

Seo, Young Ho; Kim, Sung-Su; Shin, Kwang-Soo

2015-06-01

2',4'-Dihydroxychalcone (2',4'-DHC) was identified from a heat shock protein 90 (Hsp90)-targeting library as a compound with Hsp90 inhibitory and antifungal effects. In the presence of 2',4'-DHC (8 µg/mL), radial growth of Aspergillus fumigatus was inhibited 20% compared to the control, and green pigmentation was completely blocked. The expression of the conidiation-associated genes abaA, brlA, and wetA was significantly decreased (approximately 3- to 5-fold) by treatment with 2',4'-DHC. The expression of calcineurin signaling components, cnaA and crzA, was also significantly reduced. The inhibitory effects of 2',4'-DHC on metabolic activity and mycelial growth were significantly enhanced by combination treatment with itraconazole and caspofungin. Docking studies indicated that 2',4'-DHC bind to the ATPase domain of Hsp90. These results suggest that 2',4'-DHC act as an Hsp90-calcinurin pathway inhibitor.

Porous polycarbene-bearing membrane actuator for ultrasensitive weak-acid detection and real-time chemical reaction monitoring.

PubMed

Sun, Jian-Ke; Zhang, Weiyi; Guterman, Ryan; Lin, Hui-Juan; Yuan, Jiayin

2018-04-30

Soft actuators with integration of ultrasensitivity and capability of simultaneous interaction with multiple stimuli through an entire event ask for a high level of structure complexity, adaptability, and/or multi-responsiveness, which is a great challenge. Here, we develop a porous polycarbene-bearing membrane actuator built up from ionic complexation between a poly(ionic liquid) and trimesic acid (TA). The actuator features two concurrent structure gradients, i.e., an electrostatic complexation (EC) degree and a density distribution of a carbene-NH 3 adduct (CNA) along the membrane cross-section. The membrane actuator performs the highest sensitivity among the state-of-the-art soft proton actuators toward acetic acid at 10 -6  mol L -1 (M) level in aqueous media. Through competing actuation of the two gradients, it is capable of monitoring an entire process of proton-involved chemical reactions that comprise multiple stimuli and operational steps. The present achievement constitutes a significant step toward real-life application of soft actuators in chemical sensing and reaction technology.

Light-Sensitive Ruthenium Complex-Loaded Cross-linked Polymeric Nanoassemblies for the Treatment of Cancer

PubMed Central

Dickerson, M; Howerton, B.; Bae, Y.; Glazer, E.

2016-01-01

This work focuses on improving the efficacy of photoactivatable Ru complexes for photodynamic therapy by employing cross-linked nanoassemblies (CNAs) as a delivery approach. The effects of complex photoactivation, hydrophobicity, and solution ionic strength and pH on complex loading and release from CNAs were analyzed. The cell cytotoxicity of CNA formulations was similar to free Ru complexes despite reduced or eliminated DNA interactions. The release rate and the amount of each Ru complex released (%) varied inversely with complex hydrophobicity, while the effect of solution ionic strength was dependent on complex hydrophobicity. Premature release of two photoactivatable prodrugs prior to irradiation was believed to account for higher activity in cells studies compared to DNA interaction studies; however, for photostable 1O2 generator-loaded CNAs this cannot explain the high cytotoxicity and lack of DNA interactions because release was incomplete after 48 hrs. The cause remains unclear, but among other possibilities, accelerated release in a cell culture environment may be responsible. PMID:26855780

Honeycomb: Visual Analysis of Large Scale Social Networks

NASA Astrophysics Data System (ADS)

van Ham, Frank; Schulz, Hans-Jörg; Dimicco, Joan M.

The rise in the use of social network sites allows us to collect large amounts of user reported data on social structures and analysis of this data could provide useful insights for many of the social sciences. This analysis is typically the domain of Social Network Analysis, and visualization of these structures often proves invaluable in understanding them. However, currently available visual analysis tools are not very well suited to handle the massive scale of this network data, and often resolve to displaying small ego networks or heavily abstracted networks. In this paper, we present Honeycomb, a visualization tool that is able to deal with much larger scale data (with millions of connections), which we illustrate by using a large scale corporate social networking site as an example. Additionally, we introduce a new probability based network metric to guide users to potentially interesting or anomalous patterns and discuss lessons learned during design and implementation.

Visual analysis and exploration of complex corporate shareholder networks

NASA Astrophysics Data System (ADS)

Tekušová, Tatiana; Kohlhammer, Jörn

2008-01-01

The analysis of large corporate shareholder network structures is an important task in corporate governance, in financing, and in financial investment domains. In a modern economy, large structures of cross-corporation, cross-border shareholder relationships exist, forming complex networks. These networks are often difficult to analyze with traditional approaches. An efficient visualization of the networks helps to reveal the interdependent shareholding formations and the controlling patterns. In this paper, we propose an effective visualization tool that supports the financial analyst in understanding complex shareholding networks. We develop an interactive visual analysis system by combining state-of-the-art visualization technologies with economic analysis methods. Our system is capable to reveal patterns in large corporate shareholder networks, allows the visual identification of the ultimate shareholders, and supports the visual analysis of integrated cash flow and control rights. We apply our system on an extensive real-world database of shareholder relationships, showing its usefulness for effective visual analysis.

Evaluating the Quality of Evidence from a Network Meta-Analysis

PubMed Central

Salanti, Georgia; Del Giovane, Cinzia; Chaimani, Anna; Caldwell, Deborah M.; Higgins, Julian P. T.

2014-01-01

Systematic reviews that collate data about the relative effects of multiple interventions via network meta-analysis are highly informative for decision-making purposes. A network meta-analysis provides two types of findings for a specific outcome: the relative treatment effect for all pairwise comparisons, and a ranking of the treatments. It is important to consider the confidence with which these two types of results can enable clinicians, policy makers and patients to make informed decisions. We propose an approach to determining confidence in the output of a network meta-analysis. Our proposed approach is based on methodology developed by the Grading of Recommendations Assessment, Development and Evaluation (GRADE) Working Group for pairwise meta-analyses. The suggested framework for evaluating a network meta-analysis acknowledges (i) the key role of indirect comparisons (ii) the contributions of each piece of direct evidence to the network meta-analysis estimates of effect size; (iii) the importance of the transitivity assumption to the validity of network meta-analysis; and (iv) the possibility of disagreement between direct evidence and indirect evidence. We apply our proposed strategy to a systematic review comparing topical antibiotics without steroids for chronically discharging ears with underlying eardrum perforations. The proposed framework can be used to determine confidence in the results from a network meta-analysis. Judgements about evidence from a network meta-analysis can be different from those made about evidence from pairwise meta-analyses. PMID:24992266

Unified functional network and nonlinear time series analysis for complex systems science: The pyunicorn package

NASA Astrophysics Data System (ADS)

Donges, Jonathan; Heitzig, Jobst; Beronov, Boyan; Wiedermann, Marc; Runge, Jakob; Feng, Qing Yi; Tupikina, Liubov; Stolbova, Veronika; Donner, Reik; Marwan, Norbert; Dijkstra, Henk; Kurths, Jürgen

2016-04-01

We introduce the pyunicorn (Pythonic unified complex network and recurrence analysis toolbox) open source software package for applying and combining modern methods of data analysis and modeling from complex network theory and nonlinear time series analysis. pyunicorn is a fully object-oriented and easily parallelizable package written in the language Python. It allows for the construction of functional networks such as climate networks in climatology or functional brain networks in neuroscience representing the structure of statistical interrelationships in large data sets of time series and, subsequently, investigating this structure using advanced methods of complex network theory such as measures and models for spatial networks, networks of interacting networks, node-weighted statistics, or network surrogates. Additionally, pyunicorn provides insights into the nonlinear dynamics of complex systems as recorded in uni- and multivariate time series from a non-traditional perspective by means of recurrence quantification analysis, recurrence networks, visibility graphs, and construction of surrogate time series. The range of possible applications of the library is outlined, drawing on several examples mainly from the field of climatology. pyunicorn is available online at https://github.com/pik-copan/pyunicorn. Reference: J.F. Donges, J. Heitzig, B. Beronov, M. Wiedermann, J. Runge, Q.-Y. Feng, L. Tupikina, V. Stolbova, R.V. Donner, N. Marwan, H.A. Dijkstra, and J. Kurths, Unified functional network and nonlinear time series analysis for complex systems science: The pyunicorn package, Chaos 25, 113101 (2015), DOI: 10.1063/1.4934554, Preprint: arxiv.org:1507.01571 [physics.data-an].

Organizational network analysis for two networks in the Washington State Department of Transportation.

DOT National Transportation Integrated Search

2010-10-01

Organizational network analysis (ONA) consists of gathering data on information sharing and : connectivity in a group, calculating network measures, creating network maps, and using this : information to analyze and improve the functionality of the g...

Spatial Distribution Characteristics of Healthcare Facilities in Nanjing: Network Point Pattern Analysis and Correlation Analysis.

PubMed

Ni, Jianhua; Qian, Tianlu; Xi, Changbai; Rui, Yikang; Wang, Jiechen

2016-08-18

The spatial distribution of urban service facilities is largely constrained by the road network. In this study, network point pattern analysis and correlation analysis were used to analyze the relationship between road network and healthcare facility distribution. The weighted network kernel density estimation method proposed in this study identifies significant differences between the outside and inside areas of the Ming city wall. The results of network K-function analysis show that private hospitals are more evenly distributed than public hospitals, and pharmacy stores tend to cluster around hospitals along the road network. After computing the correlation analysis between different categorized hospitals and street centrality, we find that the distribution of these hospitals correlates highly with the street centralities, and that the correlations are higher with private and small hospitals than with public and large hospitals. The comprehensive analysis results could help examine the reasonability of existing urban healthcare facility distribution and optimize the location of new healthcare facilities.

NAP: The Network Analysis Profiler, a web tool for easier topological analysis and comparison of medium-scale biological networks.

PubMed

Theodosiou, Theodosios; Efstathiou, Georgios; Papanikolaou, Nikolas; Kyrpides, Nikos C; Bagos, Pantelis G; Iliopoulos, Ioannis; Pavlopoulos, Georgios A

2017-07-14

Nowadays, due to the technological advances of high-throughput techniques, Systems Biology has seen a tremendous growth of data generation. With network analysis, looking at biological systems at a higher level in order to better understand a system, its topology and the relationships between its components is of a great importance. Gene expression, signal transduction, protein/chemical interactions, biomedical literature co-occurrences, are few of the examples captured in biological network representations where nodes represent certain bioentities and edges represent the connections between them. Today, many tools for network visualization and analysis are available. Nevertheless, most of them are standalone applications that often (i) burden users with computing and calculation time depending on the network's size and (ii) focus on handling, editing and exploring a network interactively. While such functionality is of great importance, limited efforts have been made towards the comparison of the topological analysis of multiple networks. Network Analysis Provider (NAP) is a comprehensive web tool to automate network profiling and intra/inter-network topology comparison. It is designed to bridge the gap between network analysis, statistics, graph theory and partially visualization in a user-friendly way. It is freely available and aims to become a very appealing tool for the broader community. It hosts a great plethora of topological analysis methods such as node and edge rankings. Few of its powerful characteristics are: its ability to enable easy profile comparisons across multiple networks, find their intersection and provide users with simplified, high quality plots of any of the offered topological characteristics against any other within the same network. It is written in R and Shiny, it is based on the igraph library and it is able to handle medium-scale weighted/unweighted, directed/undirected and bipartite graphs. NAP is available at http://bioinformatics.med.uoc.gr/NAP .

Nested Neural Networks

NASA Technical Reports Server (NTRS)

Baram, Yoram

1992-01-01

Report presents analysis of nested neural networks, consisting of interconnected subnetworks. Analysis based on simplified mathematical models more appropriate for artificial electronic neural networks, partly applicable to biological neural networks. Nested structure allows for retrieval of individual subpatterns. Requires fewer wires and connection devices than fully connected networks, and allows for local reconstruction of damaged subnetworks without rewiring entire network.

Analysing Health Professionals' Learning Interactions in an Online Social Network: A Longitudinal Study.

PubMed

Li, Xin; Verspoor, Karin; Gray, Kathleen; Barnett, Stephen

2016-01-01

This paper summarises a longitudinal analysis of learning interactions occurring over three years among health professionals in an online social network. The study employs the techniques of Social Network Analysis (SNA) and statistical modeling to identify the changes in patterns of interaction over time and test associated structural network effects. SNA results indicate overall low participation in the network, although some participants became active over time and even led discussions. In particular, the analysis has shown that a change of lead contributor results in a change in learning interaction and network structure. The analysis of structural network effects demonstrates that the interaction dynamics slow down over time, indicating that interactions in the network are more stable. The health professionals may be reluctant to share knowledge and collaborate in groups but were interested in building personal learning networks or simply seeking information.

WGCNA: an R package for weighted correlation network analysis.

PubMed

Langfelder, Peter; Horvath, Steve

2008-12-29

Correlation networks are increasingly being used in bioinformatics applications. For example, weighted gene co-expression network analysis is a systems biology method for describing the correlation patterns among genes across microarray samples. Weighted correlation network analysis (WGCNA) can be used for finding clusters (modules) of highly correlated genes, for summarizing such clusters using the module eigengene or an intramodular hub gene, for relating modules to one another and to external sample traits (using eigengene network methodology), and for calculating module membership measures. Correlation networks facilitate network based gene screening methods that can be used to identify candidate biomarkers or therapeutic targets. These methods have been successfully applied in various biological contexts, e.g. cancer, mouse genetics, yeast genetics, and analysis of brain imaging data. While parts of the correlation network methodology have been described in separate publications, there is a need to provide a user-friendly, comprehensive, and consistent software implementation and an accompanying tutorial. The WGCNA R software package is a comprehensive collection of R functions for performing various aspects of weighted correlation network analysis. The package includes functions for network construction, module detection, gene selection, calculations of topological properties, data simulation, visualization, and interfacing with external software. Along with the R package we also present R software tutorials. While the methods development was motivated by gene expression data, the underlying data mining approach can be applied to a variety of different settings. The WGCNA package provides R functions for weighted correlation network analysis, e.g. co-expression network analysis of gene expression data. The R package along with its source code and additional material are freely available at http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA.

A methodological approach to the analysis of egocentric social networks in public health research: a practical example.

PubMed

Djomba, Janet Klara; Zaletel-Kragelj, Lijana

2016-12-01

Research on social networks in public health focuses on how social structures and relationships influence health and health-related behaviour. While the sociocentric approach is used to study complete social networks, the egocentric approach is gaining popularity because of its focus on individuals, groups and communities. One of the participants of the healthy lifestyle health education workshop 'I'm moving', included in the study of social support for exercise was randomly selected. The participant was denoted as the ego and members of her/his social network as the alteri. Data were collected by personal interviews using a self-made questionnaire. Numerical methods and computer programmes for the analysis of social networks were used for the demonstration of analysis. The size, composition and structure of the egocentric social network were obtained by a numerical analysis. The analysis of composition included homophily and homogeneity. Moreover, the analysis of the structure included the degree of the egocentric network, the strength of the ego-alter ties and the average strength of ties. Visualisation of the network was performed by three freely available computer programmes, namely: Egonet.QF, E-net and Pajek. The computer programmes were described and compared by their usefulness. Both numerical analysis and visualisation have their benefits. The decision what approach to use is depending on the purpose of the social network analysis. While the numerical analysis can be used in large-scale population-based studies, visualisation of personal networks can help health professionals at creating, performing and evaluation of preventive programmes, especially if focused on behaviour change.

Statistical parsimony networks and species assemblages in Cephalotrichid nemerteans (nemertea).

PubMed

Chen, Haixia; Strand, Malin; Norenburg, Jon L; Sun, Shichun; Kajihara, Hiroshi; Chernyshev, Alexey V; Maslakova, Svetlana A; Sundberg, Per

2010-09-21

It has been suggested that statistical parsimony network analysis could be used to get an indication of species represented in a set of nucleotide data, and the approach has been used to discuss species boundaries in some taxa. Based on 635 base pairs of the mitochondrial protein-coding gene cytochrome c oxidase I (COI), we analyzed 152 nemertean specimens using statistical parsimony network analysis with the connection probability set to 95%. The analysis revealed 15 distinct networks together with seven singletons. Statistical parsimony yielded three networks supporting the species status of Cephalothrix rufifrons, C. major and C. spiralis as they currently have been delineated by morphological characters and geographical location. Many other networks contained haplotypes from nearby geographical locations. Cladistic structure by maximum likelihood analysis overall supported the network analysis, but indicated a false positive result where subnetworks should have been connected into one network/species. This probably is caused by undersampling of the intraspecific haplotype diversity. Statistical parsimony network analysis provides a rapid and useful tool for detecting possible undescribed/cryptic species among cephalotrichid nemerteans based on COI gene. It should be combined with phylogenetic analysis to get indications of false positive results, i.e., subnetworks that would have been connected with more extensive haplotype sampling.

Orthoscape: a cytoscape application for grouping and visualization KEGG based gene networks by taxonomy and homology principles.

PubMed

Mustafin, Zakhar Sergeevich; Lashin, Sergey Alexandrovich; Matushkin, Yury Georgievich; Gunbin, Konstantin Vladimirovich; Afonnikov, Dmitry Arkadievich

2017-01-27

There are many available software tools for visualization and analysis of biological networks. Among them, Cytoscape ( http://cytoscape.org/ ) is one of the most comprehensive packages, with many plugins and applications which extends its functionality by providing analysis of protein-protein interaction, gene regulatory and gene co-expression networks, metabolic, signaling, neural as well as ecological-type networks including food webs, communities networks etc. Nevertheless, only three plugins tagged 'network evolution' found in Cytoscape official app store and in literature. We have developed a new Cytoscape 3.0 application Orthoscape aimed to facilitate evolutionary analysis of gene networks and visualize the results. Orthoscape aids in analysis of evolutionary information available for gene sets and networks by highlighting: (1) the orthology relationships between genes; (2) the evolutionary origin of gene network components; (3) the evolutionary pressure mode (diversifying or stabilizing, negative or positive selection) of orthologous groups in general and/or branch-oriented mode. The distinctive feature of Orthoscape is the ability to control all data analysis steps via user-friendly interface. Orthoscape allows its users to analyze gene networks or separated gene sets in the context of evolution. At each step of data analysis, Orthoscape also provides for convenient visualization and data manipulation.

NEAT: an efficient network enrichment analysis test.

PubMed

Signorelli, Mirko; Vinciotti, Veronica; Wit, Ernst C

2016-09-05

Network enrichment analysis is a powerful method, which allows to integrate gene enrichment analysis with the information on relationships between genes that is provided by gene networks. Existing tests for network enrichment analysis deal only with undirected networks, they can be computationally slow and are based on normality assumptions. We propose NEAT, a test for network enrichment analysis. The test is based on the hypergeometric distribution, which naturally arises as the null distribution in this context. NEAT can be applied not only to undirected, but to directed and partially directed networks as well. Our simulations indicate that NEAT is considerably faster than alternative resampling-based methods, and that its capacity to detect enrichments is at least as good as the one of alternative tests. We discuss applications of NEAT to network analyses in yeast by testing for enrichment of the Environmental Stress Response target gene set with GO Slim and KEGG functional gene sets, and also by inspecting associations between functional sets themselves. NEAT is a flexible and efficient test for network enrichment analysis that aims to overcome some limitations of existing resampling-based tests. The method is implemented in the R package neat, which can be freely downloaded from CRAN ( https://cran.r-project.org/package=neat ).

Software Defined Network Monitoring Scheme Using Spectral Graph Theory and Phantom Nodes

DTIC Science & Technology

2014-09-01

networks is the emergence of software - defined networking ( SDN ) [1]. SDN has existed for the...Chapter III for network monitoring. A. SOFTWARE DEFINED NETWORKS SDNs provide a new and innovative method to simplify network hardware by logically...and R. Giladi, “Performance analysis of software - defined networking ( SDN ),” in Proc. of IEEE 21st International Symposium on Modeling, Analysis

Kinetics of cisplatin binding to short r(GG) containing miRNA mimics - influence of Na(+)versus K(+), temperature and hydrophobicity on reactivity.

PubMed

Alshiekh, Alak; Clausén, Maria; Elmroth, Sofi K C

2015-07-28

Nucleic acids are well recognized targets for platinum-based anticancer drugs, with RNA and DNA being kinetically comparable. In the case of RNA, previous studies have shown that the reaction between small duplex RNAs (dsRNAs) and monoaquated cisplatin (cis-Pt(NH3)2Cl(OH2)(+), ) can be followed by the metal induced hyperchromicity occurring directly after addition of to e.g. microRNA mimics. In the present study, we have used this approach to compare thermal stability and reactivity between intracellularly- and extracellularly relevant salt concentration (CNa(+) and CK(+)ca. 0.1 M), and also as a function of increased hydrophobicity (10% v/v EtOH). In addition, reactivity was studied as a function of temperature in the interval ca. 5-20 °C below the respective dsRNA melting temperatures (Tms). Four different 13- to 20-mer dsRNAs with two different central sequence motifs were used as targets containing either a central r(GG)·r(CC)- or r(GG)·r(UAU)-sequence. The reactions exhibited half-lives in the minute- to hour range at 38 °C in the presence of excess in the μM range. Further, a linear dependence was found between C and the observed pseudo-first-order rate constants. The resulting apparent second-order rate constants were significantly larger for the lower melting r(GG)·r(UAU)-containing sequences compared with that of the fully complementary ones; the higher and lower reactivities represented by RNA-1-3 and RNA-1-1 with k2,appca. 30 and 8 M(-1) s(-1) respectively at CNa(+) = 122 mM. For all RNAs a common small, but significant, trend was observed with increased reactivity in the presence of K(+) compared with Na(+), and decreased reactivity in the presence of EtOH. Finally, the temperature dependence of k2,app was evaluated using the Eyring equation. The retrieved activation parameters reveal positive values for both ΔH(≠) and ΔS(≠) for all dsRNAs, in the range ca. 23-34 kcal mol(-1) and 22-57 cal K(-1) mol(-1) respectively. These values indicate solvational effects to be important for the rate determining step of the reaction, and thus in support of a structural change of the dsRNA to take place in parallel with the adduct formation step.

Transportation Network Analysis and Decomposition Methods

DOT National Transportation Integrated Search

1978-03-01

The report outlines research in transportation network analysis using decomposition techniques as a basis for problem solutions. Two transportation network problems were considered in detail: a freight network flow problem and a scheduling problem fo...

Protocol vulnerability detection based on network traffic analysis and binary reverse engineering.

PubMed

Wen, Shameng; Meng, Qingkun; Feng, Chao; Tang, Chaojing

2017-01-01

Network protocol vulnerability detection plays an important role in many domains, including protocol security analysis, application security, and network intrusion detection. In this study, by analyzing the general fuzzing method of network protocols, we propose a novel approach that combines network traffic analysis with the binary reverse engineering method. For network traffic analysis, the block-based protocol description language is introduced to construct test scripts, while the binary reverse engineering method employs the genetic algorithm with a fitness function designed to focus on code coverage. This combination leads to a substantial improvement in fuzz testing for network protocols. We build a prototype system and use it to test several real-world network protocol implementations. The experimental results show that the proposed approach detects vulnerabilities more efficiently and effectively than general fuzzing methods such as SPIKE.

Neural Networks for Rapid Design and Analysis

NASA Technical Reports Server (NTRS)

Sparks, Dean W., Jr.; Maghami, Peiman G.

1998-01-01

Artificial neural networks have been employed for rapid and efficient dynamics and control analysis of flexible systems. Specifically, feedforward neural networks are designed to approximate nonlinear dynamic components over prescribed input ranges, and are used in simulations as a means to speed up the overall time response analysis process. To capture the recursive nature of dynamic components with artificial neural networks, recurrent networks, which use state feedback with the appropriate number of time delays, as inputs to the networks, are employed. Once properly trained, neural networks can give very good approximations to nonlinear dynamic components, and by their judicious use in simulations, allow the analyst the potential to speed up the analysis process considerably. To illustrate this potential speed up, an existing simulation model of a spacecraft reaction wheel system is executed, first conventionally, and then with an artificial neural network in place.

Topological Vulnerability Analysis

NASA Astrophysics Data System (ADS)

Jajodia, Sushil; Noel, Steven

Traditionally, network administrators rely on labor-intensive processes for tracking network configurations and vulnerabilities. This requires a great deal of expertise, and is error prone because of the complexity of networks and associated security data. The interdependencies of network vulnerabilities make traditional point-wise vulnerability analysis inadequate. We describe a Topological Vulnerability Analysis (TVA) approach that analyzes vulnerability dependencies and shows all possible attack paths into a network. From models of the network vulnerabilities and potential attacker exploits, we compute attack graphs that convey the impact of individual and combined vulnerabilities on overall security. TVA finds potential paths of vulnerability through a network, showing exactly how attackers may penetrate a network. From this, we identify key vulnerabilities and provide strategies for protection of critical network assets.

Conducting indirect-treatment-comparison and network-meta-analysis studies: report of the ISPOR Task Force on Indirect Treatment Comparisons Good Research Practices: part 2.

PubMed

Hoaglin, David C; Hawkins, Neil; Jansen, Jeroen P; Scott, David A; Itzler, Robbin; Cappelleri, Joseph C; Boersma, Cornelis; Thompson, David; Larholt, Kay M; Diaz, Mireya; Barrett, Annabel

2011-06-01

Evidence-based health care decision making requires comparison of all relevant competing interventions. In the absence of randomized controlled trials involving a direct comparison of all treatments of interest, indirect treatment comparisons and network meta-analysis provide useful evidence for judiciously selecting the best treatment(s). Mixed treatment comparisons, a special case of network meta-analysis, combine direct evidence and indirect evidence for particular pairwise comparisons, thereby synthesizing a greater share of the available evidence than traditional meta-analysis. This report from the International Society for Pharmacoeconomics and Outcomes Research Indirect Treatment Comparisons Good Research Practices Task Force provides guidance on technical aspects of conducting network meta-analyses (our use of this term includes most methods that involve meta-analysis in the context of a network of evidence). We start with a discussion of strategies for developing networks of evidence. Next we briefly review assumptions of network meta-analysis. Then we focus on the statistical analysis of the data: objectives, models (fixed-effects and random-effects), frequentist versus Bayesian approaches, and model validation. A checklist highlights key components of network meta-analysis, and substantial examples illustrate indirect treatment comparisons (both frequentist and Bayesian approaches) and network meta-analysis. A further section discusses eight key areas for future research. Copyright © 2011 International Society for Pharmacoeconomics and Outcomes Research (ISPOR). Published by Elsevier Inc. All rights reserved.

Network analysis for the visualization and analysis of qualitative data.

PubMed

Pokorny, Jennifer J; Norman, Alex; Zanesco, Anthony P; Bauer-Wu, Susan; Sahdra, Baljinder K; Saron, Clifford D

2018-03-01

We present a novel manner in which to visualize the coding of qualitative data that enables representation and analysis of connections between codes using graph theory and network analysis. Network graphs are created from codes applied to a transcript or audio file using the code names and their chronological location. The resulting network is a representation of the coding data that characterizes the interrelations of codes. This approach enables quantification of qualitative codes using network analysis and facilitates examination of associations of network indices with other quantitative variables using common statistical procedures. Here, as a proof of concept, we applied this method to a set of interview transcripts that had been coded in 2 different ways and the resultant network graphs were examined. The creation of network graphs allows researchers an opportunity to view and share their qualitative data in an innovative way that may provide new insights and enhance transparency of the analytical process by which they reach their conclusions. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

Interdependent Multi-Layer Networks: Modeling and Survivability Analysis with Applications to Space-Based Networks

PubMed Central

Castet, Jean-Francois; Saleh, Joseph H.

2013-01-01

This article develops a novel approach and algorithmic tools for the modeling and survivability analysis of networks with heterogeneous nodes, and examines their application to space-based networks. Space-based networks (SBNs) allow the sharing of spacecraft on-orbit resources, such as data storage, processing, and downlink. Each spacecraft in the network can have different subsystem composition and functionality, thus resulting in node heterogeneity. Most traditional survivability analyses of networks assume node homogeneity and as a result, are not suited for the analysis of SBNs. This work proposes that heterogeneous networks can be modeled as interdependent multi-layer networks, which enables their survivability analysis. The multi-layer aspect captures the breakdown of the network according to common functionalities across the different nodes, and it allows the emergence of homogeneous sub-networks, while the interdependency aspect constrains the network to capture the physical characteristics of each node. Definitions of primitives of failure propagation are devised. Formal characterization of interdependent multi-layer networks, as well as algorithmic tools for the analysis of failure propagation across the network are developed and illustrated with space applications. The SBN applications considered consist of several networked spacecraft that can tap into each other's Command and Data Handling subsystem, in case of failure of its own, including the Telemetry, Tracking and Command, the Control Processor, and the Data Handling sub-subsystems. Various design insights are derived and discussed, and the capability to perform trade-space analysis with the proposed approach for various network characteristics is indicated. The select results here shown quantify the incremental survivability gains (with respect to a particular class of threats) of the SBN over the traditional monolith spacecraft. Failure of the connectivity between nodes is also examined, and the results highlight the importance of the reliability of the wireless links between spacecraft (nodes) to enable any survivability improvements for space-based networks. PMID:23599835

Interdependent multi-layer networks: modeling and survivability analysis with applications to space-based networks.

PubMed

Castet, Jean-Francois; Saleh, Joseph H

2013-01-01

This article develops a novel approach and algorithmic tools for the modeling and survivability analysis of networks with heterogeneous nodes, and examines their application to space-based networks. Space-based networks (SBNs) allow the sharing of spacecraft on-orbit resources, such as data storage, processing, and downlink. Each spacecraft in the network can have different subsystem composition and functionality, thus resulting in node heterogeneity. Most traditional survivability analyses of networks assume node homogeneity and as a result, are not suited for the analysis of SBNs. This work proposes that heterogeneous networks can be modeled as interdependent multi-layer networks, which enables their survivability analysis. The multi-layer aspect captures the breakdown of the network according to common functionalities across the different nodes, and it allows the emergence of homogeneous sub-networks, while the interdependency aspect constrains the network to capture the physical characteristics of each node. Definitions of primitives of failure propagation are devised. Formal characterization of interdependent multi-layer networks, as well as algorithmic tools for the analysis of failure propagation across the network are developed and illustrated with space applications. The SBN applications considered consist of several networked spacecraft that can tap into each other's Command and Data Handling subsystem, in case of failure of its own, including the Telemetry, Tracking and Command, the Control Processor, and the Data Handling sub-subsystems. Various design insights are derived and discussed, and the capability to perform trade-space analysis with the proposed approach for various network characteristics is indicated. The select results here shown quantify the incremental survivability gains (with respect to a particular class of threats) of the SBN over the traditional monolith spacecraft. Failure of the connectivity between nodes is also examined, and the results highlight the importance of the reliability of the wireless links between spacecraft (nodes) to enable any survivability improvements for space-based networks.

Stochastic Control of Multi-Scale Networks: Modeling, Analysis and Algorithms

DTIC Science & Technology

2014-10-20

Theory, (02 2012): 0. doi: B. T. Swapna, Atilla Eryilmaz, Ness B. Shroff. Throughput-Delay Analysis of Random Linear Network Coding for Wireless ... Wireless Sensor Networks and Effects of Long-Range Dependent Data, Sequential Analysis , (10 2012): 0. doi: 10.1080/07474946.2012.719435 Stefano...Sequential Analysis , (10 2012): 0. doi: John S. Baras, Shanshan Zheng. Sequential Anomaly Detection in Wireless Sensor Networks andEffects of Long

Framework for network modularization and Bayesian network analysis to investigate the perturbed metabolic network

PubMed Central

2011-01-01

Background Genome-scale metabolic network models have contributed to elucidating biological phenomena, and predicting gene targets to engineer for biotechnological applications. With their increasing importance, their precise network characterization has also been crucial for better understanding of the cellular physiology. Results We herein introduce a framework for network modularization and Bayesian network analysis (FMB) to investigate organism’s metabolism under perturbation. FMB reveals direction of influences among metabolic modules, in which reactions with similar or positively correlated flux variation patterns are clustered, in response to specific perturbation using metabolic flux data. With metabolic flux data calculated by constraints-based flux analysis under both control and perturbation conditions, FMB, in essence, reveals the effects of specific perturbations on the biological system through network modularization and Bayesian network analysis at metabolic modular level. As a demonstration, this framework was applied to the genetically perturbed Escherichia coli metabolism, which is a lpdA gene knockout mutant, using its genome-scale metabolic network model. Conclusions After all, it provides alternative scenarios of metabolic flux distributions in response to the perturbation, which are complementary to the data obtained from conventionally available genome-wide high-throughput techniques or metabolic flux analysis. PMID:22784571

Framework for network modularization and Bayesian network analysis to investigate the perturbed metabolic network.

PubMed

Kim, Hyun Uk; Kim, Tae Yong; Lee, Sang Yup

2011-01-01

Genome-scale metabolic network models have contributed to elucidating biological phenomena, and predicting gene targets to engineer for biotechnological applications. With their increasing importance, their precise network characterization has also been crucial for better understanding of the cellular physiology. We herein introduce a framework for network modularization and Bayesian network analysis (FMB) to investigate organism's metabolism under perturbation. FMB reveals direction of influences among metabolic modules, in which reactions with similar or positively correlated flux variation patterns are clustered, in response to specific perturbation using metabolic flux data. With metabolic flux data calculated by constraints-based flux analysis under both control and perturbation conditions, FMB, in essence, reveals the effects of specific perturbations on the biological system through network modularization and Bayesian network analysis at metabolic modular level. As a demonstration, this framework was applied to the genetically perturbed Escherichia coli metabolism, which is a lpdA gene knockout mutant, using its genome-scale metabolic network model. After all, it provides alternative scenarios of metabolic flux distributions in response to the perturbation, which are complementary to the data obtained from conventionally available genome-wide high-throughput techniques or metabolic flux analysis.

Satellite image analysis using neural networks

NASA Technical Reports Server (NTRS)

Sheldon, Roger A.

1990-01-01

The tremendous backlog of unanalyzed satellite data necessitates the development of improved methods for data cataloging and analysis. Ford Aerospace has developed an image analysis system, SIANN (Satellite Image Analysis using Neural Networks) that integrates the technologies necessary to satisfy NASA's science data analysis requirements for the next generation of satellites. SIANN will enable scientists to train a neural network to recognize image data containing scenes of interest and then rapidly search data archives for all such images. The approach combines conventional image processing technology with recent advances in neural networks to provide improved classification capabilities. SIANN allows users to proceed through a four step process of image classification: filtering and enhancement, creation of neural network training data via application of feature extraction algorithms, configuring and training a neural network model, and classification of images by application of the trained neural network. A prototype experimentation testbed was completed and applied to climatological data.

Network Analysis: Applications for the Developing Brain

PubMed Central

Chu-Shore, Catherine J.; Kramer, Mark A.; Bianchi, Matt T.; Caviness, Verne S.; Cash, Sydney S.

2011-01-01

Development of the human brain follows a complex trajectory of age-specific anatomical and physiological changes. The application of network analysis provides an illuminating perspective on the dynamic interregional and global properties of this intricate and complex system. Here, we provide a critical synopsis of methods of network analysis with a focus on developing brain networks. After discussing basic concepts and approaches to network analysis, we explore the primary events of anatomical cortical development from gestation through adolescence. Upon this framework, we describe early work revealing the evolution of age-specific functional brain networks in normal neurodevelopment. Finally, we review how these relationships can be altered in disease and perhaps even rectified with treatment. While this method of description and inquiry remains in early form, there is already substantial evidence that the application of network models and analysis to understanding normal and abnormal human neural development holds tremendous promise for future discovery. PMID:21303762

An investigation of the impact of using different methods for network meta-analysis: a protocol for an empirical evaluation.

PubMed

Karahalios, Amalia Emily; Salanti, Georgia; Turner, Simon L; Herbison, G Peter; White, Ian R; Veroniki, Areti Angeliki; Nikolakopoulou, Adriani; Mckenzie, Joanne E

2017-06-24

Network meta-analysis, a method to synthesise evidence from multiple treatments, has increased in popularity in the past decade. Two broad approaches are available to synthesise data across networks, namely, arm- and contrast-synthesis models, with a range of models that can be fitted within each. There has been recent debate about the validity of the arm-synthesis models, but to date, there has been limited empirical evaluation comparing results using the methods applied to a large number of networks. We aim to address this gap through the re-analysis of a large cohort of published networks of interventions using a range of network meta-analysis methods. We will include a subset of networks from a database of network meta-analyses of randomised trials that have been identified and curated from the published literature. The subset of networks will include those where the primary outcome is binary, the number of events and participants are reported for each direct comparison, and there is no evidence of inconsistency in the network. We will re-analyse the networks using three contrast-synthesis methods and two arm-synthesis methods. We will compare the estimated treatment effects, their standard errors, treatment hierarchy based on the surface under the cumulative ranking (SUCRA) curve, the SUCRA value, and the between-trial heterogeneity variance across the network meta-analysis methods. We will investigate whether differences in the results are affected by network characteristics and baseline risk. The results of this study will inform whether, in practice, the choice of network meta-analysis method matters, and if it does, in what situations differences in the results between methods might arise. The results from this research might also inform future simulation studies.

A Network Optimization Approach for Improving Organizational Design

DTIC Science & Technology

2004-01-01

functions, Dynamic Network Analysis, Social Network Analysis Abstract Organizations are frequently designed and redesigned, often in...links between sites on the web. Hence a change in any one of the four networks in which people are involved can potentially result in a cascade of...in terms of a set of networks that open the possibility of using all networks (both social and dynamic network measures) as indicators of potential

Advantages of Social Network Analysis in Educational Research

ERIC Educational Resources Information Center

Ushakov, K. M.; Kukso, K. N.

2015-01-01

Currently one of the main tools for the large scale studies of schools is statistical analysis. Although it is the most common method and it offers greatest opportunities for analysis, there are other quantitative methods for studying schools, such as network analysis. We discuss the potential advantages that network analysis has for educational…

Living network meta-analysis compared with pairwise meta-analysis in comparative effectiveness research: empirical study

PubMed Central

Nikolakopoulou, Adriani; Mavridis, Dimitris; Furukawa, Toshi A; Cipriani, Andrea; Tricco, Andrea C; Straus, Sharon E; Siontis, George C M; Egger, Matthias

2018-01-01

Abstract Objective To examine whether the continuous updating of networks of prospectively planned randomised controlled trials (RCTs) (“living” network meta-analysis) provides strong evidence against the null hypothesis in comparative effectiveness of medical interventions earlier than the updating of conventional, pairwise meta-analysis. Design Empirical study of the accumulating evidence about the comparative effectiveness of clinical interventions. Data sources Database of network meta-analyses of RCTs identified through searches of Medline, Embase, and the Cochrane Database of Systematic Reviews until 14 April 2015. Eligibility criteria for study selection Network meta-analyses published after January 2012 that compared at least five treatments and included at least 20 RCTs. Clinical experts were asked to identify in each network the treatment comparison of greatest clinical interest. Comparisons were excluded for which direct and indirect evidence disagreed, based on side, or node, splitting test (P<0.10). Outcomes and analysis Cumulative pairwise and network meta-analyses were performed for each selected comparison. Monitoring boundaries of statistical significance were constructed and the evidence against the null hypothesis was considered to be strong when the monitoring boundaries were crossed. A significance level was defined as α=5%, power of 90% (β=10%), and an anticipated treatment effect to detect equal to the final estimate from the network meta-analysis. The frequency and time to strong evidence was compared against the null hypothesis between pairwise and network meta-analyses. Results 49 comparisons of interest from 44 networks were included; most (n=39, 80%) were between active drugs, mainly from the specialties of cardiology, endocrinology, psychiatry, and rheumatology. 29 comparisons were informed by both direct and indirect evidence (59%), 13 by indirect evidence (27%), and 7 by direct evidence (14%). Both network and pairwise meta-analysis provided strong evidence against the null hypothesis for seven comparisons, but for an additional 10 comparisons only network meta-analysis provided strong evidence against the null hypothesis (P=0.002). The median time to strong evidence against the null hypothesis was 19 years with living network meta-analysis and 23 years with living pairwise meta-analysis (hazard ratio 2.78, 95% confidence interval 1.00 to 7.72, P=0.05). Studies directly comparing the treatments of interest continued to be published for eight comparisons after strong evidence had become evident in network meta-analysis. Conclusions In comparative effectiveness research, prospectively planned living network meta-analyses produced strong evidence against the null hypothesis more often and earlier than conventional, pairwise meta-analyses. PMID:29490922

WGCNA: an R package for weighted correlation network analysis

PubMed Central

Langfelder, Peter; Horvath, Steve

2008-01-01

Background Correlation networks are increasingly being used in bioinformatics applications. For example, weighted gene co-expression network analysis is a systems biology method for describing the correlation patterns among genes across microarray samples. Weighted correlation network analysis (WGCNA) can be used for finding clusters (modules) of highly correlated genes, for summarizing such clusters using the module eigengene or an intramodular hub gene, for relating modules to one another and to external sample traits (using eigengene network methodology), and for calculating module membership measures. Correlation networks facilitate network based gene screening methods that can be used to identify candidate biomarkers or therapeutic targets. These methods have been successfully applied in various biological contexts, e.g. cancer, mouse genetics, yeast genetics, and analysis of brain imaging data. While parts of the correlation network methodology have been described in separate publications, there is a need to provide a user-friendly, comprehensive, and consistent software implementation and an accompanying tutorial. Results The WGCNA R software package is a comprehensive collection of R functions for performing various aspects of weighted correlation network analysis. The package includes functions for network construction, module detection, gene selection, calculations of topological properties, data simulation, visualization, and interfacing with external software. Along with the R package we also present R software tutorials. While the methods development was motivated by gene expression data, the underlying data mining approach can be applied to a variety of different settings. Conclusion The WGCNA package provides R functions for weighted correlation network analysis, e.g. co-expression network analysis of gene expression data. The R package along with its source code and additional material are freely available at . PMID:19114008

Structural Properties of the Brazilian Air Transportation Network.

PubMed

Couto, Guilherme S; da Silva, Ana Paula Couto; Ruiz, Linnyer B; Benevenuto, Fabrício

2015-09-01

The air transportation network in a country has a great impact on the local, national and global economy. In this paper, we analyze the air transportation network in Brazil with complex network features to better understand its characteristics. In our analysis, we built networks composed either by national or by international flights. We also consider the network when both types of flights are put together. Interesting conclusions emerge from our analysis. For instance, Viracopos Airport (Campinas City) is the most central and connected airport on the national flights network. Any operational problem in this airport separates the Brazilian national network into six distinct subnetworks. Moreover, the Brazilian air transportation network exhibits small world characteristics and national connections network follows a power law distribution. Therefore, our analysis sheds light on the current Brazilian air transportation infrastructure, bringing a novel understanding that may help face the recent fast growth in the usage of the Brazilian transport network.

Comparing Networks from a Data Analysis Perspective

NASA Astrophysics Data System (ADS)

Li, Wei; Yang, Jing-Yu

To probe network characteristics, two predominant ways of network comparison are global property statistics and subgraph enumeration. However, they suffer from limited information and exhaustible computing. Here, we present an approach to compare networks from the perspective of data analysis. Initially, the approach projects each node of original network as a high-dimensional data point, and the network is seen as clouds of data points. Then the dispersion information of the principal component analysis (PCA) projection of the generated data clouds can be used to distinguish networks. We applied this node projection method to the yeast protein-protein interaction networks and the Internet Autonomous System networks, two types of networks with several similar higher properties. The method can efficiently distinguish one from the other. The identical result of different datasets from independent sources also indicated that the method is a robust and universal framework.

Performance analysis of Aloha networks with power capture and near/far effect

NASA Astrophysics Data System (ADS)

McCartin, Joseph T.

1989-06-01

An analysis is presented for the throughput characteristics for several classes of Aloha packet networks. Specifically, the throughput for variable packet length Aloha utilizing multiple power levels to induce receiver capture is derived. The results are extended to an analysis of a selective-repeat ARQ Aloha network. Analytical results are presented which indicate a significant increase in throughput for a variable packet network implementing a random two power level capture scheme. Further research into the area of the near/far effect on Aloha networks is included. Improvements in throughput for mobile radio Aloha networks which are subject to the near/far effect are presented. Tactical Command, Control and Communications (C3) systems of the future will rely on Aloha ground mobile data networks. The incorporation of power capture and the near/far effect into future tactical networks will result in improved system analysis, design, and performance.

Angle of Arrival Detection Through Artificial Neural Network Analysis of Optical Fiber Intensity Patterns

DTIC Science & Technology

1990-12-01

ARTIFICIAL NEURAL NETWORK ANALYSIS OF OPTICAL FIBER INTENSITY PATTERNS THESIS Scott Thomas Captain, USAF AFIT/GE/ENG/90D-62 DTIC...ELECTE ao • JAN08 1991 Approved for public release; distribution unlimited. AFIT/GE/ENG/90D-62 ANGLE OF ARRIVAL DETECTION THROUGH ARTIFICIAL NEURAL NETWORK ANALYSIS... ARTIFICIAL NEURAL NETWORK ANALYSIS OF OPTICAL FIBER INTENSITY PATTERNS L Introduction The optical sensors of United States Air Force reconnaissance

Friendship Group Composition and Juvenile Institutional Misconduct.

PubMed

Reid, Shannon E

2017-02-01

The present study examines both the patterns of friendship networks and how these network characteristics relate to the risk factors of institutional misconduct for incarcerated youth. Using friendship networks collected from males incarcerated with California's Division of Juvenile Justice (DJJ), latent profile analysis was utilized to create homogeneous groups of friendship patterns based on alter attributes and network structure. The incarcerated youth provided 144 egocentric networks reporting 558 social network relationships. Latent profile analysis identified three network profiles: expected group (67%), new breed group (20%), and model citizen group (13%). The three network profiles were integrated into a multiple group analysis framework to examine the relative influence of individual-level risk factors on their rate of institutional misconduct. The analysis finds variation in predictors of institutional misconduct across profile types. These findings suggest that the close friendships of incarcerated youth are patterned across the individual characteristics of the youth's friends and that the friendship network can act as a moderator for individual risk factors for institutional misconduct.

Deep Learning Neural Networks and Bayesian Neural Networks in Data Analysis

NASA Astrophysics Data System (ADS)

Chernoded, Andrey; Dudko, Lev; Myagkov, Igor; Volkov, Petr

2017-10-01

Most of the modern analyses in high energy physics use signal-versus-background classification techniques of machine learning methods and neural networks in particular. Deep learning neural network is the most promising modern technique to separate signal and background and now days can be widely and successfully implemented as a part of physical analysis. In this article we compare Deep learning and Bayesian neural networks application as a classifiers in an instance of top quark analysis.

Combining Flux Balance and Energy Balance Analysis for Large-Scale Metabolic Network: Biochemical Circuit Theory for Analysis of Large-Scale Metabolic Networks

NASA Technical Reports Server (NTRS)

Beard, Daniel A.; Liang, Shou-Dan; Qian, Hong; Biegel, Bryan (Technical Monitor)

2001-01-01

Predicting behavior of large-scale biochemical metabolic networks represents one of the greatest challenges of bioinformatics and computational biology. Approaches, such as flux balance analysis (FBA), that account for the known stoichiometry of the reaction network while avoiding implementation of detailed reaction kinetics are perhaps the most promising tools for the analysis of large complex networks. As a step towards building a complete theory of biochemical circuit analysis, we introduce energy balance analysis (EBA), which compliments the FBA approach by introducing fundamental constraints based on the first and second laws of thermodynamics. Fluxes obtained with EBA are thermodynamically feasible and provide valuable insight into the activation and suppression of biochemical pathways.

Review: visual analytics of climate networks

NASA Astrophysics Data System (ADS)

Nocke, T.; Buschmann, S.; Donges, J. F.; Marwan, N.; Schulz, H.-J.; Tominski, C.

2015-09-01

Network analysis has become an important approach in studying complex spatiotemporal behaviour within geophysical observation and simulation data. This new field produces increasing numbers of large geo-referenced networks to be analysed. Particular focus lies currently on the network analysis of the complex statistical interrelationship structure within climatological fields. The standard procedure for such network analyses is the extraction of network measures in combination with static standard visualisation methods. Existing interactive visualisation methods and tools for geo-referenced network exploration are often either not known to the analyst or their potential is not fully exploited. To fill this gap, we illustrate how interactive visual analytics methods in combination with geovisualisation can be tailored for visual climate network investigation. Therefore, the paper provides a problem analysis relating the multiple visualisation challenges to a survey undertaken with network analysts from the research fields of climate and complex systems science. Then, as an overview for the interested practitioner, we review the state-of-the-art in climate network visualisation and provide an overview of existing tools. As a further contribution, we introduce the visual network analytics tools CGV and GTX, providing tailored solutions for climate network analysis, including alternative geographic projections, edge bundling, and 3-D network support. Using these tools, the paper illustrates the application potentials of visual analytics for climate networks based on several use cases including examples from global, regional, and multi-layered climate networks.

Review: visual analytics of climate networks

NASA Astrophysics Data System (ADS)

Nocke, T.; Buschmann, S.; Donges, J. F.; Marwan, N.; Schulz, H.-J.; Tominski, C.

2015-04-01

Network analysis has become an important approach in studying complex spatiotemporal behaviour within geophysical observation and simulation data. This new field produces increasing amounts of large geo-referenced networks to be analysed. Particular focus lies currently on the network analysis of the complex statistical interrelationship structure within climatological fields. The standard procedure for such network analyses is the extraction of network measures in combination with static standard visualisation methods. Existing interactive visualisation methods and tools for geo-referenced network exploration are often either not known to the analyst or their potential is not fully exploited. To fill this gap, we illustrate how interactive visual analytics methods in combination with geovisualisation can be tailored for visual climate network investigation. Therefore, the paper provides a problem analysis, relating the multiple visualisation challenges with a survey undertaken with network analysts from the research fields of climate and complex systems science. Then, as an overview for the interested practitioner, we review the state-of-the-art in climate network visualisation and provide an overview of existing tools. As a further contribution, we introduce the visual network analytics tools CGV and GTX, providing tailored solutions for climate network analysis, including alternative geographic projections, edge bundling, and 3-D network support. Using these tools, the paper illustrates the application potentials of visual analytics for climate networks based on several use cases including examples from global, regional, and multi-layered climate networks.

Network meta-analysis, electrical networks and graph theory.

PubMed

Rücker, Gerta

2012-12-01

Network meta-analysis is an active field of research in clinical biostatistics. It aims to combine information from all randomized comparisons among a set of treatments for a given medical condition. We show how graph-theoretical methods can be applied to network meta-analysis. A meta-analytic graph consists of vertices (treatments) and edges (randomized comparisons). We illustrate the correspondence between meta-analytic networks and electrical networks, where variance corresponds to resistance, treatment effects to voltage, and weighted treatment effects to current flows. Based thereon, we then show that graph-theoretical methods that have been routinely applied to electrical networks also work well in network meta-analysis. In more detail, the resulting consistent treatment effects induced in the edges can be estimated via the Moore-Penrose pseudoinverse of the Laplacian matrix. Moreover, the variances of the treatment effects are estimated in analogy to electrical effective resistances. It is shown that this method, being computationally simple, leads to the usual fixed effect model estimate when applied to pairwise meta-analysis and is consistent with published results when applied to network meta-analysis examples from the literature. Moreover, problems of heterogeneity and inconsistency, random effects modeling and including multi-armed trials are addressed. Copyright © 2012 John Wiley & Sons, Ltd. Copyright © 2012 John Wiley & Sons, Ltd.

Study of co-authorship network of papers in the Journal of Research in Medical Sciences using social network analysis

PubMed Central

Zare-Farashbandi, Firoozeh; Geraei, Ehsan; Siamaki, Saba

2014-01-01

Background: Co-authorship is one of the most tangible forms of research collaboration. A co-authorship network is a social network in which the authors through participation in one or more publication through an indirect path have linked to each other. The present research using the social network analysis studied co-authorship network of 681 articles published in Journal of Research in Medical Sciences (JRMS) during 2008-2012. Materials and Methods: The study was carried out with the scientometrics approach and using co-authorship network analysis of authors. The topology of the co-authorship network of 681 published articles in JRMS between 2008 and 2012 was analyzed using macro-level metrics indicators of network analysis such as density, clustering coefficient, components and mean distance. In addition, in order to evaluate the performance of each authors and countries in the network, the micro-level indicators such as degree centrality, closeness centrality and betweenness centrality as well as productivity index were used. The UCINET and NetDraw softwares were used to draw and analyze the co-authorship network of the papers. Results: The assessment of the authors productivity in this journal showed that the first ranks were belonged to only five authors, respectively. Furthermore, analysis of the co-authorship of the authors in the network demonstrated that in the betweenness centrality index, three authors of them had the good position in the network. They can be considered as the network leaders able to control the flow of information in the network compared with the other members based on the shortest paths. On the other hand, the key role of the network according to the productivity and centrality indexes was belonged to Iran, Malaysia and United States of America. Conclusion: Co-authorship network of JRMS has the characteristics of a small world network. In addition, the theory of 6° separation is valid in this network was also true. PMID:24672564

Spectral Analysis of Rich Network Topology in Social Networks

ERIC Educational Resources Information Center

Wu, Leting

2013-01-01

Social networks have received much attention these days. Researchers have developed different methods to study the structure and characteristics of the network topology. Our focus is on spectral analysis of the adjacency matrix of the underlying network. Recent work showed good properties in the adjacency spectral space but there are few…

Techno-Economic Analysis of FiWi Access Networks Based on 802.11ac WLAN and NG-PON2 Networks

NASA Astrophysics Data System (ADS)

Breskovic, Damir; Begusic, Dinko

2017-05-01

In this article, techno-economic analysis of a fiber-wireless access network is presented. With high bandwidth capacity of the gigabit passive optical network and with cost-effectiveness of very high throughput 802.11ac wireless local area networks that enable user mobility in the wireless segment, fiber-wireless access networks can be considered as an alternative to the fiber-to-the-home architecture for next generation access networks. Analysis based on the proposed scenario here, shows that a fiber-wireless access network is a more cost-effective solution in densely populated areas, but with some introduced improvements, even other geotypes can be considered as a commercially-viable solution.

Network analysis of patient flow in two UK acute care hospitals identifies key sub-networks for A&E performance

PubMed Central

Stringer, Clive; Beeknoo, Neeraj

2017-01-01

The topology of the patient flow network in a hospital is complex, comprising hundreds of overlapping patient journeys, and is a determinant of operational efficiency. To understand the network architecture of patient flow, we performed a data-driven network analysis of patient flow through two acute hospital sites of King’s College Hospital NHS Foundation Trust. Administration databases were queried for all intra-hospital patient transfers in an 18-month period and modelled as a dynamic weighted directed graph. A ‘core’ subnetwork containing only 13–17% of all edges channelled 83–90% of the patient flow, while an ‘ephemeral’ network constituted the remainder. Unsupervised cluster analysis and differential network analysis identified sub-networks where traffic is most associated with A&E performance. Increased flow to clinical decision units was associated with the best A&E performance in both sites. The component analysis also detected a weekend effect on patient transfers which was not associated with performance. We have performed the first data-driven hypothesis-free analysis of patient flow which can enhance understanding of whole healthcare systems. Such analysis can drive transformation in healthcare as it has in industries such as manufacturing. PMID:28968472

Disclosing Sexual Assault Within Social Networks: A Mixed-Method Investigation.

PubMed

Dworkin, Emily R; Pittenger, Samantha L; Allen, Nicole E

2016-03-01

Most survivors of sexual assault disclose their experiences within their social networks, and these disclosure decisions can have important implications for their entry into formal systems and well-being, but no research has directly examined these networks as a strategy to understand disclosure decisions. Using a mixed-method approach that combined survey data, social network analysis, and interview data, we investigate whom, among potential informal responders in the social networks of college students who have experienced sexual assault, survivors contact regarding their assault, and how survivors narrate the role of networks in their decisions about whom to contact. Quantitative results suggest that characteristics of survivors, their social networks, and members of these networks are associated with disclosure decisions. Using data from social network analysis, we identified that survivors tended to disclose to a smaller proportion of their network when many network members had relationships with each other or when the network had more subgroups. Our qualitative analysis helps to contextualize these findings. © Society for Community Research and Action 2016.

Living network meta-analysis compared with pairwise meta-analysis in comparative effectiveness research: empirical study.

PubMed

Nikolakopoulou, Adriani; Mavridis, Dimitris; Furukawa, Toshi A; Cipriani, Andrea; Tricco, Andrea C; Straus, Sharon E; Siontis, George C M; Egger, Matthias; Salanti, Georgia

2018-02-28

To examine whether the continuous updating of networks of prospectively planned randomised controlled trials (RCTs) ("living" network meta-analysis) provides strong evidence against the null hypothesis in comparative effectiveness of medical interventions earlier than the updating of conventional, pairwise meta-analysis. Empirical study of the accumulating evidence about the comparative effectiveness of clinical interventions. Database of network meta-analyses of RCTs identified through searches of Medline, Embase, and the Cochrane Database of Systematic Reviews until 14 April 2015. Network meta-analyses published after January 2012 that compared at least five treatments and included at least 20 RCTs. Clinical experts were asked to identify in each network the treatment comparison of greatest clinical interest. Comparisons were excluded for which direct and indirect evidence disagreed, based on side, or node, splitting test (P<0.10). Cumulative pairwise and network meta-analyses were performed for each selected comparison. Monitoring boundaries of statistical significance were constructed and the evidence against the null hypothesis was considered to be strong when the monitoring boundaries were crossed. A significance level was defined as α=5%, power of 90% (β=10%), and an anticipated treatment effect to detect equal to the final estimate from the network meta-analysis. The frequency and time to strong evidence was compared against the null hypothesis between pairwise and network meta-analyses. 49 comparisons of interest from 44 networks were included; most (n=39, 80%) were between active drugs, mainly from the specialties of cardiology, endocrinology, psychiatry, and rheumatology. 29 comparisons were informed by both direct and indirect evidence (59%), 13 by indirect evidence (27%), and 7 by direct evidence (14%). Both network and pairwise meta-analysis provided strong evidence against the null hypothesis for seven comparisons, but for an additional 10 comparisons only network meta-analysis provided strong evidence against the null hypothesis (P=0.002). The median time to strong evidence against the null hypothesis was 19 years with living network meta-analysis and 23 years with living pairwise meta-analysis (hazard ratio 2.78, 95% confidence interval 1.00 to 7.72, P=0.05). Studies directly comparing the treatments of interest continued to be published for eight comparisons after strong evidence had become evident in network meta-analysis. In comparative effectiveness research, prospectively planned living network meta-analyses produced strong evidence against the null hypothesis more often and earlier than conventional, pairwise meta-analyses. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

[Reliability theory based on quality risk network analysis for Chinese medicine injection].

PubMed

Li, Zheng; Kang, Li-Yuan; Fan, Xiao-Hui

2014-08-01

A new risk analysis method based upon reliability theory was introduced in this paper for the quality risk management of Chinese medicine injection manufacturing plants. The risk events including both cause and effect ones were derived in the framework as nodes with a Bayesian network analysis approach. It thus transforms the risk analysis results from failure mode and effect analysis (FMEA) into a Bayesian network platform. With its structure and parameters determined, the network can be used to evaluate the system reliability quantitatively with probabilistic analytical appraoches. Using network analysis tools such as GeNie and AgenaRisk, we are able to find the nodes that are most critical to influence the system reliability. The importance of each node to the system can be quantitatively evaluated by calculating the effect of the node on the overall risk, and minimization plan can be determined accordingly to reduce their influences and improve the system reliability. Using the Shengmai injection manufacturing plant of SZYY Ltd as a user case, we analyzed the quality risk with both static FMEA analysis and dynamic Bayesian Network analysis. The potential risk factors for the quality of Shengmai injection manufacturing were identified with the network analysis platform. Quality assurance actions were further defined to reduce the risk and improve the product quality.

Artificial Neural Network Analysis System

DTIC Science & Technology

2001-02-27

Contract No. DASG60-00-M-0201 Purchase request no.: Foot in the Door-01 Title Name: Artificial Neural Network Analysis System Company: Atlantic... Artificial Neural Network Analysis System 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) Powell, Bruce C 5d. PROJECT NUMBER 5e. TASK NUMBER...34) 27-02-2001 Report Type N/A Dates Covered (from... to) ("DD MON YYYY") 28-10-2000 27-02-2001 Title and Subtitle Artificial Neural Network Analysis

Google matrix analysis of directed networks

NASA Astrophysics Data System (ADS)

Ermann, Leonardo; Frahm, Klaus M.; Shepelyansky, Dima L.

2015-10-01

In the past decade modern societies have developed enormous communication and social networks. Their classification and information retrieval processing has become a formidable task for the society. Because of the rapid growth of the World Wide Web, and social and communication networks, new mathematical methods have been invented to characterize the properties of these networks in a more detailed and precise way. Various search engines extensively use such methods. It is highly important to develop new tools to classify and rank a massive amount of network information in a way that is adapted to internal network structures and characteristics. This review describes the Google matrix analysis of directed complex networks demonstrating its efficiency using various examples including the World Wide Web, Wikipedia, software architectures, world trade, social and citation networks, brain neural networks, DNA sequences, and Ulam networks. The analytical and numerical matrix methods used in this analysis originate from the fields of Markov chains, quantum chaos, and random matrix theory.

Social network models predict movement and connectivity in ecological landscapes

USGS Publications Warehouse

Fletcher, R.J.; Acevedo, M.A.; Reichert, Brian E.; Pias, Kyle E.; Kitchens, W.M.

2011-01-01

Network analysis is on the rise across scientific disciplines because of its ability to reveal complex, and often emergent, patterns and dynamics. Nonetheless, a growing concern in network analysis is the use of limited data for constructing networks. This concern is strikingly relevant to ecology and conservation biology, where network analysis is used to infer connectivity across landscapes. In this context, movement among patches is the crucial parameter for interpreting connectivity but because of the difficulty of collecting reliable movement data, most network analysis proceeds with only indirect information on movement across landscapes rather than using observed movement to construct networks. Statistical models developed for social networks provide promising alternatives for landscape network construction because they can leverage limited movement information to predict linkages. Using two mark-recapture datasets on individual movement and connectivity across landscapes, we test whether commonly used network constructions for interpreting connectivity can predict actual linkages and network structure, and we contrast these approaches to social network models. We find that currently applied network constructions for assessing connectivity consistently, and substantially, overpredict actual connectivity, resulting in considerable overestimation of metapopulation lifetime. Furthermore, social network models provide accurate predictions of network structure, and can do so with remarkably limited data on movement. Social network models offer a flexible and powerful way for not only understanding the factors influencing connectivity but also for providing more reliable estimates of connectivity and metapopulation persistence in the face of limited data.

Effects of altitude on the energetics of human best performances in 100 m running: a theoretical analysis.

PubMed

Arsac, Laurent M

2002-05-01

The present study was designed to investigate the role of reduced air density on the energetics of 100 m running at altitude. A mathematical supply-demand model was used where supply had two components, aerobic and anaerobic and demand had three components: the cost of overcoming non-aerodynamic forces (C(na)), the cost of overcoming air resistance (C(aero)), and the cost due to changes in the runner's kinetic energy (C(kin)). Actual instantaneous-speed curves recorded in 100 m world champions were modelled at sea level. Then I calculated improvements in 100 m running times and changes in the components of the energy cost with changes in altitude from 0 m to 4,000 m. For the 100 m world championship for men, the model predicted times of 9.88 s at sea level, 9.80 s at 1,000 m, 9.73 s at 2,000 m, 9.64 s at 4,000 m and 9.15 s in the hypothetical situation where the air resistance was nil. In the counterpart for women the corresponding times were 10.85 s, 10.76 s, 10.70 s, 10.60 s and 10.04 s. The C(aero) was 12%-13% of demand at sea level, 10%-11% at 2,000 m and 8%-9% at 4,000 m. When C(aero) decreased this led to better performance by making more energy available for acceleration. Accordingly, C(kin) increased from 20%-24% at sea level to 23%-27% at 4,000 m. There was no effect of altitude specific to body size.

Target genes discovery through copy number alteration analysis in human hepatocellular carcinoma.

PubMed

Gu, De-Leung; Chen, Yen-Hsieh; Shih, Jou-Ho; Lin, Chi-Hung; Jou, Yuh-Shan; Chen, Chian-Feng

2013-12-21

High-throughput short-read sequencing of exomes and whole cancer genomes in multiple human hepatocellular carcinoma (HCC) cohorts confirmed previously identified frequently mutated somatic genes, such as TP53, CTNNB1 and AXIN1, and identified several novel genes with moderate mutation frequencies, including ARID1A, ARID2, MLL, MLL2, MLL3, MLL4, IRF2, ATM, CDKN2A, FGF19, PIK3CA, RPS6KA3, JAK1, KEAP1, NFE2L2, C16orf62, LEPR, RAC2, and IL6ST. Functional classification of these mutated genes suggested that alterations in pathways participating in chromatin remodeling, Wnt/β-catenin signaling, JAK/STAT signaling, and oxidative stress play critical roles in HCC tumorigenesis. Nevertheless, because there are few druggable genes used in HCC therapy, the identification of new therapeutic targets through integrated genomic approaches remains an important task. Because a large amount of HCC genomic data genotyped by high density single nucleotide polymorphism arrays is deposited in the public domain, copy number alteration (CNA) analyses of these arrays is a cost-effective way to reveal target genes through profiling of recurrent and overlapping amplicons, homozygous deletions and potentially unbalanced chromosomal translocations accumulated during HCC progression. Moreover, integration of CNAs with other high-throughput genomic data, such as aberrantly coding transcriptomes and non-coding gene expression in human HCC tissues and rodent HCC models, provides lines of evidence that can be used to facilitate the identification of novel HCC target genes with the potential of improving the survival of HCC patients.

Functional Interaction Network Construction and Analysis for Disease Discovery.

PubMed

Wu, Guanming; Haw, Robin

2017-01-01

Network-based approaches project seemingly unrelated genes or proteins onto a large-scale network context, therefore providing a holistic visualization and analysis platform for genomic data generated from high-throughput experiments, reducing the dimensionality of data via using network modules and increasing the statistic analysis power. Based on the Reactome database, the most popular and comprehensive open-source biological pathway knowledgebase, we have developed a highly reliable protein functional interaction network covering around 60 % of total human genes and an app called ReactomeFIViz for Cytoscape, the most popular biological network visualization and analysis platform. In this chapter, we describe the detailed procedures on how this functional interaction network is constructed by integrating multiple external data sources, extracting functional interactions from human curated pathway databases, building a machine learning classifier called a Naïve Bayesian Classifier, predicting interactions based on the trained Naïve Bayesian Classifier, and finally constructing the functional interaction database. We also provide an example on how to use ReactomeFIViz for performing network-based data analysis for a list of genes.

Comparative analysis of quantitative efficiency evaluation methods for transportation networks

PubMed Central

He, Yuxin; Hong, Jian

2017-01-01

An effective evaluation of transportation network efficiency could offer guidance for the optimal control of urban traffic. Based on the introduction and related mathematical analysis of three quantitative evaluation methods for transportation network efficiency, this paper compares the information measured by them, including network structure, traffic demand, travel choice behavior and other factors which affect network efficiency. Accordingly, the applicability of various evaluation methods is discussed. Through analyzing different transportation network examples it is obtained that Q-H method could reflect the influence of network structure, traffic demand and user route choice behavior on transportation network efficiency well. In addition, the transportation network efficiency measured by this method and Braess’s Paradox can be explained with each other, which indicates a better evaluation of the real operation condition of transportation network. Through the analysis of the network efficiency calculated by Q-H method, it can also be drawn that a specific appropriate demand is existed to a given transportation network. Meanwhile, under the fixed demand, both the critical network structure that guarantees the stability and the basic operation of the network and a specific network structure contributing to the largest value of the transportation network efficiency can be identified. PMID:28399165

Comparative analysis of quantitative efficiency evaluation methods for transportation networks.

PubMed

He, Yuxin; Qin, Jin; Hong, Jian

2017-01-01

An effective evaluation of transportation network efficiency could offer guidance for the optimal control of urban traffic. Based on the introduction and related mathematical analysis of three quantitative evaluation methods for transportation network efficiency, this paper compares the information measured by them, including network structure, traffic demand, travel choice behavior and other factors which affect network efficiency. Accordingly, the applicability of various evaluation methods is discussed. Through analyzing different transportation network examples it is obtained that Q-H method could reflect the influence of network structure, traffic demand and user route choice behavior on transportation network efficiency well. In addition, the transportation network efficiency measured by this method and Braess's Paradox can be explained with each other, which indicates a better evaluation of the real operation condition of transportation network. Through the analysis of the network efficiency calculated by Q-H method, it can also be drawn that a specific appropriate demand is existed to a given transportation network. Meanwhile, under the fixed demand, both the critical network structure that guarantees the stability and the basic operation of the network and a specific network structure contributing to the largest value of the transportation network efficiency can be identified.

[Scale effect of Nanjing urban green infrastructure network pattern and connectivity analysis.

PubMed

Yu, Ya Ping; Yin, Hai Wei; Kong, Fan Hua; Wang, Jing Jing; Xu, Wen Bin

2016-07-01

Based on ArcGIS, Erdas, GuidosToolbox, Conefor and other software platforms, using morphological spatial pattern analysis (MSPA) and landscape connectivity analysis methods, this paper quantitatively analysed the scale effect, edge effect and distance effect of the Nanjing urban green infrastructure network pattern in 2013 by setting different pixel sizes (P) and edge widths in MSPA analysis, and setting different dispersal distance thresholds in landscape connectivity analysis. The results showed that the type of landscape acquired based on the MSPA had a clear scale effect and edge effect, and scale effects only slightly affected landscape types, whereas edge effects were more obvious. Different dispersal distances had a great impact on the landscape connectivity, 2 km or 2.5 km dispersal distance was a critical threshold for Nanjing. When selecting the pixel size 30 m of the input data and the edge wide 30 m used in the morphological model, we could get more detailed landscape information of Nanjing UGI network. Based on MSPA and landscape connectivity, analysis of the scale effect, edge effect, and distance effect on the landscape types of the urban green infrastructure (UGI) network was helpful for selecting the appropriate size, edge width, and dispersal distance when developing these networks, and for better understanding the spatial pattern of UGI networks and the effects of scale and distance on the ecology of a UGI network. This would facilitate a more scientifically valid set of design parameters for UGI network spatiotemporal pattern analysis. The results of this study provided an important reference for Nanjing UGI networks and a basis for the analysis of the spatial and temporal patterns of medium-scale UGI landscape networks in other regions.

How Social Network Position Relates to Knowledge Building in Online Learning Communities

ERIC Educational Resources Information Center

Wang, Lu

2010-01-01

Social Network Analysis, Statistical Analysis, Content Analysis and other research methods were used to research online learning communities at Capital Normal University, Beijing. Analysis of the two online courses resulted in the following conclusions: (1) Social networks of the two online courses form typical core-periphery structures; (2)…

Identification of neuronal network properties from the spectral analysis of calcium imaging signals in neuronal cultures.

PubMed

Tibau, Elisenda; Valencia, Miguel; Soriano, Jordi

2013-01-01

Neuronal networks in vitro are prominent systems to study the development of connections in living neuronal networks and the interplay between connectivity, activity and function. These cultured networks show a rich spontaneous activity that evolves concurrently with the connectivity of the underlying network. In this work we monitor the development of neuronal cultures, and record their activity using calcium fluorescence imaging. We use spectral analysis to characterize global dynamical and structural traits of the neuronal cultures. We first observe that the power spectrum can be used as a signature of the state of the network, for instance when inhibition is active or silent, as well as a measure of the network's connectivity strength. Second, the power spectrum identifies prominent developmental changes in the network such as GABAA switch. And third, the analysis of the spatial distribution of the spectral density, in experiments with a controlled disintegration of the network through CNQX, an AMPA-glutamate receptor antagonist in excitatory neurons, reveals the existence of communities of strongly connected, highly active neurons that display synchronous oscillations. Our work illustrates the interest of spectral analysis for the study of in vitro networks, and its potential use as a network-state indicator, for instance to compare healthy and diseased neuronal networks.

Probabilistic QoS Analysis In Wireless Sensor Networks

DTIC Science & Technology

2012-04-01

and A.O. Fapojuwo. TDMA scheduling with optimized energy efficiency and minimum delay in clustered wireless sensor networks . IEEE Trans. on Mobile...Research Computer Science and Engineering, Department of 5-1-2012 Probabilistic QoS Analysis in Wireless Sensor Networks Yunbo Wang University of...Wang, Yunbo, "Probabilistic QoS Analysis in Wireless Sensor Networks " (2012). Computer Science and Engineering: Theses, Dissertations, and Student

A human functional protein interaction network and its application to cancer data analysis

PubMed Central

2010-01-01

Background One challenge facing biologists is to tease out useful information from massive data sets for further analysis. A pathway-based analysis may shed light by projecting candidate genes onto protein functional relationship networks. We are building such a pathway-based analysis system. Results We have constructed a protein functional interaction network by extending curated pathways with non-curated sources of information, including protein-protein interactions, gene coexpression, protein domain interaction, Gene Ontology (GO) annotations and text-mined protein interactions, which cover close to 50% of the human proteome. By applying this network to two glioblastoma multiforme (GBM) data sets and projecting cancer candidate genes onto the network, we found that the majority of GBM candidate genes form a cluster and are closer than expected by chance, and the majority of GBM samples have sequence-altered genes in two network modules, one mainly comprising genes whose products are localized in the cytoplasm and plasma membrane, and another comprising gene products in the nucleus. Both modules are highly enriched in known oncogenes, tumor suppressors and genes involved in signal transduction. Similar network patterns were also found in breast, colorectal and pancreatic cancers. Conclusions We have built a highly reliable functional interaction network upon expert-curated pathways and applied this network to the analysis of two genome-wide GBM and several other cancer data sets. The network patterns revealed from our results suggest common mechanisms in the cancer biology. Our system should provide a foundation for a network or pathway-based analysis platform for cancer and other diseases. PMID:20482850

Stochastic flux analysis of chemical reaction networks

PubMed Central

2013-01-01

Background Chemical reaction networks provide an abstraction scheme for a broad range of models in biology and ecology. The two common means for simulating these networks are the deterministic and the stochastic approaches. The traditional deterministic approach, based on differential equations, enjoys a rich set of analysis techniques, including a treatment of reaction fluxes. However, the discrete stochastic simulations, which provide advantages in some cases, lack a quantitative treatment of network fluxes. Results We describe a method for flux analysis of chemical reaction networks, where flux is given by the flow of species between reactions in stochastic simulations of the network. Extending discrete event simulation algorithms, our method constructs several data structures, and thereby reveals a variety of statistics about resource creation and consumption during the simulation. We use these structures to quantify the causal interdependence and relative importance of the reactions at arbitrary time intervals with respect to the network fluxes. This allows us to construct reduced networks that have the same flux-behavior, and compare these networks, also with respect to their time series. We demonstrate our approach on an extended example based on a published ODE model of the same network, that is, Rho GTP-binding proteins, and on other models from biology and ecology. Conclusions We provide a fully stochastic treatment of flux analysis. As in deterministic analysis, our method delivers the network behavior in terms of species transformations. Moreover, our stochastic analysis can be applied, not only at steady state, but at arbitrary time intervals, and used to identify the flow of specific species between specific reactions. Our cases study of Rho GTP-binding proteins reveals the role played by the cyclic reverse fluxes in tuning the behavior of this network. PMID:24314153

Stochastic flux analysis of chemical reaction networks.

PubMed

Kahramanoğulları, Ozan; Lynch, James F

2013-12-07

Chemical reaction networks provide an abstraction scheme for a broad range of models in biology and ecology. The two common means for simulating these networks are the deterministic and the stochastic approaches. The traditional deterministic approach, based on differential equations, enjoys a rich set of analysis techniques, including a treatment of reaction fluxes. However, the discrete stochastic simulations, which provide advantages in some cases, lack a quantitative treatment of network fluxes. We describe a method for flux analysis of chemical reaction networks, where flux is given by the flow of species between reactions in stochastic simulations of the network. Extending discrete event simulation algorithms, our method constructs several data structures, and thereby reveals a variety of statistics about resource creation and consumption during the simulation. We use these structures to quantify the causal interdependence and relative importance of the reactions at arbitrary time intervals with respect to the network fluxes. This allows us to construct reduced networks that have the same flux-behavior, and compare these networks, also with respect to their time series. We demonstrate our approach on an extended example based on a published ODE model of the same network, that is, Rho GTP-binding proteins, and on other models from biology and ecology. We provide a fully stochastic treatment of flux analysis. As in deterministic analysis, our method delivers the network behavior in terms of species transformations. Moreover, our stochastic analysis can be applied, not only at steady state, but at arbitrary time intervals, and used to identify the flow of specific species between specific reactions. Our cases study of Rho GTP-binding proteins reveals the role played by the cyclic reverse fluxes in tuning the behavior of this network.

A network approach to policy framing: A case study of the National Aboriginal and Torres Strait Islander Health Plan.

PubMed

Browne, Jennifer; de Leeuw, Evelyne; Gleeson, Deborah; Adams, Karen; Atkinson, Petah; Hayes, Rick

2017-01-01

Aboriginal health policy in Australia represents a unique policy subsystem comprising a diverse network of Aboriginal-specific and "mainstream" organisations, often with competing interests. This paper describes the network structure of organisations attempting to influence national Aboriginal health policy and examines how the different subgroups within the network approached the policy discourse. Public submissions made as part of a policy development process for the National Aboriginal and Torres Strait Islander Health Plan were analysed using a novel combination of network analysis and qualitative framing analysis. Other organisational actors in the network in each submission were identified, and relationships between them determined; these were used to generate a network map depicting the ties between actors. A qualitative framing analysis was undertaken, using inductive coding of the policy discourses in the submissions. The frames were overlaid with the network map to identify the relationship between the structure of the network and the way in which organisations framed Aboriginal health problems. Aboriginal organisations were central to the network and strongly connected with each other. The network consisted of several densely connected subgroups, whose central nodes were closely connected to one another. Each subgroup deployed a particular policy frame, with a frame of "system dysfunction" also adopted by all but one subgroup. Analysis of submissions revealed that many of the stakeholders in Aboriginal health policy actors are connected to one another. These connections help to drive the policy discourse. The combination of network and framing analysis illuminates competing interests within a network, and can assist advocacy organisations to identify which network members are most influential. Copyright © 2016 Elsevier Ltd. All rights reserved.

Co-occurrence network analysis of Chinese and English poems

NASA Astrophysics Data System (ADS)

Liang, Wei; Wang, Yanli; Shi, Yuming; Chen, Guanrong

2015-02-01

A total of 572 co-occurrence networks of Chinese characters and words as well as English words are constructed from both Chinese and English poems. It is found that most of the networks have small-world features; more Chinese networks have scale-free properties and hierarchical structures as compared with the English networks; all the networks are disassortative, and the disassortativeness of the Chinese word networks is more prominent than those of the English networks; the spectral densities of the Chinese word networks and English networks are similar, but they are different from those of the ER, BA, and WS networks. For the above observed phenomena, analysis is provided with interpretation from a linguistic perspective.

Neural Networks for Readability Analysis.

ERIC Educational Resources Information Center

McEneaney, John E.

This paper describes and reports on the performance of six related artificial neural networks that have been developed for the purpose of readability analysis. Two networks employ counts of linguistic variables that simulate a traditional regression-based approach to readability. The remaining networks determine readability from "visual…

Finding meaning in social media: content-based social network analysis of QuitNet to identify new opportunities for health promotion.

PubMed

Myneni, Sahiti; Cobb, Nathan K; Cohen, Trevor

2013-01-01

Unhealthy behaviors increase individual health risks and are a socioeconomic burden. Harnessing social influence is perceived as fundamental for interventions to influence health-related behaviors. However, the mechanisms through which social influence occurs are poorly understood. Online social networks provide the opportunity to understand these mechanisms as they digitally archive communication between members. In this paper, we present a methodology for content-based social network analysis, combining qualitative coding, automated text analysis, and formal network analysis such that network structure is determined by the content of messages exchanged between members. We apply this approach to characterize the communication between members of QuitNet, an online social network for smoking cessation. Results indicate that the method identifies meaningful theme-based social sub-networks. Modeling social network data using this method can provide us with theme-specific insights such as the identities of opinion leaders and sub-community clusters. Implications for design of targeted social interventions are discussed.

Multi-focus and multi-level techniques for visualization and analysis of networks with thematic data

NASA Astrophysics Data System (ADS)

Cossalter, Michele; Mengshoel, Ole J.; Selker, Ted

2013-01-01

Information-rich data sets bring several challenges in the areas of visualization and analysis, even when associated with node-link network visualizations. This paper presents an integration of multi-focus and multi-level techniques that enable interactive, multi-step comparisons in node-link networks. We describe NetEx, a visualization tool that enables users to simultaneously explore different parts of a network and its thematic data, such as time series or conditional probability tables. NetEx, implemented as a Cytoscape plug-in, has been applied to the analysis of electrical power networks, Bayesian networks, and the Enron e-mail repository. In this paper we briefly discuss visualization and analysis of the Enron social network, but focus on data from an electrical power network. Specifically, we demonstrate how NetEx supports the analytical task of electrical power system fault diagnosis. Results from a user study with 25 subjects suggest that NetEx enables more accurate isolation of complex faults compared to an especially designed software tool.

Graphical tools for network meta-analysis in STATA.

PubMed

Chaimani, Anna; Higgins, Julian P T; Mavridis, Dimitris; Spyridonos, Panagiota; Salanti, Georgia

2013-01-01

Network meta-analysis synthesizes direct and indirect evidence in a network of trials that compare multiple interventions and has the potential to rank the competing treatments according to the studied outcome. Despite its usefulness network meta-analysis is often criticized for its complexity and for being accessible only to researchers with strong statistical and computational skills. The evaluation of the underlying model assumptions, the statistical technicalities and presentation of the results in a concise and understandable way are all challenging aspects in the network meta-analysis methodology. In this paper we aim to make the methodology accessible to non-statisticians by presenting and explaining a series of graphical tools via worked examples. To this end, we provide a set of STATA routines that can be easily employed to present the evidence base, evaluate the assumptions, fit the network meta-analysis model and interpret its results.

Graphical Tools for Network Meta-Analysis in STATA

PubMed Central

Chaimani, Anna; Higgins, Julian P. T.; Mavridis, Dimitris; Spyridonos, Panagiota; Salanti, Georgia

2013-01-01

Network meta-analysis synthesizes direct and indirect evidence in a network of trials that compare multiple interventions and has the potential to rank the competing treatments according to the studied outcome. Despite its usefulness network meta-analysis is often criticized for its complexity and for being accessible only to researchers with strong statistical and computational skills. The evaluation of the underlying model assumptions, the statistical technicalities and presentation of the results in a concise and understandable way are all challenging aspects in the network meta-analysis methodology. In this paper we aim to make the methodology accessible to non-statisticians by presenting and explaining a series of graphical tools via worked examples. To this end, we provide a set of STATA routines that can be easily employed to present the evidence base, evaluate the assumptions, fit the network meta-analysis model and interpret its results. PMID:24098547

Methods for network meta-analysis of continuous outcomes using individual patient data: a case study in acupuncture for chronic pain.

PubMed

Saramago, Pedro; Woods, Beth; Weatherly, Helen; Manca, Andrea; Sculpher, Mark; Khan, Kamran; Vickers, Andrew J; MacPherson, Hugh

2016-10-06

Network meta-analysis methods, which are an extension of the standard pair-wise synthesis framework, allow for the simultaneous comparison of multiple interventions and consideration of the entire body of evidence in a single statistical model. There are well-established advantages to using individual patient data to perform network meta-analysis and methods for network meta-analysis of individual patient data have already been developed for dichotomous and time-to-event data. This paper describes appropriate methods for the network meta-analysis of individual patient data on continuous outcomes. This paper introduces and describes network meta-analysis of individual patient data models for continuous outcomes using the analysis of covariance framework. Comparisons are made between this approach and change score and final score only approaches, which are frequently used and have been proposed in the methodological literature. A motivating example on the effectiveness of acupuncture for chronic pain is used to demonstrate the methods. Individual patient data on 28 randomised controlled trials were synthesised. Consistency of endpoints across the evidence base was obtained through standardisation and mapping exercises. Individual patient data availability avoided the use of non-baseline-adjusted models, allowing instead for analysis of covariance models to be applied and thus improving the precision of treatment effect estimates while adjusting for baseline imbalance. The network meta-analysis of individual patient data using the analysis of covariance approach is advocated to be the most appropriate modelling approach for network meta-analysis of continuous outcomes, particularly in the presence of baseline imbalance. Further methods developments are required to address the challenge of analysing aggregate level data in the presence of baseline imbalance.

Insights into the Ecology and Evolution of Polyploid Plants through Network Analysis.

PubMed

Gallagher, Joseph P; Grover, Corrinne E; Hu, Guanjing; Wendel, Jonathan F

2016-06-01

Polyploidy is a widespread phenomenon throughout eukaryotes, with important ecological and evolutionary consequences. Although genes operate as components of complex pathways and networks, polyploid changes in genes and gene expression have typically been evaluated as either individual genes or as a part of broad-scale analyses. Network analysis has been fruitful in associating genomic and other 'omic'-based changes with phenotype for many systems. In polyploid species, network analysis has the potential not only to facilitate a better understanding of the complex 'omic' underpinnings of phenotypic and ecological traits common to polyploidy, but also to provide novel insight into the interaction among duplicated genes and genomes. This adds perspective to the global patterns of expression (and other 'omic') change that accompany polyploidy and to the patterns of recruitment and/or loss of genes following polyploidization. While network analysis in polyploid species faces challenges common to other analyses of duplicated genomes, present technologies combined with thoughtful experimental design provide a powerful system to explore polyploid evolution. Here, we demonstrate the utility and potential of network analysis to questions pertaining to polyploidy with an example involving evolution of the transgressively superior cotton fibres found in polyploid Gossypium hirsutum. By combining network analysis with prior knowledge, we provide further insights into the role of profilins in fibre domestication and exemplify the potential for network analysis in polyploid species. © 2016 John Wiley & Sons Ltd.

Control Theoretic Modeling for Uncertain Cultural Attitudes and Unknown Adversarial Intent

DTIC Science & Technology

2009-02-01

Constructive computational tools. 15. SUBJECT TERMS social learning, social networks , multiagent systems, game theory 16. SECURITY CLASSIFICATION OF: a...over- reactionary behaviors; 3) analysis of rational social learning in networks : analysis of belief propagation in social networks in various...general methodology as a predictive device for social network formation and for communication network formation with constraints on the lengths of

Network-based machine learning and graph theory algorithms for precision oncology.

PubMed

Zhang, Wei; Chien, Jeremy; Yong, Jeongsik; Kuang, Rui

2017-01-01

Network-based analytics plays an increasingly important role in precision oncology. Growing evidence in recent studies suggests that cancer can be better understood through mutated or dysregulated pathways or networks rather than individual mutations and that the efficacy of repositioned drugs can be inferred from disease modules in molecular networks. This article reviews network-based machine learning and graph theory algorithms for integrative analysis of personal genomic data and biomedical knowledge bases to identify tumor-specific molecular mechanisms, candidate targets and repositioned drugs for personalized treatment. The review focuses on the algorithmic design and mathematical formulation of these methods to facilitate applications and implementations of network-based analysis in the practice of precision oncology. We review the methods applied in three scenarios to integrate genomic data and network models in different analysis pipelines, and we examine three categories of network-based approaches for repositioning drugs in drug-disease-gene networks. In addition, we perform a comprehensive subnetwork/pathway analysis of mutations in 31 cancer genome projects in the Cancer Genome Atlas and present a detailed case study on ovarian cancer. Finally, we discuss interesting observations, potential pitfalls and future directions in network-based precision oncology.

Metabolic reconstruction, constraint-based analysis and game theory to probe genome-scale metabolic networks.

PubMed

Ruppin, Eytan; Papin, Jason A; de Figueiredo, Luis F; Schuster, Stefan

2010-08-01

With the advent of modern omics technologies, it has become feasible to reconstruct (quasi-) whole-cell metabolic networks and characterize them in more and more detail. Computer simulations of the dynamic behavior of such networks are difficult due to a lack of kinetic data and to computational limitations. In contrast, network analysis based on appropriate constraints such as the steady-state condition (constraint-based analysis) is feasible and allows one to derive conclusions about the system's metabolic capabilities. Here, we review methods for the reconstruction of metabolic networks, modeling techniques such as flux balance analysis and elementary flux modes and current progress in their development and applications. Game-theoretical methods for studying metabolic networks are discussed as well. Copyright © 2010 Elsevier Ltd. All rights reserved.

Using Social Network Analysis to Investigate Positive EOL Communication.

PubMed

Xu, Jiayun; Yang, Rumei; Wilson, Andrew; Reblin, Maija; Clayton, Margaret F; Ellington, Lee

2018-04-30

End of life (EOL) communication is a complex process involving the whole family and multiple care providers. Applications of analysis techniques that account for communication beyond the patient and patient/provider, will improve clinical understanding of EOL communication. To introduce the use of social network analysis to EOL communication data, and to provide an example of applying social network analysis to home hospice interactions. We provide a description of social network analysis using social network analysis to model communication patterns during home hospice nursing visits. We describe three social network attributes (i.e. magnitude, directionality, and reciprocity) in the expression of positive emotion among hospice nurses, family caregivers, and hospice cancer patients. Differences in communication structure by primary family caregiver gender and across time were also examined. Magnitude (frequency) in the expression of positive emotion occurred most often between nurses and caregivers or nurses and patients. Female caregivers directed more positive emotion to nurses, and nurses directed more positive emotion to other family caregivers when the primary family caregiver was male. Reciprocity (mutuality) in positive emotion declined towards day of death, but increased on day of actual patient death. There was variation in reciprocity by the type of positive emotion expressed. Our example demonstrates that social network analysis can be used to better understand the process of EOL communication. Social network analysis can be expanded to other areas of EOL research, such as EOL decision-making and health care teamwork. Copyright © 2018. Published by Elsevier Inc.

75 FR 9158 - Proposed Information Collection; Comment Request; Identification of Northeast Regional Ocean...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-03-01

... Collection; Comment Request; Identification of Northeast Regional Ocean Council Information Network Using Social Network Analysis AGENCY: National Oceanic and Atmospheric Administration (NOAA). ACTION: Notice... in many capacities. A social network analysis will serve to identify the network of people working on...

Multiplex social ecological network analysis reveals how social changes affect community robustness more than resource depletion.

PubMed

Baggio, Jacopo A; BurnSilver, Shauna B; Arenas, Alex; Magdanz, James S; Kofinas, Gary P; De Domenico, Manlio

2016-11-29

Network analysis provides a powerful tool to analyze complex influences of social and ecological structures on community and household dynamics. Most network studies of social-ecological systems use simple, undirected, unweighted networks. We analyze multiplex, directed, and weighted networks of subsistence food flows collected in three small indigenous communities in Arctic Alaska potentially facing substantial economic and ecological changes. Our analysis of plausible future scenarios suggests that changes to social relations and key households have greater effects on community robustness than changes to specific wild food resources.

Dynamic Network-Based Epistasis Analysis: Boolean Examples

PubMed Central

Azpeitia, Eugenio; Benítez, Mariana; Padilla-Longoria, Pablo; Espinosa-Soto, Carlos; Alvarez-Buylla, Elena R.

2011-01-01

In this article we focus on how the hierarchical and single-path assumptions of epistasis analysis can bias the inference of gene regulatory networks. Here we emphasize the critical importance of dynamic analyses, and specifically illustrate the use of Boolean network models. Epistasis in a broad sense refers to gene interactions, however, as originally proposed by Bateson, epistasis is defined as the blocking of a particular allelic effect due to the effect of another allele at a different locus (herein, classical epistasis). Classical epistasis analysis has proven powerful and useful, allowing researchers to infer and assign directionality to gene interactions. As larger data sets are becoming available, the analysis of classical epistasis is being complemented with computer science tools and system biology approaches. We show that when the hierarchical and single-path assumptions are not met in classical epistasis analysis, the access to relevant information and the correct inference of gene interaction topologies is hindered, and it becomes necessary to consider the temporal dynamics of gene interactions. The use of dynamical networks can overcome these limitations. We particularly focus on the use of Boolean networks that, like classical epistasis analysis, relies on logical formalisms, and hence can complement classical epistasis analysis and relax its assumptions. We develop a couple of theoretical examples and analyze them from a dynamic Boolean network model perspective. Boolean networks could help to guide additional experiments and discern among alternative regulatory schemes that would be impossible or difficult to infer without the elimination of these assumption from the classical epistasis analysis. We also use examples from the literature to show how a Boolean network-based approach has resolved ambiguities and guided epistasis analysis. Our article complements previous accounts, not only by focusing on the implications of the hierarchical and single-path assumption, but also by demonstrating the importance of considering temporal dynamics, and specifically introducing the usefulness of Boolean network models and also reviewing some key properties of network approaches. PMID:22645556

Large-Scale Network Analysis of Whole-Brain Resting-State Functional Connectivity in Spinal Cord Injury: A Comparative Study.

PubMed

Kaushal, Mayank; Oni-Orisan, Akinwunmi; Chen, Gang; Li, Wenjun; Leschke, Jack; Ward, Doug; Kalinosky, Benjamin; Budde, Matthew; Schmit, Brian; Li, Shi-Jiang; Muqeet, Vaishnavi; Kurpad, Shekar

2017-09-01

Network analysis based on graph theory depicts the brain as a complex network that allows inspection of overall brain connectivity pattern and calculation of quantifiable network metrics. To date, large-scale network analysis has not been applied to resting-state functional networks in complete spinal cord injury (SCI) patients. To characterize modular reorganization of whole brain into constituent nodes and compare network metrics between SCI and control subjects, fifteen subjects with chronic complete cervical SCI and 15 neurologically intact controls were scanned. The data were preprocessed followed by parcellation of the brain into 116 regions of interest (ROI). Correlation analysis was performed between every ROI pair to construct connectivity matrices and ROIs were categorized into distinct modules. Subsequently, local efficiency (LE) and global efficiency (GE) network metrics were calculated at incremental cost thresholds. The application of a modularity algorithm organized the whole-brain resting-state functional network of the SCI and the control subjects into nine and seven modules, respectively. The individual modules differed across groups in terms of the number and the composition of constituent nodes. LE demonstrated statistically significant decrease at multiple cost levels in SCI subjects. GE did not differ significantly between the two groups. The demonstration of modular architecture in both groups highlights the applicability of large-scale network analysis in studying complex brain networks. Comparing modules across groups revealed differences in number and membership of constituent nodes, indicating modular reorganization due to neural plasticity.

Microbiome Networks: A Systems Framework for Identifying Candidate Microbial Assemblages for Disease Management.

PubMed

Poudel, R; Jumpponen, A; Schlatter, D C; Paulitz, T C; Gardener, B B McSpadden; Kinkel, L L; Garrett, K A

2016-10-01

Network models of soil and plant microbiomes provide new opportunities for enhancing disease management, but also challenges for interpretation. We present a framework for interpreting microbiome networks, illustrating how observed network structures can be used to generate testable hypotheses about candidate microbes affecting plant health. The framework includes four types of network analyses. "General network analysis" identifies candidate taxa for maintaining an existing microbial community. "Host-focused analysis" includes a node representing a plant response such as yield, identifying taxa with direct or indirect associations with that node. "Pathogen-focused analysis" identifies taxa with direct or indirect associations with taxa known a priori as pathogens. "Disease-focused analysis" identifies taxa associated with disease. Positive direct or indirect associations with desirable outcomes, or negative associations with undesirable outcomes, indicate candidate taxa. Network analysis provides characterization not only of taxa with direct associations with important outcomes such as disease suppression, biofertilization, or expression of plant host resistance, but also taxa with indirect associations via their association with other key taxa. We illustrate the interpretation of network structure with analyses of microbiomes in the oak phyllosphere, and in wheat rhizosphere and bulk soil associated with the presence or absence of infection by Rhizoctonia solani.

Analysis of continuous-time switching networks

NASA Astrophysics Data System (ADS)

Edwards, R.

2000-11-01

Models of a number of biological systems, including gene regulation and neural networks, can be formulated as switching networks, in which the interactions between the variables depend strongly on thresholds. An idealized class of such networks in which the switching takes the form of Heaviside step functions but variables still change continuously in time has been proposed as a useful simplification to gain analytic insight. These networks, called here Glass networks after their originator, are simple enough mathematically to allow significant analysis without restricting the range of dynamics found in analogous smooth systems. A number of results have been obtained before, particularly regarding existence and stability of periodic orbits in such networks, but important cases were not considered. Here we present a coherent method of analysis that summarizes previous work and fills in some of the gaps as well as including some new results. Furthermore, we apply this analysis to a number of examples, including surprising long and complex limit cycles involving sequences of hundreds of threshold transitions. Finally, we show how the above methods can be extended to investigate aperiodic behaviour in specific networks, though a complete analysis will have to await new results in matrix theory and symbolic dynamics.

Ecological network analysis for a virtual water network.

PubMed

Fang, Delin; Chen, Bin

2015-06-02

The notions of virtual water flows provide important indicators to manifest the water consumption and allocation between different sectors via product transactions. However, the configuration of virtual water network (VWN) still needs further investigation to identify the water interdependency among different sectors as well as the network efficiency and stability in a socio-economic system. Ecological network analysis is chosen as a useful tool to examine the structure and function of VWN and the interactions among its sectors. A balance analysis of efficiency and redundancy is also conducted to describe the robustness (RVWN) of VWN. Then, network control analysis and network utility analysis are performed to investigate the dominant sectors and pathways for virtual water circulation and the mutual relationships between pairwise sectors. A case study of the Heihe River Basin in China shows that the balance between efficiency and redundancy is situated on the left side of the robustness curve with less efficiency and higher redundancy. The forestation, herding and fishing sectors and industrial sectors are found to be the main controllers. The network tends to be more mutualistic and synergic, though some competitive relationships that weaken the virtual water circulation still exist.

Executive Leadership in School Improvement Networks: A Conceptual Framework and Agenda for Research

ERIC Educational Resources Information Center

Peurach, Donald J.; Gumus, Emine

2011-01-01

The purpose of this analysis is to improve understanding of executive leadership in school improvement networks: for example, networks supported by comprehensive school reform providers, charter management organizations, and education management organizations. In this analysis, we review the literature on networks and executive leadership. We draw…

Surrogate-assisted identification of influences of network construction on evolving weighted functional networks

NASA Astrophysics Data System (ADS)

Stahn, Kirsten; Lehnertz, Klaus

2017-12-01

We aim at identifying factors that may affect the characteristics of evolving weighted networks derived from empirical observations. To this end, we employ various chains of analysis that are often used in field studies for a data-driven derivation and characterization of such networks. As an example, we consider fully connected, weighted functional brain networks before, during, and after epileptic seizures that we derive from multichannel electroencephalographic data recorded from epilepsy patients. For these evolving networks, we estimate clustering coefficient and average shortest path length in a time-resolved manner. Lastly, we make use of surrogate concepts that we apply at various levels of the chain of analysis to assess to what extent network characteristics are dominated by properties of the electroencephalographic recordings and/or the evolving weighted networks, which may be accessible more easily. We observe that characteristics are differently affected by the unavoidable referencing of the electroencephalographic recording, by the time-series-analysis technique used to derive the properties of network links, and whether or not networks were normalized. Importantly, for the majority of analysis settings, we observe temporal evolutions of network characteristics to merely reflect the temporal evolutions of mean interaction strengths. Such a property of the data may be accessible more easily, which would render the weighted network approach—as used here—as an overly complicated description of simple aspects of the data.

BiNA: A Visual Analytics Tool for Biological Network Data

PubMed Central

Gerasch, Andreas; Faber, Daniel; Küntzer, Jan; Niermann, Peter; Kohlbacher, Oliver; Lenhof, Hans-Peter; Kaufmann, Michael

2014-01-01

Interactive visual analysis of biological high-throughput data in the context of the underlying networks is an essential task in modern biomedicine with applications ranging from metabolic engineering to personalized medicine. The complexity and heterogeneity of data sets require flexible software architectures for data analysis. Concise and easily readable graphical representation of data and interactive navigation of large data sets are essential in this context. We present BiNA - the Biological Network Analyzer - a flexible open-source software for analyzing and visualizing biological networks. Highly configurable visualization styles for regulatory and metabolic network data offer sophisticated drawings and intuitive navigation and exploration techniques using hierarchical graph concepts. The generic projection and analysis framework provides powerful functionalities for visual analyses of high-throughput omics data in the context of networks, in particular for the differential analysis and the analysis of time series data. A direct interface to an underlying data warehouse provides fast access to a wide range of semantically integrated biological network databases. A plugin system allows simple customization and integration of new analysis algorithms or visual representations. BiNA is available under the 3-clause BSD license at http://bina.unipax.info/. PMID:24551056

BioLayout(Java): versatile network visualisation of structural and functional relationships.

PubMed

Goldovsky, Leon; Cases, Ildefonso; Enright, Anton J; Ouzounis, Christos A

2005-01-01

Visualisation of biological networks is becoming a common task for the analysis of high-throughput data. These networks correspond to a wide variety of biological relationships, such as sequence similarity, metabolic pathways, gene regulatory cascades and protein interactions. We present a general approach for the representation and analysis of networks of variable type, size and complexity. The application is based on the original BioLayout program (C-language implementation of the Fruchterman-Rheingold layout algorithm), entirely re-written in Java to guarantee portability across platforms. BioLayout(Java) provides broader functionality, various analysis techniques, extensions for better visualisation and a new user interface. Examples of analysis of biological networks using BioLayout(Java) are presented.

An attempt to understand glioma stem cell biology through centrality analysis of a protein interaction network.

PubMed

Mallik, Mrinmay Kumar

2018-02-07

Biological networks can be analyzed using "Centrality Analysis" to identify the more influential nodes and interactions in the network. This study was undertaken to create and visualize a biological network comprising of protein-protein interactions (PPIs) amongst proteins which are preferentially over-expressed in glioma cancer stem cell component (GCSC) of glioblastomas as compared to the glioma non-stem cancer cell (GNSC) component and then to analyze this network through centrality analyses (CA) in order to identify the essential proteins in this network and their interactions. In addition, this study proposes a new centrality analysis method pertaining exclusively to transcription factors (TFs) and interactions amongst them. Moreover the relevant molecular functions, biological processes and biochemical pathways amongst these proteins were sought through enrichment analysis. A protein interaction network was created using a list of proteins which have been shown to be preferentially expressed or over-expressed in GCSCs isolated from glioblastomas as compared to the GNSCs. This list comprising of 38 proteins, created using manual literature mining, was submitted to the Reactome FIViz tool, a web based application integrated into Cytoscape, an open source software platform for visualizing and analyzing molecular interaction networks and biological pathways to produce the network. This network was subjected to centrality analyses utilizing ranked lists of six centrality measures using the FIViz application and (for the first time) a dedicated centrality analysis plug-in ; CytoNCA. The interactions exclusively amongst the transcription factors were nalyzed through a newly proposed centrality analysis method called "Gene Expression Associated Degree Centrality Analysis (GEADCA)". Enrichment analysis was performed using the "network function analysis" tool on Reactome. The CA was able to identify a small set of proteins with consistently high centrality ranks that is indicative of their strong influence in the protein protein interaction network. Similarly the newly proposed GEADCA helped identify the transcription factors with high centrality values indicative of their key roles in transcriptional regulation. The enrichment studies provided a list of molecular functions, biological processes and biochemical pathways associated with the constructed network. The study shows how pathway based databases may be used to create and analyze a relevant protein interaction network in glioma cancer stem cells and identify the essential elements within it to gather insights into the molecular interactions that regulate the properties of glioma stem cells. How these insights may be utilized to help the development of future research towards formulation of new management strategies have been discussed from a theoretical standpoint. Copyright © 2017 Elsevier Ltd. All rights reserved.

Analysis of Photonic Networks for a Chip Multiprocessor Using Scientific Applications

DTIC Science & Technology

2009-05-01

Analysis of Photonic Networks for a Chip Multiprocessor Using Scientific Applications Gilbert Hendry†, Shoaib Kamil‡?, Aleksandr Biberman†, Johnnie...electronic networks -on-chip warrants investigating real application traces on functionally compa- rable photonic and electronic network designs. We... network can achieve 75× improvement in energy ef- ficiency for synthetic benchmarks and up to 37× improve- ment for real scientific applications

The Network Protocol Analysis Technique in Snort

NASA Astrophysics Data System (ADS)

Wu, Qing-Xiu

Network protocol analysis is a network sniffer to capture data for further analysis and understanding of the technical means necessary packets. Network sniffing is intercepted by packet assembly binary format of the original message content. In order to obtain the information contained. Required based on TCP / IP protocol stack protocol specification. Again to restore the data packets at protocol format and content in each protocol layer. Actual data transferred, as well as the application tier.

EG-05COMBINATION OF GENE COPY GAIN AND EPIGENETIC DEREGULATION ARE ASSOCIATED WITH THE ABERRANT EXPRESSION OF A STEM CELL RELATED HOX-SIGNATURE IN GLIOBLASTOMA

PubMed Central

Kurscheid, Sebastian; Bady, Pierre; Sciuscio, Davide; Samarzija, Ivana; Shay, Tal; Vassallo, Irene; Van Criekinge, Wim; Domany, Eytan; Stupp, Roger; Delorenzi, Mauro; Hegi, Monika

2014-01-01

We previously reported a stem cell related HOX gene signature associated with resistance to chemo-radiotherapy (TMZ/RT- > TMZ) in glioblastoma. However, underlying mechanisms triggering overexpression remain mostly elusive. Interestingly, HOX genes are neither involved in the developing brain, nor expressed in normal brain, suggestive of an acquired gene expression signature during gliomagenesis. HOXA genes are located on CHR 7 that displays trisomy in most glioblastoma which strongly impacts gene expression on this chromosome, modulated by local regulatory elements. Furthermore we observed more pronounced DNA methylation across the HOXA locus as compared to non-tumoral brain (Human methylation 450K BeadChip Illumina; 59 glioblastoma, 5 non-tumoral brain sampes). CpG probes annotated for HOX-signature genes, contributing most to the variability, served as input into the analysis of DNA methylation and expression to identify key regulatory regions. The structural similarity of the observed correlation matrices between DNA methylation and gene expression in our cohort and an independent data-set from TCGA (106 glioblastoma) was remarkable (RV-coefficient, 0.84; p-value < 0.0001). We identified a CpG located in the promoter region of the HOXA10 locus exerting the strongest mean negative correlation between methylation and expression of the whole HOX-signature. Applying this analysis the same CpG emerged in the external set. We then determined the contribution of both, gene copy aberration (CNA) and methylation at the selected probe to explain expression of the HOX-signature using a linear model. Statistically significant results suggested an additive effect between gene dosage and methylation at the key CpG identified. Similarly, such an additive effect was also observed in the external data-set. Taken together, we hypothesize that overexpression of the stem-cell related HOX signature is triggered by gain of trisomy 7 and escape from compensatory DNA methylation at positions controlling the effect of enhanced gene dose on expression.

High-resolution array comparative genomic hybridization (aCGH) identifies copy number alterations in diffuse large B-cell lymphoma that predict response to immuno-chemotherapy

PubMed Central

Kreisel, F.; Kulkarni, S.; Kerns, R. T.; Hassan, A.; Deshmukh, H.; Nagarajan, R.; Frater, J. L.; Cashen, A.

2013-01-01

Despite recent attempts at sub-categorization, including gene expression profiling into prognostically different groups of “germinal center B-cell type” and “activated B-cell type”, diffuse large B-cell lymphoma (DLBCL) remains a biologically heterogenous tumor with no clear prognostic biomarkers to guide therapy. Whole genome, high resolution array comparative genomic hybridization (aCGH) was performed on 4 cases of chemoresistant DLBCL and 4 cases of chemo-responsive DLBCL to identify genetic differences which may correlate with response to R-CHOP therapy. Array CGH analysis identified 7 DNA copy number alteration (CNA) regions exclusive to the chemoresistant group, consisting of amplifications at 1p36.13, 1q42.3, 3p21.31, 7q11.23, and 16p13.3, and loss at 9p21.3, and 14p21.31. Copy number loss of the tumor suppressor genes CDKN2A (p16, p14) and CDKN2B (p15) at 9p21.3 was validated by fluorescence in situ hybridization and immunohistochemistry as independent techniques. In the chemo-sensitive group, 12 CNAs were detected consisting of segment gains on 1p36.11, 1p36.22, 2q11.2, 8q24.3, 12p13.33, and 22q13.2 and segment loss on 6p21.32. RUNX3, a tumor suppressor gene located on 1p36.11 and MTHFR, which encodes for the enzyme methylenetetrahydrofolate reductase, located on 1p36.22 are the only known genes in this group associated with lymphoma. Whole genome aCGH analysis has detected copy number alterations exclusive to either chemoresistant or chemo-responsive DLBCL that may represent consistent clonal changes predictive for prognosis and outcome of chemotherapy. PMID:21504712

Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer

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

Zhang, Hui; Liu, Tao; Zhang, Zhen

Ovarian cancer remains the most lethal gynecological malignancy in the developed world, despite recent advances in genomic information and treatment. To better understand this disease, define an integrated proteogenomic landscape, and identify factors associated with homologous repair deficiency (HRD) and overall survival, we performed a comprehensive proteomic characterization of ovarian high-grade serous carcinomas (HGSC) previously characterized by The Cancer Genome Atlas (TCGA). We observed that messenger RNA transcript abundance did not reliably predict abundance for 10,030 proteins across 174 tumors. Clustering of tumors based on protein abundance identified five subtypes, two of which correlated robustly with mesenchymal and proliferative subtypes,more » while tumors characterized as immunoreactive or differentiated at the transcript level were intermixed at the protein level. At the genome level, HGSC is characterized by a complex landscape of somatic copy number alterations (CNA), which individually do not correlate significantly with survival. Correlation of CNAs with protein abundances identified loci with significant trans regulatory effects mapping to pathways associated with proliferation, cell motility/invasion, and immune regulation, three known hallmarks of cancer. Using the trans regulated proteins we also created models significantly correlated with patient survival by multivariate analysis. Integrating protein abundance with specific post-translational modification data identified subnetworks correlated with HRD status; specifically, acetylation of Lys12 and Lys16 on histone H4 was associated with HRD status. Using quantitative phosphoproteomics data covering 4,420 proteins as reflective of pathway activity, we identified the PDGFR and VEGFR signaling pathways as significantly up-regulated in patients with short overall survival, independent of PDGFR and VEGFR protein levels, potentially informing the use of anti-angiogenic therapies. Components of the Rho/Rac/Cdc42 cell motility pathways were also significantly enriched for short survival. Overall, proteomics provided new insights into ovarian cancer not apparent from genomic analysis and enabling a deeper understanding of HGSC with the potential to inform targeted therapeutics.« less

A review of network analysis terminology and its application to foot-and-mouth disease modelling and policy development.

PubMed

Dubé, C; Ribble, C; Kelton, D; McNab, B

2009-04-01

Livestock movements are important in spreading infectious diseases and many countries have developed regulations that require farmers to report livestock movements to authorities. This has led to the availability of large amounts of data for analysis and inclusion in computer simulation models developed to support policy formulation. Social network analysis has become increasingly popular to study and characterize the networks resulting from the movement of livestock from farm-to-farm and through other types of livestock operations. Network analysis is a powerful tool that allows one to study the relationships created among these operations, providing information on the role that they play in acquiring and spreading infectious diseases, information that is not readily available from more traditional livestock movement studies. Recent advances in the study of real-world complex networks are now being applied to veterinary epidemiology and infectious disease modelling and control. A review of the principles of network analysis and of the relevance of various complex network theories to infectious disease modelling and control is presented in this paper.

Synergistic Modification Induced Specific Recognition between Histone and TRIM24 via Fluctuation Correlation Network Analysis

NASA Astrophysics Data System (ADS)

Zhang, Jinmai; Luo, Huajie; Liu, Hao; Ye, Wei; Luo, Ray; Chen, Hai-Feng

2016-04-01

Histone modification plays a key role in gene regulation and gene expression. TRIM24 as a histone reader can recognize histone modification. However the specific recognition mechanism between TRIM24 and histone modification is unsolved. Here, systems biology method of dynamics correlation network based on molecular dynamics simulation was used to answer the question. Our network analysis shows that the dynamics correlation network of H3K23ac is distinctly different from that of wild type and other modifications. A hypothesis of “synergistic modification induced recognition” is then proposed to link histone modification and TRIM24 binding. These observations were further confirmed from community analysis of networks with mutation and network perturbation. Finally, a possible recognition pathway is also identified based on the shortest path search for H3K23ac. Significant difference of recognition pathway was found among different systems due to methylation and acetylation modifications. The analysis presented here and other studies show that the dynamic network-based analysis might be a useful general strategy to study the biology of protein post-translational modification and associated recognition.

Computer Code for Transportation Network Design and Analysis

DOT National Transportation Integrated Search

1977-01-01

This document describes the results of research into the application of the mathematical programming technique of decomposition to practical transportation network problems. A computer code called Catnap (for Control Analysis Transportation Network A...

The Network Structure of Human Personality According to the NEO-PI-R: Matching Network Community Structure to Factor Structure

PubMed Central

Goekoop, Rutger; Goekoop, Jaap G.; Scholte, H. Steven

2012-01-01

Introduction Human personality is described preferentially in terms of factors (dimensions) found using factor analysis. An alternative and highly related method is network analysis, which may have several advantages over factor analytic methods. Aim To directly compare the ability of network community detection (NCD) and principal component factor analysis (PCA) to examine modularity in multidimensional datasets such as the neuroticism-extraversion-openness personality inventory revised (NEO-PI-R). Methods 434 healthy subjects were tested on the NEO-PI-R. PCA was performed to extract factor structures (FS) of the current dataset using both item scores and facet scores. Correlational network graphs were constructed from univariate correlation matrices of interactions between both items and facets. These networks were pruned in a link-by-link fashion while calculating the network community structure (NCS) of each resulting network using the Wakita Tsurumi clustering algorithm. NCSs were matched against FS and networks of best matches were kept for further analysis. Results At facet level, NCS showed a best match (96.2%) with a ‘confirmatory’ 5-FS. At item level, NCS showed a best match (80%) with the standard 5-FS and involved a total of 6 network clusters. Lesser matches were found with ‘confirmatory’ 5-FS and ‘exploratory’ 6-FS of the current dataset. Network analysis did not identify facets as a separate level of organization in between items and clusters. A small-world network structure was found in both item- and facet level networks. Conclusion We present the first optimized network graph of personality traits according to the NEO-PI-R: a ‘Personality Web’. Such a web may represent the possible routes that subjects can take during personality development. NCD outperforms PCA by producing plausible modularity at item level in non-standard datasets, and can identify the key roles of individual items and clusters in the network. PMID:23284713

The network structure of human personality according to the NEO-PI-R: matching network community structure to factor structure.

PubMed

Goekoop, Rutger; Goekoop, Jaap G; Scholte, H Steven

2012-01-01

Human personality is described preferentially in terms of factors (dimensions) found using factor analysis. An alternative and highly related method is network analysis, which may have several advantages over factor analytic methods. To directly compare the ability of network community detection (NCD) and principal component factor analysis (PCA) to examine modularity in multidimensional datasets such as the neuroticism-extraversion-openness personality inventory revised (NEO-PI-R). 434 healthy subjects were tested on the NEO-PI-R. PCA was performed to extract factor structures (FS) of the current dataset using both item scores and facet scores. Correlational network graphs were constructed from univariate correlation matrices of interactions between both items and facets. These networks were pruned in a link-by-link fashion while calculating the network community structure (NCS) of each resulting network using the Wakita Tsurumi clustering algorithm. NCSs were matched against FS and networks of best matches were kept for further analysis. At facet level, NCS showed a best match (96.2%) with a 'confirmatory' 5-FS. At item level, NCS showed a best match (80%) with the standard 5-FS and involved a total of 6 network clusters. Lesser matches were found with 'confirmatory' 5-FS and 'exploratory' 6-FS of the current dataset. Network analysis did not identify facets as a separate level of organization in between items and clusters. A small-world network structure was found in both item- and facet level networks. We present the first optimized network graph of personality traits according to the NEO-PI-R: a 'Personality Web'. Such a web may represent the possible routes that subjects can take during personality development. NCD outperforms PCA by producing plausible modularity at item level in non-standard datasets, and can identify the key roles of individual items and clusters in the network.

Introduction to Social Network Analysis

NASA Astrophysics Data System (ADS)

Zaphiris, Panayiotis; Ang, Chee Siang

Social Network analysis focuses on patterns of relations between and among people, organizations, states, etc. It aims to describe networks of relations as fully as possible, identify prominent patterns in such networks, trace the flow of information through them, and discover what effects these relations and networks have on people and organizations. Social network analysis offers a very promising potential for analyzing human-human interactions in online communities (discussion boards, newsgroups, virtual organizations). This Tutorial provides an overview of this analytic technique and demonstrates how it can be used in Human Computer Interaction (HCI) research and practice, focusing especially on Computer Mediated Communication (CMC). This topic acquires particular importance these days, with the increasing popularity of social networking websites (e.g., youtube, myspace, MMORPGs etc.) and the research interest in studying them.

Landscape Characterization and Representativeness Analysis for Understanding Sampling Network Coverage

DOE Data Explorer

Maddalena, Damian; Hoffman, Forrest; Kumar, Jitendra; Hargrove, William

2014-08-01

Sampling networks rarely conform to spatial and temporal ideals, often comprised of network sampling points which are unevenly distributed and located in less than ideal locations due to access constraints, budget limitations, or political conflict. Quantifying the global, regional, and temporal representativeness of these networks by quantifying the coverage of network infrastructure highlights the capabilities and limitations of the data collected, facilitates upscaling and downscaling for modeling purposes, and improves the planning efforts for future infrastructure investment under current conditions and future modeled scenarios. The work presented here utilizes multivariate spatiotemporal clustering analysis and representativeness analysis for quantitative landscape characterization and assessment of the Fluxnet, RAINFOR, and ForestGEO networks. Results include ecoregions that highlight patterns of bioclimatic, topographic, and edaphic variables and quantitative representativeness maps of individual and combined networks.

Unified Approach to Modeling and Simulation of Space Communication Networks and Systems

NASA Technical Reports Server (NTRS)

Barritt, Brian; Bhasin, Kul; Eddy, Wesley; Matthews, Seth

2010-01-01

Network simulator software tools are often used to model the behaviors and interactions of applications, protocols, packets, and data links in terrestrial communication networks. Other software tools that model the physics, orbital dynamics, and RF characteristics of space systems have matured to allow for rapid, detailed analysis of space communication links. However, the absence of a unified toolset that integrates the two modeling approaches has encumbered the systems engineers tasked with the design, architecture, and analysis of complex space communication networks and systems. This paper presents the unified approach and describes the motivation, challenges, and our solution - the customization of the network simulator to integrate with astronautical analysis software tools for high-fidelity end-to-end simulation. Keywords space; communication; systems; networking; simulation; modeling; QualNet; STK; integration; space networks

Co-Inheritance Analysis within the Domains of Life Substantially Improves Network Inference by Phylogenetic Profiling

PubMed Central

Shin, Junha; Lee, Insuk

2015-01-01

Phylogenetic profiling, a network inference method based on gene inheritance profiles, has been widely used to construct functional gene networks in microbes. However, its utility for network inference in higher eukaryotes has been limited. An improved algorithm with an in-depth understanding of pathway evolution may overcome this limitation. In this study, we investigated the effects of taxonomic structures on co-inheritance analysis using 2,144 reference species in four query species: Escherichia coli, Saccharomyces cerevisiae, Arabidopsis thaliana, and Homo sapiens. We observed three clusters of reference species based on a principal component analysis of the phylogenetic profiles, which correspond to the three domains of life—Archaea, Bacteria, and Eukaryota—suggesting that pathways inherit primarily within specific domains or lower-ranked taxonomic groups during speciation. Hence, the co-inheritance pattern within a taxonomic group may be eroded by confounding inheritance patterns from irrelevant taxonomic groups. We demonstrated that co-inheritance analysis within domains substantially improved network inference not only in microbe species but also in the higher eukaryotes, including humans. Although we observed two sub-domain clusters of reference species within Eukaryota, co-inheritance analysis within these sub-domain taxonomic groups only marginally improved network inference. Therefore, we conclude that co-inheritance analysis within domains is the optimal approach to network inference with the given reference species. The construction of a series of human gene networks with increasing sample sizes of the reference species for each domain revealed that the size of the high-accuracy networks increased as additional reference species genomes were included, suggesting that within-domain co-inheritance analysis will continue to expand human gene networks as genomes of additional species are sequenced. Taken together, we propose that co-inheritance analysis within the domains of life will greatly potentiate the use of the expected onslaught of sequenced genomes in the study of molecular pathways in higher eukaryotes. PMID:26394049

A study of the electrical properties of complex resistor network based on NW model

NASA Astrophysics Data System (ADS)

Chang, Yunfeng; Li, Yunting; Yang, Liu; Guo, Lu; Liu, Gaochao

2015-04-01

The power and resistance of two-port complex resistor network based on NW small world network model are studied in this paper. Mainly, we study the dependence of the network power and resistance on the degree of port vertices, the connection probability and the shortest distance. Qualitative analysis and a simplified formula for network resistance are given out. Finally, we define a branching parameter and give out its physical meaning in the analysis of complex resistor network.

Network-Based Visual Analysis of Tabular Data

ERIC Educational Resources Information Center

Liu, Zhicheng

2012-01-01

Tabular data is pervasive in the form of spreadsheets and relational databases. Although tables often describe multivariate data without explicit network semantics, it may be advantageous to explore the data modeled as a graph or network for analysis. Even when a given table design conveys some static network semantics, analysts may want to look…

Social Network Analysis in E-Learning Environments: A Preliminary Systematic Review

ERIC Educational Resources Information Center

Cela, Karina L.; Sicilia, Miguel Ángel; Sánchez, Salvador

2015-01-01

E-learning occupies an increasingly prominent place in education. It provides the learner with a rich virtual network where he or she can exchange ideas and information and create synergies through interactions with other members of the network, whether fellow learners or teachers. Social network analysis (SNA) has proven extremely powerful at…

Traffic Driven Analysis of Cellular and WiFi Networks

ERIC Educational Resources Information Center

Paul, Utpal Kumar

2012-01-01

Since the days Internet traffic proliferated, measurement, monitoring and analysis of network traffic have been critical to not only the basic understanding of large networks, but also to seek improvements in resource management, traffic engineering and security. At the current times traffic in wireless local and wide area networks are facing…

Flory-Stockmayer analysis on reprocessable polymer networks

NASA Astrophysics Data System (ADS)

Li, Lingqiao; Chen, Xi; Jin, Kailong; Torkelson, John

Reprocessable polymer networks can undergo structure rearrangement through dynamic chemistries under proper conditions, making them a promising candidate for recyclable crosslinked materials, e.g. tires. This research field has been focusing on various chemistries. However, there has been lacking of an essential physical theory explaining the relationship between abundancy of dynamic linkages and reprocessability. Based on the classical Flory-Stockmayer analysis on network gelation, we developed a similar analysis on reprocessable polymer networks to quantitatively predict the critical condition for reprocessability. Our theory indicates that it is unnecessary for all bonds to be dynamic to make the resulting network reprocessable. As long as there is no percolated permanent network in the system, the material can fully rearrange. To experimentally validate our theory, we used a thiol-epoxy network model system with various dynamic linkage compositions. The stress relaxation behavior of resulting materials supports our theoretical prediction: only 50 % of linkages between crosslinks need to be dynamic for a tri-arm network to be reprocessable. Therefore, this analysis provides the first fundamental theoretical platform for designing and evaluating reprocessable polymer networks. We thank McCormick Research Catalyst Award Fund and ISEN cluster fellowship (L. L.) for funding support.

Using network analysis to study behavioural phenotypes: an example using domestic dogs.

PubMed

Goold, Conor; Vas, Judit; Olsen, Christine; Newberry, Ruth C

2016-10-01

Phenotypic integration describes the complex interrelationships between organismal traits, traditionally focusing on morphology. Recently, research has sought to represent behavioural phenotypes as composed of quasi-independent latent traits. Concurrently, psychologists have opposed latent variable interpretations of human behaviour, proposing instead a network perspective envisaging interrelationships between behaviours as emerging from causal dependencies. Network analysis could also be applied to understand integrated behavioural phenotypes in animals. Here, we assimilate this cross-disciplinary progression of ideas by demonstrating the use of network analysis on survey data collected on behavioural and motivational characteristics of police patrol and detection dogs ( Canis lupus familiaris ). Networks of conditional independence relationships illustrated a number of functional connections between descriptors, which varied between dog types. The most central descriptors denoted desirable characteristics in both patrol and detection dog networks, with 'Playful' being widely correlated and possessing mediating relationships between descriptors. Bootstrap analyses revealed the stability of network results. We discuss the results in relation to previous research on dog personality, and benefits of using network analysis to study behavioural phenotypes. We conclude that a network perspective offers widespread opportunities for advancing the understanding of phenotypic integration in animal behaviour.

Visibility Graph Based Time Series Analysis.

PubMed

Stephen, Mutua; Gu, Changgui; Yang, Huijie

2015-01-01

Network based time series analysis has made considerable achievements in the recent years. By mapping mono/multivariate time series into networks, one can investigate both it's microscopic and macroscopic behaviors. However, most proposed approaches lead to the construction of static networks consequently providing limited information on evolutionary behaviors. In the present paper we propose a method called visibility graph based time series analysis, in which series segments are mapped to visibility graphs as being descriptions of the corresponding states and the successively occurring states are linked. This procedure converts a time series to a temporal network and at the same time a network of networks. Findings from empirical records for stock markets in USA (S&P500 and Nasdaq) and artificial series generated by means of fractional Gaussian motions show that the method can provide us rich information benefiting short-term and long-term predictions. Theoretically, we propose a method to investigate time series from the viewpoint of network of networks.

Electrode systems for in situ vitrification

DOEpatents

Buelt, James L.; Carter, John G.; Eschbach, Eugene A.; FitzPatrick, Vincent F.; Koehmstedt, Paul L.; Morgan, William C.; Oma, Kenton H.; Timmerman, Craig L.

1990-01-01

An electrode comprising a molybdenum rod is received within a conductive collar formed of graphite. The molybdenum rod and the graphite collar may be physically joined at the bottom. A pair of such electrodes are placed in soil containing buried waste material and an electric current is passed therebetween for vitrifying the soil. The graphite collar enhances the thermal conductivity of the combination, bringing heat to the surface, and preventing formation of a cold cap of material above the ground surface. The annulus between the molybdenum rod electrode and the graphite collar is suitably filled with a conductive ceramic powder that sinters upon the molybdenum rod, protecting the same from oxidation as graphite material is consumed, or a metal powder which liquefies at operating temperatures. The center of the molybdenum rod, used with a collar of separately, can be hollow and filled with a powdered metal, such as copper, which liquefies at operating temperatures. Connection to electrodes can be provided below ground level to avoid open circuit due to electrode deterioration, or sacrificial electrodes may be employed when operation is started. Outboard electrodes cna be utilized to square up a vitrified area.

Electron precipitation response to geomagnetic pulsations: Riometer revelation

NASA Astrophysics Data System (ADS)

Honary, Farideh; Kavanagh, Andrew

Electron precipitation modulations by geomagnetic pulsation have been observed in cosmic noise absorption (CNA) as early as 1965 by widebeam riometers (Barcus and Rosenberg, 1965). The first observation of pulsation with high m-number was reported by Kikuchi et al.(1988) em-ploying a scanning narrow-beam riometer to investigate the spatial structure in one dimension with a high resolution. However, the advances in high spatial resolution imaging riometers has provided the ability to observe pulsating cosmic noise absorption with azimuthal wave numbers as high as 380 as well as providing the capability of mapping their structures. These waves are commonly observed during the morning and early afternoon and exhibit eastward propagation. In this presentation a complete generating mechanism for these high m-number waves is dis-cussed as a five step process, beginning with the solar wind as a source for the excitation of dayside magnetospheric cavity modes, mode conversion, energisation of drift-bounce protons by Landau damping, followed by inverse Landau damping as a driving mechanism for the high m number secondary waves that ultimately modulate the electron precipitation. This modulation is observed as pulsations in cosmic noise absorption.

The imperative for new approaches for managing and leading in healthcare for the 21st century--observations from the Canadian Nurses Association's National Expert Commission Experience and Report.

PubMed

McTeer, Maureen

2014-12-01

The Canadian healthcare system must change to meet current and future realities, particularly to respond effectively to changing age and cultural demographics and new medical/scientific technologies. To meet its ongoing policy role, the Canadian Nurses Association established a National Expert Commission in 2011, mandated to prepare a report on healthcare reform and transformation, with a clear focus on the role individual nurses and the nursing profession generally could play in ensuring better health, better care and better value for Canadians. In this paper, Commission co-chair, health law specialist Maureen McTeer, outlines the key findings and recommendations of their final report, titled A Nursing Call to Action: The Health of our Nation, the Future of our Health System which she and co-chair Dr. Marlene Smadu presented originally at the CNA's biennial meeting in Vancouver, in June, 2012. The discussion focuses on the rationale behind the commission's recommendation for a new registered nursing education curriculum and approach to training.

Evaluation model of distribution network development based on ANP and grey correlation analysis

NASA Astrophysics Data System (ADS)

Ma, Kaiqiang; Zhan, Zhihong; Zhou, Ming; Wu, Qiang; Yan, Jun; Chen, Genyong

2018-06-01

The existing distribution network evaluation system cannot scientifically and comprehensively reflect the distribution network development status. Furthermore, the evaluation model is monotonous and it is not suitable for horizontal analysis of many regional power grids. For these reason, this paper constructs a set of universal adaptability evaluation index system and model of distribution network development. Firstly, distribution network evaluation system is set up by power supply capability, power grid structure, technical equipment, intelligent level, efficiency of the power grid and development benefit of power grid. Then the comprehensive weight of indices is calculated by combining the AHP with the grey correlation analysis. Finally, the index scoring function can be obtained by fitting the index evaluation criterion to the curve, and then using the multiply plus operator to get the result of sample evaluation. The example analysis shows that the model can reflect the development of distribution network and find out the advantages and disadvantages of distribution network development. Besides, the model provides suggestions for the development and construction of distribution network.

Social Networks, Engagement and Resilience in University Students.

PubMed

Fernández-Martínez, Elena; Andina-Díaz, Elena; Fernández-Peña, Rosario; García-López, Rosa; Fulgueiras-Carril, Iván; Liébana-Presa, Cristina

2017-12-01

Analysis of social networks may be a useful tool for understanding the relationship between resilience and engagement, and this could be applied to educational methodologies, not only to improve academic performance, but also to create emotionally sustainable networks. This descriptive study was carried out on 134 university students. We collected the network structural variables, degree of resilience (CD-RISC 10), and engagement (UWES-S). The computer programs used were excel, UCINET for network analysis, and SPSS for statistical analysis. The analysis revealed results of means of 28.61 for resilience, 2.98 for absorption, 4.82 for dedication, and 3.13 for vigour. The students had two preferred places for sharing information: the classroom and WhatsApp. The greater the value for engagement, the greater the degree of centrality in the friendship network among students who are beginning their university studies. This relationship becomes reversed as the students move to later academic years. In terms of resilience, the highest values correspond to greater centrality in the friendship networks. The variables of engagement and resilience influenced the university students' support networks.

Social Networks, Engagement and Resilience in University Students

PubMed Central

García-López, Rosa; Fulgueiras-Carril, Iván

2017-01-01

Analysis of social networks may be a useful tool for understanding the relationship between resilience and engagement, and this could be applied to educational methodologies, not only to improve academic performance, but also to create emotionally sustainable networks. This descriptive study was carried out on 134 university students. We collected the network structural variables, degree of resilience (CD-RISC 10), and engagement (UWES-S). The computer programs used were excel, UCINET for network analysis, and SPSS for statistical analysis. The analysis revealed results of means of 28.61 for resilience, 2.98 for absorption, 4.82 for dedication, and 3.13 for vigour. The students had two preferred places for sharing information: the classroom and WhatsApp. The greater the value for engagement, the greater the degree of centrality in the friendship network among students who are beginning their university studies. This relationship becomes reversed as the students move to later academic years. In terms of resilience, the highest values correspond to greater centrality in the friendship networks. The variables of engagement and resilience influenced the university students’ support networks. PMID:29194361

Developing an Effective Plan for Smart Sanctions: A Network Analysis Approach

DTIC Science & Technology

2012-10-31

data and a network model that realistically simulates the Iranian nuclear development program. We then utilize several network analysis techniques...the Iran Watch (iranwatch.org) watchdog website. Using this data, which at first glance seems obtuse and unwieldy, we constructed network models in... model is created, nodes were evaluated using several measures of centrality. The team then analyzed this network utilizing four of the most common

Social Insects: A Model System for Network Dynamics

NASA Astrophysics Data System (ADS)

Charbonneau, Daniel; Blonder, Benjamin; Dornhaus, Anna

Social insect colonies (ants, bees, wasps, and termites) show sophisticated collective problem-solving in the face of variable constraints. Individuals exchange information and materials such as food. The resulting network structure and dynamics can inform us about the mechanisms by which the insects achieve particular collective behaviors and these can be transposed to man-made and social networks. We discuss how network analysis can answer important questions about social insects, such as how effective task allocation or information flow is realized. We put forward the idea that network analysis methods are under-utilized in social insect research, and that they can provide novel ways to view the complexity of collective behavior, particularly if network dynamics are taken into account. To illustrate this, we present an example of network tasks performed by ant workers, linked by instances of workers switching from one task to another. We show how temporal network analysis can propose and test new hypotheses on mechanisms of task allocation, and how adding temporal elements to static networks can drastically change results. We discuss the benefits of using social insects as models for complex systems in general. There are multiple opportunities emergent technologies and analysis methods in facilitating research on social insect network. The potential for interdisciplinary work could significantly advance diverse fields such as behavioral ecology, computer sciences, and engineering.

A reliability analysis tool for SpaceWire network

NASA Astrophysics Data System (ADS)

Zhou, Qiang; Zhu, Longjiang; Fei, Haidong; Wang, Xingyou

2017-04-01

A SpaceWire is a standard for on-board satellite networks as the basis for future data-handling architectures. It is becoming more and more popular in space applications due to its technical advantages, including reliability, low power and fault protection, etc. High reliability is the vital issue for spacecraft. Therefore, it is very important to analyze and improve the reliability performance of the SpaceWire network. This paper deals with the problem of reliability modeling and analysis with SpaceWire network. According to the function division of distributed network, a reliability analysis method based on a task is proposed, the reliability analysis of every task can lead to the system reliability matrix, the reliability result of the network system can be deduced by integrating these entire reliability indexes in the matrix. With the method, we develop a reliability analysis tool for SpaceWire Network based on VC, where the computation schemes for reliability matrix and the multi-path-task reliability are also implemented. By using this tool, we analyze several cases on typical architectures. And the analytic results indicate that redundancy architecture has better reliability performance than basic one. In practical, the dual redundancy scheme has been adopted for some key unit, to improve the reliability index of the system or task. Finally, this reliability analysis tool will has a directive influence on both task division and topology selection in the phase of SpaceWire network system design.

Multilayer motif analysis of brain networks

NASA Astrophysics Data System (ADS)

Battiston, Federico; Nicosia, Vincenzo; Chavez, Mario; Latora, Vito

2017-04-01

In the last decade, network science has shed new light both on the structural (anatomical) and on the functional (correlations in the activity) connectivity among the different areas of the human brain. The analysis of brain networks has made possible to detect the central areas of a neural system and to identify its building blocks by looking at overabundant small subgraphs, known as motifs. However, network analysis of the brain has so far mainly focused on anatomical and functional networks as separate entities. The recently developed mathematical framework of multi-layer networks allows us to perform an analysis of the human brain where the structural and functional layers are considered together. In this work, we describe how to classify the subgraphs of a multiplex network, and we extend the motif analysis to networks with an arbitrary number of layers. We then extract multi-layer motifs in brain networks of healthy subjects by considering networks with two layers, anatomical and functional, respectively, obtained from diffusion and functional magnetic resonance imaging. Results indicate that subgraphs in which the presence of a physical connection between brain areas (links at the structural layer) coexists with a non-trivial positive correlation in their activities are statistically overabundant. Finally, we investigate the existence of a reinforcement mechanism between the two layers by looking at how the probability to find a link in one layer depends on the intensity of the connection in the other one. Showing that functional connectivity is non-trivially constrained by the underlying anatomical network, our work contributes to a better understanding of the interplay between the structure and function in the human brain.

Measuring Road Network Vulnerability with Sensitivity Analysis

PubMed Central

Jun-qiang, Leng; Long-hai, Yang; Liu, Wei-yi; Zhao, Lin

2017-01-01

This paper focuses on the development of a method for road network vulnerability analysis, from the perspective of capacity degradation, which seeks to identify the critical infrastructures in the road network and the operational performance of the whole traffic system. This research involves defining the traffic utility index and modeling vulnerability of road segment, route, OD (Origin Destination) pair and road network. Meanwhile, sensitivity analysis method is utilized to calculate the change of traffic utility index due to capacity degradation. This method, compared to traditional traffic assignment, can improve calculation efficiency and make the application of vulnerability analysis to large actual road network possible. Finally, all the above models and calculation method is applied to actual road network evaluation to verify its efficiency and utility. This approach can be used as a decision-supporting tool for evaluating the performance of road network and identifying critical infrastructures in transportation planning and management, especially in the resource allocation for mitigation and recovery. PMID:28125706

Linear and nonlinear ARMA model parameter estimation using an artificial neural network

NASA Technical Reports Server (NTRS)

Chon, K. H.; Cohen, R. J.

1997-01-01

This paper addresses parametric system identification of linear and nonlinear dynamic systems by analysis of the input and output signals. Specifically, we investigate the relationship between estimation of the system using a feedforward neural network model and estimation of the system by use of linear and nonlinear autoregressive moving-average (ARMA) models. By utilizing a neural network model incorporating a polynomial activation function, we show the equivalence of the artificial neural network to the linear and nonlinear ARMA models. We compare the parameterization of the estimated system using the neural network and ARMA approaches by utilizing data generated by means of computer simulations. Specifically, we show that the parameters of a simulated ARMA system can be obtained from the neural network analysis of the simulated data or by conventional least squares ARMA analysis. The feasibility of applying neural networks with polynomial activation functions to the analysis of experimental data is explored by application to measurements of heart rate (HR) and instantaneous lung volume (ILV) fluctuations.

Network analysis of mesoscale optical recordings to assess regional, functional connectivity.

PubMed

Lim, Diana H; LeDue, Jeffrey M; Murphy, Timothy H

2015-10-01

With modern optical imaging methods, it is possible to map structural and functional connectivity. Optical imaging studies that aim to describe large-scale neural connectivity often need to handle large and complex datasets. In order to interpret these datasets, new methods for analyzing structural and functional connectivity are being developed. Recently, network analysis, based on graph theory, has been used to describe and quantify brain connectivity in both experimental and clinical studies. We outline how to apply regional, functional network analysis to mesoscale optical imaging using voltage-sensitive-dye imaging and channelrhodopsin-2 stimulation in a mouse model. We include links to sample datasets and an analysis script. The analyses we employ can be applied to other types of fluorescence wide-field imaging, including genetically encoded calcium indicators, to assess network properties. We discuss the benefits and limitations of using network analysis for interpreting optical imaging data and define network properties that may be used to compare across preparations or other manipulations such as animal models of disease.

Optimization Techniques for Analysis of Biological and Social Networks

DTIC Science & Technology

2012-03-28

analyzing a new metaheuristic technique, variable objective search. 3. Experimentation and application: Implement the proposed algorithms , test and fine...alternative mathematical programming formulations, their theoretical analysis, the development of exact algorithms , and heuristics. Originally, clusters...systematic fashion under a unifying theoretical and algorithmic framework. Optimization, Complex Networks, Social Network Analysis, Computational

Understanding Classrooms through Social Network Analysis: A Primer for Social Network Analysis in Education Research

ERIC Educational Resources Information Center

Grunspan, Daniel Z.; Wiggins, Benjamin L.; Goodreau, Steven M.

2014-01-01

Social interactions between students are a major and underexplored part of undergraduate education. Understanding how learning relationships form in undergraduate classrooms, as well as the impacts these relationships have on learning outcomes, can inform educators in unique ways and improve educational reform. Social network analysis (SNA)…

Network Analysis of a Demonstration Program for the Developmentally Disabled

ERIC Educational Resources Information Center

Fredericks, Kimberly A.

2005-01-01

This chapter presents the findings from a network analysis of a demonstration program for the developmentally disabled to show the application of graphical network analysis in program evaluation. The developmentally disabled demonstration (DDD) program was a five-year pilot project to provide person-centered service environments to people with …

A systematic review protocol: social network analysis of tobacco use.

PubMed

Maddox, Raglan; Davey, Rachel; Lovett, Ray; van der Sterren, Anke; Corbett, Joan; Cochrane, Tom

2014-08-08

Tobacco use is the single most preventable cause of death in the world. Evidence indicates that behaviours such as tobacco use can influence social networks, and that social network structures can influence behaviours. Social network analysis provides a set of analytic tools to undertake methodical analysis of social networks. We will undertake a systematic review to provide a comprehensive synthesis of the literature regarding social network analysis and tobacco use. The review will answer the following research questions: among participants who use tobacco, does social network structure/position influence tobacco use? Does tobacco use influence peer selection? Does peer selection influence tobacco use? We will follow the Preferred Reporting Items for Systemic Reviews and Meta-Analyses (PRISMA) guidelines and search the following databases for relevant articles: CINAHL (Cumulative Index to Nursing and Allied Health Literature); Informit Health Collection; PsycINFO; PubMed/MEDLINE; Scopus/Embase; Web of Science; and the Wiley Online Library. Keywords include tobacco; smoking; smokeless; cigarettes; cigar and 'social network' and reference lists of included articles will be hand searched. Studies will be included that provide descriptions of social network analysis of tobacco use.Qualitative, quantitative and mixed method data that meets the inclusion criteria for the review, including methodological rigour, credibility and quality standards, will be synthesized using narrative synthesis. Results will be presented using outcome statistics that address each of the research questions. This systematic review will provide a timely evidence base on the role of social network analysis of tobacco use, forming a basis for future research, policy and practice in this area. This systematic review will synthesise the evidence, supporting the hypothesis that social network structures can influence tobacco use. This will also include exploring the relationship between social network structure, social network position, peer selection, peer influence and tobacco use across all age groups, and across different demographics. The research will increase our understanding of social networks and their impact on tobacco use, informing policy and practice while highlighting gaps in the literature and areas for further research.

Network Analysis of Earth's Co-Evolving Geosphere and Biosphere

NASA Astrophysics Data System (ADS)

Hazen, R. M.; Eleish, A.; Liu, C.; Morrison, S. M.; Meyer, M.; Consortium, K. D.

2017-12-01

A fundamental goal of Earth science is the deep understanding of Earth's dynamic, co-evolving geosphere and biosphere through deep time. Network analysis of geo- and bio- `big data' provides an interactive, quantitative, and predictive visualization framework to explore complex and otherwise hidden high-dimension features of diversity, distribution, and change in the evolution of Earth's geochemistry, mineralogy, paleobiology, and biochemistry [1]. Networks also facilitate quantitative comparison of different geological time periods, tectonic settings, and geographical regions, as well as different planets and moons, through network metrics, including density, centralization, diameter, and transitivity.We render networks by employing data related to geographical, paragenetic, environmental, or structural relationships among minerals, fossils, proteins, and microbial taxa. An important recent finding is that the topography of many networks reflects parameters not explicitly incorporated in constructing the network. For example, networks for minerals, fossils, and protein structures reveal embedded qualitative time axes, with additional network geometries possibly related to extinction and/or other punctuation events (see Figure). Other axes related to chemical activities and volatile fugacities, as well as pressure and/or depth of formation, may also emerge from network analysis. These patterns provide new insights into the way planets evolve, especially Earth's co-evolving geosphere and biosphere. 1. Morrison, S.M. et al. (2017) Network analysis of mineralogical systems. American Mineralogist 102, in press. Figure Caption: A network of Phanerozoic Era fossil animals from the past 540 million years includes blue, red, and black circles (nodes) representing family-level taxa and grey lines (links) between coexisting families. Age information was not used in the construction of this network; nevertheless an intrinsic timeline is embedded in the network topology. In addition, two mass extinction events appear as "pinch points" in the network.

Top-down network analysis characterizes hidden termite-termite interactions.

PubMed

Campbell, Colin; Russo, Laura; Marins, Alessandra; DeSouza, Og; Schönrogge, Karsten; Mortensen, David; Tooker, John; Albert, Réka; Shea, Katriona

2016-09-01

The analysis of ecological networks is generally bottom-up, where networks are established by observing interactions between individuals. Emergent network properties have been indicated to reflect the dominant mode of interactions in communities that might be mutualistic (e.g., pollination) or antagonistic (e.g., host-parasitoid communities). Many ecological communities, however, comprise species interactions that are difficult to observe directly. Here, we propose that a comparison of the emergent properties from detail-rich reference communities with known modes of interaction can inform our understanding of detail-sparse focal communities. With this top-down approach, we consider patterns of coexistence between termite species that live as guests in mounds built by other host termite species as a case in point. Termite societies are extremely sensitive to perturbations, which precludes determining the nature of their interactions through direct observations. We perform a literature review to construct two networks representing termite mound cohabitation in a Brazilian savanna and in the tropical forest of Cameroon. We contrast the properties of these cohabitation networks with a total of 197 geographically diverse mutualistic plant-pollinator and antagonistic host-parasitoid networks. We analyze network properties for the networks, perform a principal components analysis (PCA), and compute the Mahalanobis distance of the termite networks to the cloud of mutualistic and antagonistic networks to assess the extent to which the termite networks overlap with the properties of the reference networks. Both termite networks overlap more closely with the mutualistic plant-pollinator communities than the antagonistic host-parasitoid communities, although the Brazilian community overlap with mutualistic communities is stronger. The analysis raises the hypothesis that termite-termite cohabitation networks may be overall mutualistic. More broadly, this work provides support for the argument that cryptic communities may be analyzed via comparison to well-characterized communities.

"Us and them": a social network analysis of physicians' professional networks and their attitudes towards EBM.

PubMed

Mascia, Daniele; Cicchetti, Americo; Damiani, Gianfranco

2013-10-22

Extant research suggests that there is a strong social component to Evidence-Based Medicine (EBM) adoption since professional networks amongst physicians are strongly associated with their attitudes towards EBM. Despite this evidence, it is still unknown whether individual attitudes to use scientific evidence in clinical decision-making influence the position that physicians hold in their professional network. This paper explores how physicians' attitudes towards EBM is related to the network position they occupy within healthcare organizations. Data pertain to a sample of Italian physicians, whose professional network relationships, demographics and work-profile characteristics were collected. A social network analysis was performed to capture the structural importance of physicians in the collaboration network by the means of a core-periphery analysis and the computation of network centrality indicators. Then, regression analysis was used to test the association between the network position of individual clinicians and their attitudes towards EBM. Findings documented that the overall network structure is made up of a dense cohesive core of physicians and of less connected clinicians who occupy the periphery. A negative association between the physicians' attitudes towards EBM and the coreness they exhibited in the professional network was also found. Network centrality indicators confirmed these results documenting a negative association between physicians' propensity to use EBM and their structural importance in the professional network. Attitudes that physicians show towards EBM are related to the part (core or periphery) of the professional networks to which they belong as well as to their structural importance. By identifying virtuous attitudes and behaviors of professionals within their organizations, policymakers and executives may avoid marginalization and stimulate integration and continuity of care, both within and across the boundaries of healthcare providers.

Cross-species transcriptional network analysis reveals conservation and variation in response to metal stress in cyanobacteria

PubMed Central

2013-01-01

Background As one of the most dominant bacterial groups on Earth, cyanobacteria play a pivotal role in the global carbon cycling and the Earth atmosphere composition. Understanding their molecular responses to environmental perturbations has important scientific and environmental values. Since important biological processes or networks are often evolutionarily conserved, the cross-species transcriptional network analysis offers a useful strategy to decipher conserved and species-specific transcriptional mechanisms that cells utilize to deal with various biotic and abiotic disturbances, and it will eventually lead to a better understanding of associated adaptation and regulatory networks. Results In this study, the Weighted Gene Co-expression Network Analysis (WGCNA) approach was used to establish transcriptional networks for four important cyanobacteria species under metal stress, including iron depletion and high copper conditions. Cross-species network comparison led to discovery of several core response modules and genes possibly essential to metal stress, as well as species-specific hub genes for metal stresses in different cyanobacteria species, shedding light on survival strategies of cyanobacteria responding to different environmental perturbations. Conclusions The WGCNA analysis demonstrated that the application of cross-species transcriptional network analysis will lead to novel insights to molecular response to environmental changes which will otherwise not be achieved by analyzing data from a single species. PMID:23421563

atBioNet--an integrated network analysis tool for genomics and biomarker discovery.

PubMed

Ding, Yijun; Chen, Minjun; Liu, Zhichao; Ding, Don; Ye, Yanbin; Zhang, Min; Kelly, Reagan; Guo, Li; Su, Zhenqiang; Harris, Stephen C; Qian, Feng; Ge, Weigong; Fang, Hong; Xu, Xiaowei; Tong, Weida

2012-07-20

Large amounts of mammalian protein-protein interaction (PPI) data have been generated and are available for public use. From a systems biology perspective, Proteins/genes interactions encode the key mechanisms distinguishing disease and health, and such mechanisms can be uncovered through network analysis. An effective network analysis tool should integrate different content-specific PPI databases into a comprehensive network format with a user-friendly platform to identify key functional modules/pathways and the underlying mechanisms of disease and toxicity. atBioNet integrates seven publicly available PPI databases into a network-specific knowledge base. Knowledge expansion is achieved by expanding a user supplied proteins/genes list with interactions from its integrated PPI network. The statistically significant functional modules are determined by applying a fast network-clustering algorithm (SCAN: a Structural Clustering Algorithm for Networks). The functional modules can be visualized either separately or together in the context of the whole network. Integration of pathway information enables enrichment analysis and assessment of the biological function of modules. Three case studies are presented using publicly available disease gene signatures as a basis to discover new biomarkers for acute leukemia, systemic lupus erythematosus, and breast cancer. The results demonstrated that atBioNet can not only identify functional modules and pathways related to the studied diseases, but this information can also be used to hypothesize novel biomarkers for future analysis. atBioNet is a free web-based network analysis tool that provides a systematic insight into proteins/genes interactions through examining significant functional modules. The identified functional modules are useful for determining underlying mechanisms of disease and biomarker discovery. It can be accessed at: http://www.fda.gov/ScienceResearch/BioinformaticsTools/ucm285284.htm.

Principal Component Analysis Based Measure of Structural Holes

NASA Astrophysics Data System (ADS)

Deng, Shiguo; Zhang, Wenqing; Yang, Huijie

2013-02-01

Based upon principal component analysis, a new measure called compressibility coefficient is proposed to evaluate structural holes in networks. This measure incorporates a new effect from identical patterns in networks. It is found that compressibility coefficient for Watts-Strogatz small-world networks increases monotonically with the rewiring probability and saturates to that for the corresponding shuffled networks. While compressibility coefficient for extended Barabasi-Albert scale-free networks decreases monotonically with the preferential effect and is significantly large compared with that for corresponding shuffled networks. This measure is helpful in diverse research fields to evaluate global efficiency of networks.

Content-specific network analysis of peer-to-peer communication in an online community for smoking cessation.

PubMed

Myneni, Sahiti; Cobb, Nathan K; Cohen, Trevor

2016-01-01

Analysis of user interactions in online communities could improve our understanding of health-related behaviors and inform the design of technological solutions that support behavior change. However, to achieve this we would need methods that provide granular perspective, yet are scalable. In this paper, we present a methodology for high-throughput semantic and network analysis of large social media datasets, combining semi-automated text categorization with social network analytics. We apply this method to derive content-specific network visualizations of 16,492 user interactions in an online community for smoking cessation. Performance of the categorization system was reasonable (average F-measure of 0.74, with system-rater reliability approaching rater-rater reliability). The resulting semantically specific network analysis of user interactions reveals content- and behavior-specific network topologies. Implications for socio-behavioral health and wellness platforms are also discussed.

Assessing Group Interaction with Social Language Network Analysis

NASA Astrophysics Data System (ADS)

Scholand, Andrew J.; Tausczik, Yla R.; Pennebaker, James W.

In this paper we discuss a new methodology, social language network analysis (SLNA), that combines tools from social language processing and network analysis to assess socially situated working relationships within a group. Specifically, SLNA aims to identify and characterize the nature of working relationships by processing artifacts generated with computer-mediated communication systems, such as instant message texts or emails. Because social language processing is able to identify psychological, social, and emotional processes that individuals are not able to fully mask, social language network analysis can clarify and highlight complex interdependencies between group members, even when these relationships are latent or unrecognized.

Multivariate analysis: A statistical approach for computations

NASA Astrophysics Data System (ADS)

Michu, Sachin; Kaushik, Vandana

2014-10-01

Multivariate analysis is a type of multivariate statistical approach commonly used in, automotive diagnosis, education evaluating clusters in finance etc and more recently in the health-related professions. The objective of the paper is to provide a detailed exploratory discussion about factor analysis (FA) in image retrieval method and correlation analysis (CA) of network traffic. Image retrieval methods aim to retrieve relevant images from a collected database, based on their content. The problem is made more difficult due to the high dimension of the variable space in which the images are represented. Multivariate correlation analysis proposes an anomaly detection and analysis method based on the correlation coefficient matrix. Anomaly behaviors in the network include the various attacks on the network like DDOs attacks and network scanning.

Mapping Extension's Networks: Using Social Network Analysis to Explore Extension's Outreach

ERIC Educational Resources Information Center

Bartholomay, Tom; Chazdon, Scott; Marczak, Mary S.; Walker, Kathrin C.

2011-01-01

The University of Minnesota Extension conducted a social network analysis (SNA) to examine its outreach to organizations external to the University of Minnesota. The study found that its outreach network was both broad in its reach and strong in its connections. The study found that SNA offers a unique method for describing and measuring Extension…

Understanding the Dynamics of MOOC Discussion Forums with Simulation Investigation for Empirical Network Analysis (SIENA)

ERIC Educational Resources Information Center

Zhang, Jingjing; Skryabin, Maxim; Song, Xiongwei

2016-01-01

This study attempts to make inferences about the mechanisms that drive network change over time. It adopts simulation investigation for empirical network analysis to examine the patterns and evolution of relationships formed in the context of a massive open online course (MOOC) discussion forum. Four network effects--"homophily,"…

A Network Text Analysis of David Ayer's "Fury"

ERIC Educational Resources Information Center

Hunter, Starling David; Smith, Susan

2015-01-01

Network Text Analysis (NTA) involves the creation of networks of words and/or concepts from linguistic data. Its key insight is that the position of words and concepts in a text network provides vital clues to the central and underlying themes of the text as a whole. Recent research has relied on inductive approaches to identify these themes. In…

Combinatorial complexity of pathway analysis in metabolic networks.

PubMed

Klamt, Steffen; Stelling, Jörg

2002-01-01

Elementary flux mode analysis is a promising approach for a pathway-oriented perspective of metabolic networks. However, in larger networks it is hampered by the combinatorial explosion of possible routes. In this work we give some estimations on the combinatorial complexity including theoretical upper bounds for the number of elementary flux modes in a network of a given size. In a case study, we computed the elementary modes in the central metabolism of Escherichia coli while utilizing four different substrates. Interestingly, although the number of modes occurring in this complex network can exceed half a million, it is still far below the upper bound. Hence, to a certain extent, pathway analysis of central catabolism is feasible to assess network properties such as flexibility and functionality.

A network approach for distinguishing ethical issues in research and development.

PubMed

Zwart, Sjoerd D; van de Poel, Ibo; van Mil, Harald; Brumsen, Michiel

2006-10-01

In this paper we report on our experiences with using network analysis to discern and analyse ethical issues in research into, and the development of, a new wastewater treatment technology. Using network analysis, we preliminarily interpreted some of our observations in a Group Decision Room (GDR) session where we invited important stakeholders to think about the risks of this new technology. We show how a network approach is useful for understanding the observations, and suggests some relevant ethical issues. We argue that a network approach is also useful for ethical analysis of issues in other fields of research and development. The abandoning of the overarching rationality assumption, which is central to network approaches, does not have to lead to ethical relativism.

75 FR 48369 - Notice of Intent To Seek Approval To Establish an Information Collection

Federal Register 2010, 2011, 2012, 2013, 2014

2010-08-10

... INFORMATION: Title of Collection: A Social Network Analysis of the National Science Foundation's Research and... Office of Management and Budget (OMB) for review and approval. A Social Network Analysis of the National... programs. The primary objectives of the study are to conduct a social network analysis of the REESE and DR...

Research on two-port network of wavelet transform processor using surface acoustic wavelet devices and its application.

PubMed

Liu, Shoubing; Lu, Wenke; Zhu, Changchun

2017-11-01

The goal of this research is to study two-port network of wavelet transform processor (WTP) using surface acoustic wave (SAW) devices and its application. The motive was prompted by the inconvenience of the long research and design cycle and the huge research funding involved with traditional method in this field, which were caused by the lack of the simulation and emulation method of WTP using SAW devices. For this reason, we introduce the two-port network analysis tool, which has been widely used in the design and analysis of SAW devices with uniform interdigital transducers (IDTs). Because the admittance parameters calculation formula of the two-port network can only be used for the SAW devices with uniform IDTs, this analysis tool cannot be directly applied into the design and analysis of the processor using SAW devices, whose input interdigital transducer (IDT) is apodized weighting. Therefore, in this paper, we propose the channel segmentation method, which can convert the WTP using SAW devices into parallel channels, and also provide with the calculation formula of the number of channels, the number of finger pairs and the static capacitance of an interdigital period in each parallel channel firstly. From the parameters given above, we can calculate the admittance parameters of the two port network for each channel, so that we can obtain the admittance parameter of the two-port network of the WTP using SAW devices on the basis of the simplification rule of parallel two-port network. Through this analysis tool, not only can we get the impulse response function of the WTP using SAW devices but we can also get the matching circuit of it. Large numbers of studies show that the parameters of the two-port network obtained by this paper are consistent with those measured by network analyzer E5061A, and the impulse response function obtained by the two-port network analysis tool is also consistent with that measured by network analyzer E5061A, which can meet the accuracy requirements of the analysis of the WTP using SAW devices. Therefore the two-port network analysis tool discussed in this paper has comparatively higher theoretical and practical value. Copyright © 2017 Elsevier B.V. All rights reserved.

CoryneRegNet 4.0 – A reference database for corynebacterial gene regulatory networks

PubMed Central

Baumbach, Jan

2007-01-01

Background Detailed information on DNA-binding transcription factors (the key players in the regulation of gene expression) and on transcriptional regulatory interactions of microorganisms deduced from literature-derived knowledge, computer predictions and global DNA microarray hybridization experiments, has opened the way for the genome-wide analysis of transcriptional regulatory networks. The large-scale reconstruction of these networks allows the in silico analysis of cell behavior in response to changing environmental conditions. We previously published CoryneRegNet, an ontology-based data warehouse of corynebacterial transcription factors and regulatory networks. Initially, it was designed to provide methods for the analysis and visualization of the gene regulatory network of Corynebacterium glutamicum. Results Now we introduce CoryneRegNet release 4.0, which integrates data on the gene regulatory networks of 4 corynebacteria, 2 mycobacteria and the model organism Escherichia coli K12. As the previous versions, CoryneRegNet provides a web-based user interface to access the database content, to allow various queries, and to support the reconstruction, analysis and visualization of regulatory networks at different hierarchical levels. In this article, we present the further improved database content of CoryneRegNet along with novel analysis features. The network visualization feature GraphVis now allows the inter-species comparisons of reconstructed gene regulatory networks and the projection of gene expression levels onto that networks. Therefore, we added stimulon data directly into the database, but also provide Web Service access to the DNA microarray analysis platform EMMA. Additionally, CoryneRegNet now provides a SOAP based Web Service server, which can easily be consumed by other bioinformatics software systems. Stimulons (imported from the database, or uploaded by the user) can be analyzed in the context of known transcriptional regulatory networks to predict putative contradictions or further gene regulatory interactions. Furthermore, it integrates protein clusters by means of heuristically solving the weighted graph cluster editing problem. In addition, it provides Web Service based access to up to date gene annotation data from GenDB. Conclusion The release 4.0 of CoryneRegNet is a comprehensive system for the integrated analysis of procaryotic gene regulatory networks. It is a versatile systems biology platform to support the efficient and large-scale analysis of transcriptional regulation of gene expression in microorganisms. It is publicly available at . PMID:17986320

Drug target identification using network analysis: Taking active components in Sini decoction as an example

NASA Astrophysics Data System (ADS)

Chen, Si; Jiang, Hailong; Cao, Yan; Wang, Yun; Hu, Ziheng; Zhu, Zhenyu; Chai, Yifeng

2016-04-01

Identifying the molecular targets for the beneficial effects of active small-molecule compounds simultaneously is an important and currently unmet challenge. In this study, we firstly proposed network analysis by integrating data from network pharmacology and metabolomics to identify targets of active components in sini decoction (SND) simultaneously against heart failure. To begin with, 48 potential active components in SND against heart failure were predicted by serum pharmacochemistry, text mining and similarity match. Then, we employed network pharmacology including text mining and molecular docking to identify the potential targets of these components. The key enriched processes, pathways and related diseases of these target proteins were analyzed by STRING database. At last, network analysis was conducted to identify most possible targets of components in SND. Among the 25 targets predicted by network analysis, tumor necrosis factor α (TNF-α) was firstly experimentally validated in molecular and cellular level. Results indicated that hypaconitine, mesaconitine, higenamine and quercetin in SND can directly bind to TNF-α, reduce the TNF-α-mediated cytotoxicity on L929 cells and exert anti-myocardial cell apoptosis effects. We envisage that network analysis will also be useful in target identification of a bioactive compound.

Drug target identification using network analysis: Taking active components in Sini decoction as an example

PubMed Central

Chen, Si; Jiang, Hailong; Cao, Yan; Wang, Yun; Hu, Ziheng; Zhu, Zhenyu; Chai, Yifeng

2016-01-01

Identifying the molecular targets for the beneficial effects of active small-molecule compounds simultaneously is an important and currently unmet challenge. In this study, we firstly proposed network analysis by integrating data from network pharmacology and metabolomics to identify targets of active components in sini decoction (SND) simultaneously against heart failure. To begin with, 48 potential active components in SND against heart failure were predicted by serum pharmacochemistry, text mining and similarity match. Then, we employed network pharmacology including text mining and molecular docking to identify the potential targets of these components. The key enriched processes, pathways and related diseases of these target proteins were analyzed by STRING database. At last, network analysis was conducted to identify most possible targets of components in SND. Among the 25 targets predicted by network analysis, tumor necrosis factor α (TNF-α) was firstly experimentally validated in molecular and cellular level. Results indicated that hypaconitine, mesaconitine, higenamine and quercetin in SND can directly bind to TNF-α, reduce the TNF-α-mediated cytotoxicity on L929 cells and exert anti-myocardial cell apoptosis effects. We envisage that network analysis will also be useful in target identification of a bioactive compound. PMID:27095146

Graph analysis of functional brain networks: practical issues in translational neuroscience

PubMed Central

De Vico Fallani, Fabrizio; Richiardi, Jonas; Chavez, Mario; Achard, Sophie

2014-01-01

The brain can be regarded as a network: a connected system where nodes, or units, represent different specialized regions and links, or connections, represent communication pathways. From a functional perspective, communication is coded by temporal dependence between the activities of different brain areas. In the last decade, the abstract representation of the brain as a graph has allowed to visualize functional brain networks and describe their non-trivial topological properties in a compact and objective way. Nowadays, the use of graph analysis in translational neuroscience has become essential to quantify brain dysfunctions in terms of aberrant reconfiguration of functional brain networks. Despite its evident impact, graph analysis of functional brain networks is not a simple toolbox that can be blindly applied to brain signals. On the one hand, it requires the know-how of all the methodological steps of the pipeline that manipulate the input brain signals and extract the functional network properties. On the other hand, knowledge of the neural phenomenon under study is required to perform physiologically relevant analysis. The aim of this review is to provide practical indications to make sense of brain network analysis and contrast counterproductive attitudes. PMID:25180301

African American Extended Family and Church-Based Social Network Typologies.

PubMed

Nguyen, Ann W; Chatters, Linda M; Taylor, Robert Joseph

2016-12-01

We examined social network typologies among African American adults and their sociodemographic correlates. Network types were derived from indicators of the family and church networks. Latent class analysis was based on a nationally representative sample of African Americans from the National Survey of American Life. Results indicated four distinct network types: ambivalent, optimal, family centered, and strained. These four types were distinguished by (a) degree of social integration, (b) network composition, and (c) level of negative interactions. In a departure from previous work, a network type composed solely of nonkin was not identified, which may reflect racial differences in social network typologies. Further, the analysis indicated that network types varied by sociodemographic characteristics. Social network typologies have several promising practice implications, as they can inform the development of prevention and intervention programs.

Network Analysis on Attitudes: A Brief Tutorial.

PubMed

Dalege, Jonas; Borsboom, Denny; van Harreveld, Frenk; van der Maas, Han L J

2017-07-01

In this article, we provide a brief tutorial on the estimation, analysis, and simulation on attitude networks using the programming language R. We first discuss what a network is and subsequently show how one can estimate a regularized network on typical attitude data. For this, we use open-access data on the attitudes toward Barack Obama during the 2012 American presidential election. Second, we show how one can calculate standard network measures such as community structure, centrality, and connectivity on this estimated attitude network. Third, we show how one can simulate from an estimated attitude network to derive predictions from attitude networks. By this, we highlight that network theory provides a framework for both testing and developing formalized hypotheses on attitudes and related core social psychological constructs.

Network Analysis on Attitudes

PubMed Central

Borsboom, Denny; van Harreveld, Frenk; van der Maas, Han L. J.

2017-01-01

In this article, we provide a brief tutorial on the estimation, analysis, and simulation on attitude networks using the programming language R. We first discuss what a network is and subsequently show how one can estimate a regularized network on typical attitude data. For this, we use open-access data on the attitudes toward Barack Obama during the 2012 American presidential election. Second, we show how one can calculate standard network measures such as community structure, centrality, and connectivity on this estimated attitude network. Third, we show how one can simulate from an estimated attitude network to derive predictions from attitude networks. By this, we highlight that network theory provides a framework for both testing and developing formalized hypotheses on attitudes and related core social psychological constructs. PMID:28919944