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

Genomic suppression subtractive hybridization as a tool to identify differences in mycorrhizal fungal genomes.

PubMed

Murat, Claude; Zampieri, Elisa; Vallino, Marta; Daghino, Stefania; Perotto, Silvia; Bonfante, Paola

2011-05-01

Characterization of genomic variation among different microbial species, or different strains of the same species, is a field of significant interest with a wide range of potential applications. We have investigated the genomic variation in mycorrhizal fungal genomes through genomic suppressive subtractive hybridization. The comparison was between phylogenetically distant and close truffle species (Tuber spp.), and between isolates of the ericoid mycorrhizal fungus Oidiodendron maius featuring different degrees of metal tolerance. In the interspecies experiment, almost all the sequences that were identified in the Tuber melanosporum genome and absent in Tuber borchii and Tuber indicum corresponded to transposable elements. In the intraspecies comparison, some specific sequences corresponded to regions coding for enzymes, among them a glutathione synthetase known to be involved in metal tolerance. This approach is a quick and rather inexpensive tool to develop molecular markers for mycorrhizal fungi tracking and barcoding, to identify functional genes and to investigate the genome plasticity, adaptation and evolution. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Genome-wide association study for rotator cuff tears identifies two significant single-nucleotide polymorphisms.

PubMed

Tashjian, Robert Z; Granger, Erin K; Farnham, James M; Cannon-Albright, Lisa A; Teerlink, Craig C

2016-02-01

The precise etiology of rotator cuff disease is unknown, but prior evidence suggests a role for genetic factors. Limited data exist identifying specific genes associated with rotator cuff tearing. The purpose of this study was to identify specific genes or genetic variants associated with rotator cuff tearing by a genome-wide association study with an independent set of rotator cuff tear cases. A set of 311 full-thickness rotator cuff tear cases genotyped on the Illumina 5M single-nucleotide polymorphism (SNP) platform were used in a genome-wide association study with 2641 genetically matched white population controls available from the Illumina iControls database. Tests of association were performed with GEMMA software at 257,558 SNPs that compose the intersection of Illumina SNP platforms and that passed general quality control metrics. SNPs were considered significant if P < 1.94 × 10(-7) (Bonferroni correction: 0.05/257,558). Tests of association revealed 2 significantly associated SNPs, one occurring in SAP30BP (rs820218; P = 3.8E-9) on chromosome 17q25 and another occurring in SASH1 (rs12527089; P = 1.9E-7) on chromosome 6q24. This study represents the first attempt to identify genetic factors influencing rotator cuff tearing by a genome-wide association study using a dense/complete set of SNPs. Two SNPs were significantly associated with rotator cuff tearing, residing in SAP30BP on chromosome 17 and SASH1 on chromosome 6. Both genes are associated with the cellular process of apoptosis. Identification of potential genes or genetic variants associated with rotator cuff tearing may help in identifying individuals at risk for the development of rotator cuff tearing. Copyright © 2016 Journal of Shoulder and Elbow Surgery Board of Trustees. Published by Elsevier Inc. All rights reserved.

Combining a nontargeted and targeted metabolomics approach to identify metabolic pathways significantly altered in polycystic ovary syndrome.

PubMed

Chang, Alice Y; Lalia, Antigoni Z; Jenkins, Gregory D; Dutta, Tumpa; Carter, Rickey E; Singh, Ravinder J; Nair, K Sreekumaran

2017-06-01

Polycystic ovary syndrome (PCOS) is a condition of androgen excess and chronic anovulation frequently associated with insulin resistance. We combined a nontargeted and targeted metabolomics approach to identify pathways and metabolites that distinguished PCOS from metabolic syndrome (MetS). Twenty obese women with PCOS were compared with 18 obese women without PCOS. Both groups met criteria for MetS but could not have diabetes mellitus or take medications that treat PCOS or affect lipids or insulin sensitivity. Insulin sensitivity was derived from the frequently sampled intravenous glucose tolerance test. A nontargeted metabolomics approach was performed on fasting plasma samples to identify differentially expressed metabolites, which were further evaluated by principal component and pathway enrichment analysis. Quantitative targeted metabolomics was then applied on candidate metabolites. Measured metabolites were tested for associations with PCOS and clinical variables by logistic and linear regression analyses. This multiethnic, obese sample was matched by age (PCOS, 37±6; MetS, 40±6years) and body mass index (BMI) (PCOS, 34.6±5.1; MetS, 33.7±5.2kg/m 2 ). Principal component analysis of the nontargeted metabolomics data showed distinct group separation of PCOS from MetS controls. From the subset of 385 differentially expressed metabolites, 22% were identified by accurate mass, resulting in 19 canonical pathways significantly altered in PCOS, including amino acid, lipid, steroid, carbohydrate, and vitamin D metabolism. Targeted metabolomics identified many essential amino acids, including branched-chain amino acids (BCAA) that were elevated in PCOS compared with MetS. PCOS was most associated with BCAA (P=.02), essential amino acids (P=.03), the essential amino acid lysine (P=.02), and the lysine metabolite α-aminoadipic acid (P=.02) in models adjusted for surrogate variables representing technical variation in metabolites. No significant differences between

Combining a Nontargeted and Targeted Metabolomics Approach to Identify Metabolic Pathways Significantly Altered in Polycystic Ovary Syndrome

PubMed Central

Chang, Alice Y.; Lalia, Antigoni Z.; Jenkins, Gregory D.; Dutta, Tumpa; Carter, Rickey E.; Singh, Ravinder J.; Sreekumaran Nair, K.

2017-01-01

Objective Polycystic ovary syndrome (PCOS) is a condition of androgen excess and chronic anovulation frequently associated with insulin resistance. We combined a nontargeted and targeted metabolomics approach to identify pathways and metabolites that distinguished PCOS from metabolic syndrome (MetS). Methods Twenty obese women with PCOS were compared with 18 obese women without PCOS. Both groups met criteria for MetS but could not have diabetes mellitus or take medications that treat PCOS or affect lipids or insulin sensitivity. Insulin sensitivity was derived from the frequently sampled intravenous glucose tolerance test. A nontargeted metabolomics approach was performed on fasting plasma samples to identify differentially expressed metabolites, which were further evaluated by principal component and pathway enrichment analysis. Quantitative targeted metabolomics was then applied on candidate metabolites. Measured metabolites were tested for associations with PCOS and clinical variables by logistic and linear regression analyses. Results This multiethnic, obese sample was matched by age (PCOS, 37 ± 6; MetS, 40 ± 6 years) and body mass index (BMI) (PCOS, 34.6 ± 5.1; MetS, 33.7 ± 5.2 kg/m2). Principal component analysis of the nontargeted metabolomics data showed distinct group separation of PCOS from MetS controls. From the subset of 385 differentially expressed metabolites, 22% were identified by accurate mass, resulting in 19 canonical pathways significantly altered in PCOS, including amino acid, lipid, steroid, carbohydrate, and vitamin D metabolism. Targeted metabolomics identified many essential amino acids, including branched-chain amino acids (BCAA) that were elevated in PCOS compared with MetS. PCOS was most associated with BCAA (P = .02), essential amino acids (P = .03), the essential amino acid lysine (P = .02), and the lysine metabolite α-aminoadipic acid (P = .02) in models adjusted for surrogate variables representing technical variation in

40 CFR 141.723 - Requirements to respond to significant deficiencies identified in sanitary surveys performed by EPA.

Code of Federal Regulations, 2011 CFR

2011-07-01

... deficiencies identified in sanitary surveys performed by EPA. 141.723 Section 141.723 Protection of Environment... REGULATIONS Enhanced Treatment for Cryptosporidium Requirements for Sanitary Surveys Performed by Epa § 141.723 Requirements to respond to significant deficiencies identified in sanitary surveys performed by...

40 CFR 141.723 - Requirements to respond to significant deficiencies identified in sanitary surveys performed by EPA.

Code of Federal Regulations, 2014 CFR

2014-07-01

... deficiencies identified in sanitary surveys performed by EPA. 141.723 Section 141.723 Protection of Environment... REGULATIONS Enhanced Treatment for Cryptosporidium Requirements for Sanitary Surveys Performed by Epa § 141.723 Requirements to respond to significant deficiencies identified in sanitary surveys performed by...

40 CFR 141.723 - Requirements to respond to significant deficiencies identified in sanitary surveys performed by EPA.

Code of Federal Regulations, 2013 CFR

2013-07-01

... deficiencies identified in sanitary surveys performed by EPA. 141.723 Section 141.723 Protection of Environment... REGULATIONS Enhanced Treatment for Cryptosporidium Requirements for Sanitary Surveys Performed by Epa § 141.723 Requirements to respond to significant deficiencies identified in sanitary surveys performed by...

40 CFR 141.723 - Requirements to respond to significant deficiencies identified in sanitary surveys performed by EPA.

Code of Federal Regulations, 2012 CFR

2012-07-01

... deficiencies identified in sanitary surveys performed by EPA. 141.723 Section 141.723 Protection of Environment... REGULATIONS Enhanced Treatment for Cryptosporidium Requirements for Sanitary Surveys Performed by Epa § 141.723 Requirements to respond to significant deficiencies identified in sanitary surveys performed by...

40 CFR 141.723 - Requirements to respond to significant deficiencies identified in sanitary surveys performed by EPA.

Code of Federal Regulations, 2010 CFR

2010-07-01

... deficiencies identified in sanitary surveys performed by EPA. 141.723 Section 141.723 Protection of Environment... REGULATIONS Enhanced Treatment for Cryptosporidium Requirements for Sanitary Surveys Performed by Epa § 141.723 Requirements to respond to significant deficiencies identified in sanitary surveys performed by...

Protein phosphorylation differs significantly among ontogenetic phases in Malus seedlings

PubMed Central

2014-01-01

Background Although protein phosphorylation is an important post-translational modification affecting protein function and metabolism, dynamic changes in this process during ontogenesis remain unexplored in woody angiosperms. Methods Phosphorylated proteins from leaves of three apple seedlings at juvenile, adult vegetative and reproductive stages were extracted and subjected to alkaline phosphatase pre-treatment. After separating the proteins by two-dimensional gel electrophoresis and phosphoprotein-specific Pro-Q Diamond staining, differentially expressed phosphoproteins were identified by MALDI-TOF-TOF mass spectrometry. Results A total of 107 phosphorylated protein spots on nine gels (three ontogenetic phases × three seedlings) were identified by MALDI-TOF-TOF mass spectrometry. The 55 spots of ribulose-1, 5-bisphosphate carboxylase/oxygenase (Rubisco) large-chain fragments varied significantly in protein abundance and degree of phosphorylation among ontogenetic phases. Abundances of the 27 spots corresponding to Rubisco activase declined between juvenile and reproductive phases. More extensively, phosphorylated β-tubulin chain spots with lower isoelectric points were most abundant during juvenile and adult vegetative phases. Conclusions Protein phosphorylation varied significantly during vegetative phase change and floral transition in apple seedlings. Most of the observed changes were consistent among seedlings and between hybrid populations. PMID:24904238

Personality Characteristics of Leaders Identifying with Different Student Subcultures.

ERIC Educational Resources Information Center

Brainard, Stephen R.

This study was conducted to discover differences in personality characteristics among student leaders. The personality characteristics of presidents of campus organizations affiliated with one of four distinguishable student subcultures, identified by previous research as vocational, academic, collegiate, and nonconformist, were measured by the…

[The significance of the interaural latency difference of VEMP].

PubMed

Wu, Ziming; Zhang, Suzhen; Ji, Fei; Zhou, Na; Guo, Weiwei; Yang, Weiyan; Han, Dongyi

2005-05-01

To investigate the significance of the interaural latency (IAL) difference of the latency of VEMP and to raise the sensitivity of the test. Vestibular evoked myogenic potentials (VEMP) were tested in 20 healthy subjects; 13 patients with acoustic neuromaor cerebellopontile angle occupying lesions and 1 patient with multiple sclerosis. IAL differences of the wave p13,n23 and p13-n23 (abbreviatd as /delta p13/, /delta n23/ and /delta p13-n23/, respectively) were analysed to determine the normal range and the upper limit of the norm data. Four illustrative cases with the abnormality of the IAL difference were given as examples. The upper limit of the IAL of /delta p13/ was 1.13 ms; that of the /delta n23/ was 1.38 ms and that of /delta p13-n23/ was 1.54 ms. The /p13-n23/ latency between the right and left side had no significant difference (P > 0.05). /delta p13/, /delta n23/ and /delta p13-n23/, especially /delta p13/ of VEMP can suggest abnormality in the neural pathway and it may be applicable in practice.

Evolutionary analysis of vision genes identifies potential drivers of visual differences between giraffe and okapi

PubMed Central

Agaba, Morris; Cavener, Douglas R.

2017-01-01

Background The capacity of visually oriented species to perceive and respond to visual signal is integral to their evolutionary success. Giraffes are closely related to okapi, but the two species have broad range of phenotypic differences including their visual capacities. Vision studies rank giraffe’s visual acuity higher than all other artiodactyls despite sharing similar vision ecological determinants with many of them. The extent to which the giraffe’s unique visual capacity and its difference with okapi is reflected by changes in their vision genes is not understood. Methods The recent availability of giraffe and okapi genomes provided opportunity to identify giraffe and okapi vision genes. Multiple strategies were employed to identify thirty-six candidate mammalian vision genes in giraffe and okapi genomes. Quantification of selection pressure was performed by a combination of branch-site tests of positive selection and clade models of selection divergence through comparing giraffe and okapi vision genes and orthologous sequences from other mammals. Results Signatures of selection were identified in key genes that could potentially underlie giraffe and okapi visual adaptations. Importantly, some genes that contribute to optical transparency of the eye and those that are critical in light signaling pathway were found to show signatures of adaptive evolution or selection divergence. Comparison between giraffe and other ruminants identifies significant selection divergence in CRYAA and OPN1LW. Significant selection divergence was identified in SAG while positive selection was detected in LUM when okapi is compared with ruminants and other mammals. Sequence analysis of OPN1LW showed that at least one of the sites known to affect spectral sensitivity of the red pigment is uniquely divergent between giraffe and other ruminants. Discussion By taking a systemic approach to gene function in vision, the results provide the first molecular clues associated with

Evolutionary analysis of vision genes identifies potential drivers of visual differences between giraffe and okapi.

PubMed

Ishengoma, Edson; Agaba, Morris; Cavener, Douglas R

2017-01-01

The capacity of visually oriented species to perceive and respond to visual signal is integral to their evolutionary success. Giraffes are closely related to okapi, but the two species have broad range of phenotypic differences including their visual capacities. Vision studies rank giraffe's visual acuity higher than all other artiodactyls despite sharing similar vision ecological determinants with many of them. The extent to which the giraffe's unique visual capacity and its difference with okapi is reflected by changes in their vision genes is not understood. The recent availability of giraffe and okapi genomes provided opportunity to identify giraffe and okapi vision genes. Multiple strategies were employed to identify thirty-six candidate mammalian vision genes in giraffe and okapi genomes. Quantification of selection pressure was performed by a combination of branch-site tests of positive selection and clade models of selection divergence through comparing giraffe and okapi vision genes and orthologous sequences from other mammals. Signatures of selection were identified in key genes that could potentially underlie giraffe and okapi visual adaptations. Importantly, some genes that contribute to optical transparency of the eye and those that are critical in light signaling pathway were found to show signatures of adaptive evolution or selection divergence. Comparison between giraffe and other ruminants identifies significant selection divergence in CRYAA and OPN1LW . Significant selection divergence was identified in SAG while positive selection was detected in LUM when okapi is compared with ruminants and other mammals. Sequence analysis of OPN1LW showed that at least one of the sites known to affect spectral sensitivity of the red pigment is uniquely divergent between giraffe and other ruminants. By taking a systemic approach to gene function in vision, the results provide the first molecular clues associated with giraffe and okapi vision adaptations. At

Clinical Significance and Characteristic Clinical Differences of Cytolytic Vaginosis in Recurrent Vulvovaginitis.

PubMed

Yang, Shuhua; Zhang, Yuexiang; Liu, Ying; Wang, Jianhong; Chen, Shuqin; Li, Shuxia

2017-01-01

The study aimed to evaluate whether cytolytic vaginosis (CV) has important clinical implications for recurrent vulvovaginitis and to identify clinical differences between CV and vulvovaginal candidosis (VVC). Medical histories, physical examinations and laboratory findings were used to diagnose and assess the prevalence rates of various vulvovaginal infections among 536 women with recurrent vulvovaginitis. Chi-square and Fisher exact tests were used to compare age, menstrual cycle phase at episode onset, symptoms/signs of infection and discharge characteristics between CV and VVC with single infection. Among the 484 women with a single-infection recurrent vulvovaginitis, the prevalence of CV (n = 143; 26.7%) was second only to VVC (n = 196; 36.6%). CV symptoms occurred predominantly during the ovulatory and luteal phases. Meanwhile, VVC episodes were not concentrated premenstrually, but rather occurred throughout the menstrual cycle. Significant differences were found in the vaginal pH, discharge characteristics and frequency of inflammatory symptoms between the 2 groups. CV is clinically important, because it is a common cause of recurrent vulvovaginitis. To distinguish CV from VVC, gynecologists should consider the patient's medical history, physical and laboratory findings, vaginal pH and vaginal discharge characteristics. © 2016 S. Karger AG, Basel.

The Urinary Microbiome Differs Significantly Between Patients With Chronic Prostatitis/Chronic Pelvic Pain Syndrome and Controls as Well as Between Patients With Different Clinical Phenotypes.

PubMed

Shoskes, Daniel A; Altemus, Jessica; Polackwich, Alan S; Tucky, Barbara; Wang, Hannah; Eng, Charis

2016-06-01

To study the urinary microbiome of patients with Chronic Prostatitis/Chronic Pelvic Pain Syndrome (CP/CPPS) compared with controls. We identified 25 patients with CP/CPPS and 25 men who were either asymptomatic or only had urinary symptoms. Midstream urine was collected. Symptom severity was measured with the National Institutes of Health Chronic Prostatitis Symptom Index and clinical phenotype with UPOINT. Total DNA was extracted from the urine pellet and bacterial-specific 16Sr-DNA-capture identified by MiSeq sequencing. Taxonomic and functional bioinformatic analyses used principal coordinate analysis (PCoA)/MacQIIME, LEfSe, and PiCRUSt algorithms. Patients and controls were similar ages (52.3 vs 57.0 years, P = .27). For patients, median duration was 48 months, mean Chronic Prostatitis Symptom Index was 26.0, and mean UPOINT domains was 3.6. Weighted 3D UniFrac PCoA revealed tighter clustering of controls distinct from the wider clustering of cases (P = .001; α-diversity P = .005). Seventeen clades were overrepresented in patients, for example, Clostridia, and 5 were underrepresented, eg, Bacilli, resulting in predicted perturbations in functional pathways. PiCRUSt inferred differentially regulated pathways between cases and controls that may be of relevance including sporulation, chemotaxis, and pyruvate metabolism. PCoA-derived microbiomic differences were noted for neurologic/systemic domains (P = .06), whereas LEfSe identified differences associated with each of the 6 clinical features. Urinary microbiomes from patients with CP/CPPS have significantly higher alpha(phylogenetic) diversity which cluster differently from controls, and higher counts of Clostridia compared with controls, resulting in predicted perturbations of functional pathways which could suggest metabolite-specific targeted treatment. Several measures of severity and clinical phenotype have significant microbiome differences. Copyright © 2016 Elsevier Inc. All rights

Determining coding CpG islands by identifying regions significant for pattern statistics on Markov chains.

PubMed

Singer, Meromit; Engström, Alexander; Schönhuth, Alexander; Pachter, Lior

2011-09-23

Recent experimental and computational work confirms that CpGs can be unmethylated inside coding exons, thereby showing that codons may be subjected to both genomic and epigenomic constraint. It is therefore of interest to identify coding CpG islands (CCGIs) that are regions inside exons enriched for CpGs. The difficulty in identifying such islands is that coding exons exhibit sequence biases determined by codon usage and constraints that must be taken into account. We present a method for finding CCGIs that showcases a novel approach we have developed for identifying regions of interest that are significant (with respect to a Markov chain) for the counts of any pattern. Our method begins with the exact computation of tail probabilities for the number of CpGs in all regions contained in coding exons, and then applies a greedy algorithm for selecting islands from among the regions. We show that the greedy algorithm provably optimizes a biologically motivated criterion for selecting islands while controlling the false discovery rate. We applied this approach to the human genome (hg18) and annotated CpG islands in coding exons. The statistical criterion we apply to evaluating islands reduces the number of false positives in existing annotations, while our approach to defining islands reveals significant numbers of undiscovered CCGIs in coding exons. Many of these appear to be examples of functional epigenetic specialization in coding exons.

Identifying Gifted Children: Congruence among Different IQ Measures

PubMed Central

Fernández, Estrella; García, Trinidad; Arias-Gundín, Olga; Vázquez, Almudena; Rodríguez, Celestino

2017-01-01

This study has two main aims: (1) analysing the relationship between intellectual capacities and levels of creativity in a sample of Spanish students from the third and sixth grades; and (2) examining the discrimination capacities and degree of congruence among different tests of intellectual ability that are commonly used to identify high-ability students. The study sample comprised 236 primary school students. Participants completed different tests of intellectual ability, which were based on both fluid and crystallized intelligence, as well as creativity. Results indicated that it is advisable to use varying tests in the assessment process, and a complementary measure (i.e., creativity) in order to create a multi-criteria means of detection that can more efficiently distinguish this population of students. PMID:28775702

Testing the Difference of Correlated Agreement Coefficients for Statistical Significance

ERIC Educational Resources Information Center

Gwet, Kilem L.

2016-01-01

This article addresses the problem of testing the difference between two correlated agreement coefficients for statistical significance. A number of authors have proposed methods for testing the difference between two correlated kappa coefficients, which require either the use of resampling methods or the use of advanced statistical modeling…

Drosophila Cancer Models Identify Functional Differences between Ret Fusions.

PubMed

Levinson, Sarah; Cagan, Ross L

2016-09-13

We generated and compared Drosophila models of RET fusions CCDC6-RET and NCOA4-RET. Both RET fusions directed cells to migrate, delaminate, and undergo EMT, and both resulted in lethality when broadly expressed. In all phenotypes examined, NCOA4-RET was more severe than CCDC6-RET, mirroring their effects on patients. A functional screen against the Drosophila kinome and a library of cancer drugs found that CCDC6-RET and NCOA4-RET acted through different signaling networks and displayed distinct drug sensitivities. Combining data from the kinome and drug screens identified the WEE1 inhibitor AZD1775 plus the multi-kinase inhibitor sorafenib as a synergistic drug combination that is specific for NCOA4-RET. Our work emphasizes the importance of identifying and tailoring a patient's treatment to their specific RET fusion isoform and identifies a multi-targeted therapy that may prove effective against tumors containing the NCOA4-RET fusion. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Cloud-based solution to identify statistically significant MS peaks differentiating sample categories.

PubMed

Ji, Jun; Ling, Jeffrey; Jiang, Helen; Wen, Qiaojun; Whitin, John C; Tian, Lu; Cohen, Harvey J; Ling, Xuefeng B

2013-03-23

Mass spectrometry (MS) has evolved to become the primary high throughput tool for proteomics based biomarker discovery. Until now, multiple challenges in protein MS data analysis remain: large-scale and complex data set management; MS peak identification, indexing; and high dimensional peak differential analysis with the concurrent statistical tests based false discovery rate (FDR). "Turnkey" solutions are needed for biomarker investigations to rapidly process MS data sets to identify statistically significant peaks for subsequent validation. Here we present an efficient and effective solution, which provides experimental biologists easy access to "cloud" computing capabilities to analyze MS data. The web portal can be accessed at http://transmed.stanford.edu/ssa/. Presented web application supplies large scale MS data online uploading and analysis with a simple user interface. This bioinformatic tool will facilitate the discovery of the potential protein biomarkers using MS.

Coagulation tests show significant differences in patients with breast cancer.

PubMed

Tas, Faruk; Kilic, Leyla; Duranyildiz, Derya

2014-06-01

Activated coagulation and fibrinolytic system in cancer patients is associated with tumor stroma formation and metastasis in different cancer types. The aim of this study is to explore the correlation of blood coagulation assays for various clinicopathologic factors in breast cancer patients. A total of 123 female breast cancer patients were enrolled into the study. All the patients were treatment naïve. Pretreatment blood coagulation tests including PT, APTT, PTA, INR, D-dimer, fibrinogen levels, and platelet counts were evaluated. Median age of diagnosis was 51 years old (range 26-82). Twenty-two percent of the group consisted of metastatic breast cancer patients. The plasma level of all coagulation tests revealed statistically significant difference between patient and control group except for PT (p<0.001 for all variables except for PT; p=0.08). Elderly age (>50 years) was associated with higher D-dimer levels (p=0.003). Metastatic patients exhibited significantly higher D-dimer values when compared with early breast cancer patients (p=0.049). Advanced tumor stage (T3 and T4) was associated with higher INR (p=0.05) and lower PTA (p=0.025). In conclusion, coagulation tests show significant differences in patients with breast cancer.

Relating genes to function: identifying enriched transcription factors using the ENCODE ChIP-Seq significance tool.

PubMed

Auerbach, Raymond K; Chen, Bin; Butte, Atul J

2013-08-01

Biological analysis has shifted from identifying genes and transcripts to mapping these genes and transcripts to biological functions. The ENCODE Project has generated hundreds of ChIP-Seq experiments spanning multiple transcription factors and cell lines for public use, but tools for a biomedical scientist to analyze these data are either non-existent or tailored to narrow biological questions. We present the ENCODE ChIP-Seq Significance Tool, a flexible web application leveraging public ENCODE data to identify enriched transcription factors in a gene or transcript list for comparative analyses. The ENCODE ChIP-Seq Significance Tool is written in JavaScript on the client side and has been tested on Google Chrome, Apple Safari and Mozilla Firefox browsers. Server-side scripts are written in PHP and leverage R and a MySQL database. The tool is available at http://encodeqt.stanford.edu. abutte@stanford.edu Supplementary material is available at Bioinformatics online.

Identifying biologically relevant differences between metagenomic communities.

PubMed

Parks, Donovan H; Beiko, Robert G

2010-03-15

Metagenomics is the study of genetic material recovered directly from environmental samples. Taxonomic and functional differences between metagenomic samples can highlight the influence of ecological factors on patterns of microbial life in a wide range of habitats. Statistical hypothesis tests can help us distinguish ecological influences from sampling artifacts, but knowledge of only the P-value from a statistical hypothesis test is insufficient to make inferences about biological relevance. Current reporting practices for pairwise comparative metagenomics are inadequate, and better tools are needed for comparative metagenomic analysis. We have developed a new software package, STAMP, for comparative metagenomics that supports best practices in analysis and reporting. Examination of a pair of iron mine metagenomes demonstrates that deeper biological insights can be gained using statistical techniques available in our software. An analysis of the functional potential of 'Candidatus Accumulibacter phosphatis' in two enhanced biological phosphorus removal metagenomes identified several subsystems that differ between the A.phosphatis stains in these related communities, including phosphate metabolism, secretion and metal transport. Python source code and binaries are freely available from our website at http://kiwi.cs.dal.ca/Software/STAMP CONTACT: beiko@cs.dal.ca Supplementary data are available at Bioinformatics online.

Two distinct groups within the Bacillus subtilis group display significantly different spore heat resistance properties.

PubMed

Berendsen, Erwin M; Zwietering, Marcel H; Kuipers, Oscar P; Wells-Bennik, Marjon H J

2015-02-01

The survival of bacterial spores after heat treatment and the subsequent germination and outgrowth in a food product can lead to spoilage of the food product and economical losses. Prediction of time-temperature conditions that lead to sufficient inactivation requires access to detailed spore thermal inactivation kinetics of relevant model strains. In this study, the thermal inactivation kinetics of spores of fourteen strains belonging to the Bacillus subtilis group were determined in detail, using both batch heating in capillary tubes and continuous flow heating in a micro heater. The inactivation data were fitted using a log linear model. Based on the spore heat resistance data, two distinct groups (p < 0.001) within the B. subtilis group could be identified. One group of strains had spores with an average D120 °C of 0.33 s, while the spores of the other group displayed significantly higher heat resistances, with an average D120 °C of 45.7 s. When comparing spore inactivation data obtained using batch- and continuous flow heating, the z-values were significantly different, hence extrapolation from one system to the other was not justified. This study clearly shows that heat resistances of spores from different strains in the B. subtilis group can vary greatly. Strains can be separated into two groups, to which different spore heat inactivation kinetics apply. Copyright © 2014 Elsevier Ltd. All rights reserved.

Use of computed tomography to identify atrial fibrillation associated differences in left atrial wall thickness and density.

PubMed

Dewland, Thomas A; Wintermark, Max; Vaysman, Anna; Smith, Lisa M; Tong, Elizabeth; Vittinghoff, Eric; Marcus, Gregory M

2013-01-01

Left atrial (LA) tissue characteristics may play an important role in atrial fibrillation (AF) induction and perpetuation. Although frequently used in clinical practice, computed tomography (CT) has not been employed to describe differences in LA wall properties between AF patients and controls. We sought to noninvasively characterize AF-associated differences in LA tissue using CT. CT images of the LA were obtained in 98 consecutive patients undergoing AF ablation and in 89 controls. A custom software algorithm was used to measure wall thickness and density in four prespecified regions of the LA. On average, LA walls were thinner (-15.5%, 95% confidence interval [CI] -23.2 to -7.8%, P < 0.001) and demonstrated significantly lower density (-19.7 Hounsfield Units [HU], 95% CI -27.0 to -12.5 HU, P < 0.001) in AF patients compared to controls. In linear mixed models adjusting for demographics, clinical variables, and other CT measurements, the average LA, interatrial septum, LA appendage, and anterior walls remained significantly thinner in AF patients. After adjusting for the same potential confounders, history of AF was associated with reduced density in the LA anterior wall and increased density below the right inferior pulmonary vein and in the LA appendage. Application of an automated measurement algorithm to CT imaging of the atrium identified significant thinning of the LA wall and regional alterations in tissue density in patients with a history of AF. These findings suggest differences in LA tissue composition can be noninvasively identified and quantified using CT. ©2012, The Authors. Journal compilation ©2012 Wiley Periodicals, Inc.

One arm exercise induces significant interarm diastolic blood pressure difference.

PubMed

Hong, Dezhi; Wang, Jiwei; Su, Hai; Xu, Jingsong; Liu, Yanna; Peng, Qiang; Wang, Lijuan

2011-06-01

This study is designed to investigate the inducing effect of one arm exercise on interarm difference (IAD) in the blood pressure (BP). Fifty healthy young participants were included in the study. Three-minute exercises of the right arm elbow flexion and extension were performed. The bilateral brachial BP was simultaneously measured with two automatic BP measurement devices before (basic) and immediately 0, 5, 10, 15, 20, and 30 min after exercise. The absolute difference in the systolic BP (SBP) and diastolic BP (DBP) between the left and right BP of at least 10 mmHg was recognized as sIAD and dIAD. The baseline data of the SBP and DBP in left and right arms revealed no significant difference (SBP: 110 ± 10 vs. 111 ± 11 mmHg; DBP: 66 ± 8 vs. 66 ± 9 mmHg, both not significant). The prevalence of dIAD was 2% at the baseline. However, this prevalence increased to 80% at 0 min, as right arm exercise induced the right DBP decrease and left DBP increase, and then the prevalence decreased gradually within a 30-min recovery period. The prevalence of sIAD was zero at the baseline and the maximal prevalence was 8% during the 20-min postexercise period. One arm exercise can lead to a significant IAD in DBP. Any arm exercise should be avoided before BP measurement.

Comparison of Four Views to Single-view Ultrasound Protocols to Identify Clinically Significant Pneumothorax.

PubMed

Helland, Gregg; Gaspari, Romolo; Licciardo, Samuel; Sanseverino, Alexandra; Torres, Ulises; Emhoff, Timothy; Blehar, David

2016-10-01

Ultrasound (US) has been shown to be effective at identifying a pneumothorax (PTX); however, the additional value of adding multiple views has not been studied. Single- and four-view protocols have both been described in the literature. The objective of this study was to compare the diagnostic accuracy of single-view versus four-view lung US to detect clinically significant PTX in trauma patients. This was a randomized, prospective trial on trauma patients. Adult patients with acute traumatic injury undergoing computed tomography (CT) scan of the chest were eligible for enrollment. Patients were randomized to a single view or four views of each hemithorax prior to any imaging. USs were performed and interpreted by credentialed physicians using a 7.5-Mhz linear array transducer on a portable US machine with digital clips recorded for later review. Attending radiologist interpretation of the chest CT was reviewed for presence or absence of PTX with descriptions of small foci of air or minimal PTX categorized as clinically insignificant. A total of 260 patients were enrolled over a 2-year period. A total of 139 patients received a single view of each chest wall and 121 patients received four views. There were a total of 49 patients that had a PTX (19%), and 29 of these were clinically significant (11%). In diagnosis of any PTX, both single-view and four-view techniques showed poor sensitivity (54.2 and 68%) but high specificity (99 and 98%). For clinically significant PTX, single-view US demonstrated a sensitivity of 93% (95% confidence interval [CI] = 64.1% to 99.6%) and a specificity of 99.2% (95% CI = 95.5% to 99.9%), with sensitivity of 93.3% (95% CI = 66% to 99.7%) and specificity of 98% (95% CI = 92.1% to 99.7%) for four views. Single-view and four-view chest wall USs demonstrate comparable sensitivity and specificity for PTX. The additional time to obtain four views should be weighed against the absence of additional diagnostic yield over a single view when

COMPARATIVE DIVERSITY OF FECAL BACTERIA IN AGRICULTURALLY SIGNIFICANT ANIMALS TO IDENTIFY ALTERNATIVE TARGETS FOR MICROBIAL SOURCE TRACKING

EPA Science Inventory

Animals of agricultural significance contribute a large percentage of fecal pollution to waterways via runoff contamination. The premise of microbial source tracking is to utilize fecal bacteria to identify target populations which are directly correlated to specific animal feces...

A Large-Scale Multi-ancestry Genome-wide Study Accounting for Smoking Behavior Identifies Multiple Significant Loci for Blood Pressure.

PubMed

Sung, Yun J; Winkler, Thomas W; de Las Fuentes, Lisa; Bentley, Amy R; Brown, Michael R; Kraja, Aldi T; Schwander, Karen; Ntalla, Ioanna; Guo, Xiuqing; Franceschini, Nora; Lu, Yingchang; Cheng, Ching-Yu; Sim, Xueling; Vojinovic, Dina; Marten, Jonathan; Musani, Solomon K; Li, Changwei; Feitosa, Mary F; Kilpeläinen, Tuomas O; Richard, Melissa A; Noordam, Raymond; Aslibekyan, Stella; Aschard, Hugues; Bartz, Traci M; Dorajoo, Rajkumar; Liu, Yongmei; Manning, Alisa K; Rankinen, Tuomo; Smith, Albert Vernon; Tajuddin, Salman M; Tayo, Bamidele O; Warren, Helen R; Zhao, Wei; Zhou, Yanhua; Matoba, Nana; Sofer, Tamar; Alver, Maris; Amini, Marzyeh; Boissel, Mathilde; Chai, Jin Fang; Chen, Xu; Divers, Jasmin; Gandin, Ilaria; Gao, Chuan; Giulianini, Franco; Goel, Anuj; Harris, Sarah E; Hartwig, Fernando Pires; Horimoto, Andrea R V R; Hsu, Fang-Chi; Jackson, Anne U; Kähönen, Mika; Kasturiratne, Anuradhani; Kühnel, Brigitte; Leander, Karin; Lee, Wen-Jane; Lin, Keng-Hung; 'an Luan, Jian; McKenzie, Colin A; Meian, He; Nelson, Christopher P; Rauramaa, Rainer; Schupf, Nicole; Scott, Robert A; Sheu, Wayne H H; Stančáková, Alena; Takeuchi, Fumihiko; van der Most, Peter J; Varga, Tibor V; Wang, Heming; Wang, Yajuan; Ware, Erin B; Weiss, Stefan; Wen, Wanqing; Yanek, Lisa R; Zhang, Weihua; Zhao, Jing Hua; Afaq, Saima; Alfred, Tamuno; Amin, Najaf; Arking, Dan; Aung, Tin; Barr, R Graham; Bielak, Lawrence F; Boerwinkle, Eric; Bottinger, Erwin P; Braund, Peter S; Brody, Jennifer A; Broeckel, Ulrich; Cabrera, Claudia P; Cade, Brian; Caizheng, Yu; Campbell, Archie; Canouil, Mickaël; Chakravarti, Aravinda; Chauhan, Ganesh; Christensen, Kaare; Cocca, Massimiliano; Collins, Francis S; Connell, John M; de Mutsert, Renée; de Silva, H Janaka; Debette, Stephanie; Dörr, Marcus; Duan, Qing; Eaton, Charles B; Ehret, Georg; Evangelou, Evangelos; Faul, Jessica D; Fisher, Virginia A; Forouhi, Nita G; Franco, Oscar H; Friedlander, Yechiel; Gao, He; Gigante, Bruna; Graff, Misa; Gu, C Charles; Gu, Dongfeng; Gupta, Preeti; Hagenaars, Saskia P; Harris, Tamara B; He, Jiang; Heikkinen, Sami; Heng, Chew-Kiat; Hirata, Makoto; Hofman, Albert; Howard, Barbara V; Hunt, Steven; Irvin, Marguerite R; Jia, Yucheng; Joehanes, Roby; Justice, Anne E; Katsuya, Tomohiro; Kaufman, Joel; Kerrison, Nicola D; Khor, Chiea Chuen; Koh, Woon-Puay; Koistinen, Heikki A; Komulainen, Pirjo; Kooperberg, Charles; Krieger, Jose E; Kubo, Michiaki; Kuusisto, Johanna; Langefeld, Carl D; Langenberg, Claudia; Launer, Lenore J; Lehne, Benjamin; Lewis, Cora E; Li, Yize; Lim, Sing Hui; Lin, Shiow; Liu, Ching-Ti; Liu, Jianjun; Liu, Jingmin; Liu, Kiang; Liu, Yeheng; Loh, Marie; Lohman, Kurt K; Long, Jirong; Louie, Tin; Mägi, Reedik; Mahajan, Anubha; Meitinger, Thomas; Metspalu, Andres; Milani, Lili; Momozawa, Yukihide; Morris, Andrew P; Mosley, Thomas H; Munson, Peter; Murray, Alison D; Nalls, Mike A; Nasri, Ubaydah; Norris, Jill M; North, Kari; Ogunniyi, Adesola; Padmanabhan, Sandosh; Palmas, Walter R; Palmer, Nicholette D; Pankow, James S; Pedersen, Nancy L; Peters, Annette; Peyser, Patricia A; Polasek, Ozren; Raitakari, Olli T; Renström, Frida; Rice, Treva K; Ridker, Paul M; Robino, Antonietta; Robinson, Jennifer G; Rose, Lynda M; Rudan, Igor; Sabanayagam, Charumathi; Salako, Babatunde L; Sandow, Kevin; Schmidt, Carsten O; Schreiner, Pamela J; Scott, William R; Seshadri, Sudha; Sever, Peter; Sitlani, Colleen M; Smith, Jennifer A; Snieder, Harold; Starr, John M; Strauch, Konstantin; Tang, Hua; Taylor, Kent D; Teo, Yik Ying; Tham, Yih Chung; Uitterlinden, André G; Waldenberger, Melanie; Wang, Lihua; Wang, Ya X; Wei, Wen Bin; Williams, Christine; Wilson, Gregory; Wojczynski, Mary K; Yao, Jie; Yuan, Jian-Min; Zonderman, Alan B; Becker, Diane M; Boehnke, Michael; Bowden, Donald W; Chambers, John C; Chen, Yii-Der Ida; de Faire, Ulf; Deary, Ian J; Esko, Tõnu; Farrall, Martin; Forrester, Terrence; Franks, Paul W; Freedman, Barry I; Froguel, Philippe; Gasparini, Paolo; Gieger, Christian; Horta, Bernardo Lessa; Hung, Yi-Jen; Jonas, Jost B; Kato, Norihiro; Kooner, Jaspal S; Laakso, Markku; Lehtimäki, Terho; Liang, Kae-Woei; Magnusson, Patrik K E; Newman, Anne B; Oldehinkel, Albertine J; Pereira, Alexandre C; Redline, Susan; Rettig, Rainer; Samani, Nilesh J; Scott, James; Shu, Xiao-Ou; van der Harst, Pim; Wagenknecht, Lynne E; Wareham, Nicholas J; Watkins, Hugh; Weir, David R; Wickremasinghe, Ananda R; Wu, Tangchun; Zheng, Wei; Kamatani, Yoichiro; Laurie, Cathy C; Bouchard, Claude; Cooper, Richard S; Evans, Michele K; Gudnason, Vilmundur; Kardia, Sharon L R; Kritchevsky, Stephen B; Levy, Daniel; O'Connell, Jeff R; Psaty, Bruce M; van Dam, Rob M; Sims, Mario; Arnett, Donna K; Mook-Kanamori, Dennis O; Kelly, Tanika N; Fox, Ervin R; Hayward, Caroline; Fornage, Myriam; Rotimi, Charles N; Province, Michael A; van Duijn, Cornelia M; Tai, E Shyong; Wong, Tien Yin; Loos, Ruth J F; Reiner, Alex P; Rotter, Jerome I; Zhu, Xiaofeng; Bierut, Laura J; Gauderman, W James; Caulfield, Mark J; Elliott, Paul; Rice, Kenneth; Munroe, Patricia B; Morrison, Alanna C; Cupples, L Adrienne; Rao, Dabeeru C; Chasman, Daniel I

2018-03-01

Genome-wide association analysis advanced understanding of blood pressure (BP), a major risk factor for vascular conditions such as coronary heart disease and stroke. Accounting for smoking behavior may help identify BP loci and extend our knowledge of its genetic architecture. We performed genome-wide association meta-analyses of systolic and diastolic BP incorporating gene-smoking interactions in 610,091 individuals. Stage 1 analysis examined ∼18.8 million SNPs and small insertion/deletion variants in 129,913 individuals from four ancestries (European, African, Asian, and Hispanic) with follow-up analysis of promising variants in 480,178 additional individuals from five ancestries. We identified 15 loci that were genome-wide significant (p < 5 × 10 -8 ) in stage 1 and formally replicated in stage 2. A combined stage 1 and 2 meta-analysis identified 66 additional genome-wide significant loci (13, 35, and 18 loci in European, African, and trans-ancestry, respectively). A total of 56 known BP loci were also identified by our results (p < 5 × 10 -8 ). Of the newly identified loci, ten showed significant interaction with smoking status, but none of them were replicated in stage 2. Several loci were identified in African ancestry, highlighting the importance of genetic studies in diverse populations. The identified loci show strong evidence for regulatory features and support shared pathophysiology with cardiometabolic and addiction traits. They also highlight a role in BP regulation for biological candidates such as modulators of vascular structure and function (CDKN1B, BCAR1-CFDP1, PXDN, EEA1), ciliopathies (SDCCAG8, RPGRIP1L), telomere maintenance (TNKS, PINX1, AKTIP), and central dopaminergic signaling (MSRA, EBF2). Copyright © 2018 American Society of Human Genetics. All rights reserved.

SigTree: A Microbial Community Analysis Tool to Identify and Visualize Significantly Responsive Branches in a Phylogenetic Tree.

PubMed

Stevens, John R; Jones, Todd R; Lefevre, Michael; Ganesan, Balasubramanian; Weimer, Bart C

2017-01-01

Microbial community analysis experiments to assess the effect of a treatment intervention (or environmental change) on the relative abundance levels of multiple related microbial species (or operational taxonomic units) simultaneously using high throughput genomics are becoming increasingly common. Within the framework of the evolutionary phylogeny of all species considered in the experiment, this translates to a statistical need to identify the phylogenetic branches that exhibit a significant consensus response (in terms of operational taxonomic unit abundance) to the intervention. We present the R software package SigTree , a collection of flexible tools that make use of meta-analysis methods and regular expressions to identify and visualize significantly responsive branches in a phylogenetic tree, while appropriately adjusting for multiple comparisons.

Improved system identification using artificial neural networks and analysis of individual differences in responses of an identified neuron.

PubMed

Costalago Meruelo, Alicia; Simpson, David M; Veres, Sandor M; Newland, Philip L

2016-03-01

Mathematical modelling is used routinely to understand the coding properties and dynamics of responses of neurons and neural networks. Here we analyse the effectiveness of Artificial Neural Networks (ANNs) as a modelling tool for motor neuron responses. We used ANNs to model the synaptic responses of an identified motor neuron, the fast extensor motor neuron, of the desert locust in response to displacement of a sensory organ, the femoral chordotonal organ, which monitors movements of the tibia relative to the femur of the leg. The aim of the study was threefold: first to determine the potential value of ANNs as tools to model and investigate neural networks, second to understand the generalisation properties of ANNs across individuals and to different input signals and third, to understand individual differences in responses of an identified neuron. A metaheuristic algorithm was developed to design the ANN architectures. The performance of the models generated by the ANNs was compared with those generated through previous mathematical models of the same neuron. The results suggest that ANNs are significantly better than LNL and Wiener models in predicting specific neural responses to Gaussian White Noise, but not significantly different when tested with sinusoidal inputs. They are also able to predict responses of the same neuron in different individuals irrespective of which animal was used to develop the model, although notable differences between some individuals were evident. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

Significant differences in pediatric psychotropic side effects: Implications for school performance.

PubMed

Kubiszyn, Thomas; Mire, Sarah; Dutt, Sonia; Papathopoulos, Katina; Burridge, Andrea Backsheider

2012-03-01

Some side effects (SEs) of increasingly prescribed psychotropic medications can impact student performance in school. SE risk varies, even among drugs from the same class (e.g., antidepressants). Knowing which SEs occur significantly more often than others may enable school psychologists to enhance collaborative risk-benefit analysis, medication monitoring, data-based decision-making, and inform mitigation efforts. SE data from Full Prescribing Information (PI) on the FDA website for ADHD drugs, atypical antipsychotics, and antidepressants with pediatric indications were analyzed. Risk ratios (RR) are reported for each drug within a category compared with placebo. RR tables and graphs inform the reader about SE incidence differences for each drug and provide clear evidence of the wide variability in SE incidence in the FDA data. Breslow-Day and Cochran Mantel-Haenszel methods were used to test for drug-placebo SE differences and to test for significance across drugs within each category based on odds ratios (ORs). Significant drug-placebo differences were found for each drug compared with placebo, when odds were pooled across all drugs in a category compared with placebo, and between some drugs within categories. Unexpectedly, many large RR differences did not reach significance. Potential explanations are offered, including limitations of the FDA data sets and statistical and methodological issues. Future research directions are offered. The potential impact of certain SEs on school performance, mitigation strategies, and the potential role of the school psychologist is discussed, with consideration for ethical and legal limitations. (c) 2012 APA, all rights reserved.

Are Mammographically Occult Additional Tumors Identified More Than 2 Cm Away From the Primary Breast Cancer on MRI Clinically Significant?

PubMed

Goodman, Sarah; Mango, Victoria; Friedlander, Lauren; Desperito, Elise; Wynn, Ralph; Ha, Richard

2018-06-08

To evaluate the clinical significance of mammographically occult additional tumors identified more than 2cm away from the primary breast cancer on preoperative magnetic resonance imaging (MRI). An Institutional Review Board approved review of consecutive preoperative breast MRIs performed from 1/1/08 to 12/31/14, yielded 667 patients with breast cancer. These patients underwent further assessment to identify biopsy proven mammographically occult breast tumors located more than 2cm away from the edge of the primary tumor. Additional MRI characteristics of the primary and secondary tumors and pathology were reviewed. Statistical analysis was performed using SPSS (v. 24). Of 667 patients with breast cancer, 129 patients had 150 additional ipsilateral mammographically occult tumors that were more than 2cm away from the edge of the primary tumor. One hundred twelve of 129 (86.8%) patients had one additional tumor and 17/129 (13.2%) had two or more additional tumors. In 71/129 (55.0%), additional tumors were located in a different quadrant and in 58/129 (45.0%) additional tumors were in the same quadrant but ≥2cm away. Overall, primary tumor size was significantly larger (mean 1.87± 1.25 cm) than the additional tumors (mean 0.79 ± 0.61cm, p < 0.001). However, in 20/129 (15.5%) the additional tumor was larger and in 26/129 (20.2%) the additional tumor was ≥1cm. The primary tumor was significantly more likely to be invasive (81.4%, 105/129) compared to additional tumors (70%, 105/150, p = 0.03). In 9/129 (7.0%) patients, additional tumors yielded unsuspected invasive cancer orhigher tumor grade. The additional tumor was more likely to be nonmass lesion type (37.3% vs 24% p = 0.02) and focus lesion type (10% vs 0.08%, p < 0.001) compared to primary tumor. Mammographically occult additional tumors identified more than 2cm away from the primary breast tumor on MRI are unlikely to be surgically treated if undiagnosed and may be clinically significant. Copyright �

Kernel Density Surface Modelling as a Means to Identify Significant Concentrations of Vulnerable Marine Ecosystem Indicators

PubMed Central

Kenchington, Ellen; Murillo, Francisco Javier; Lirette, Camille; Sacau, Mar; Koen-Alonso, Mariano; Kenny, Andrew; Ollerhead, Neil; Wareham, Vonda; Beazley, Lindsay

2014-01-01

The United Nations General Assembly Resolution 61/105, concerning sustainable fisheries in the marine ecosystem, calls for the protection of vulnerable marine ecosystems (VME) from destructive fishing practices. Subsequently, the Food and Agriculture Organization (FAO) produced guidelines for identification of VME indicator species/taxa to assist in the implementation of the resolution, but recommended the development of case-specific operational definitions for their application. We applied kernel density estimation (KDE) to research vessel trawl survey data from inside the fishing footprint of the Northwest Atlantic Fisheries Organization (NAFO) Regulatory Area in the high seas of the northwest Atlantic to create biomass density surfaces for four VME indicator taxa: large-sized sponges, sea pens, small and large gorgonian corals. These VME indicator taxa were identified previously by NAFO using the fragility, life history characteristics and structural complexity criteria presented by FAO, along with an evaluation of their recovery trajectories. KDE, a non-parametric neighbour-based smoothing function, has been used previously in ecology to identify hotspots, that is, areas of relatively high biomass/abundance. We present a novel approach of examining relative changes in area under polygons created from encircling successive biomass categories on the KDE surface to identify “significant concentrations” of biomass, which we equate to VMEs. This allows identification of the VMEs from the broader distribution of the species in the study area. We provide independent assessments of the VMEs so identified using underwater images, benthic sampling with other gear types (dredges, cores), and/or published species distribution models of probability of occurrence, as available. For each VME indicator taxon we provide a brief review of their ecological function which will be important in future assessments of significant adverse impact on these habitats here and

Kernel density surface modelling as a means to identify significant concentrations of vulnerable marine ecosystem indicators.

PubMed

Kenchington, Ellen; Murillo, Francisco Javier; Lirette, Camille; Sacau, Mar; Koen-Alonso, Mariano; Kenny, Andrew; Ollerhead, Neil; Wareham, Vonda; Beazley, Lindsay

2014-01-01

The United Nations General Assembly Resolution 61/105, concerning sustainable fisheries in the marine ecosystem, calls for the protection of vulnerable marine ecosystems (VME) from destructive fishing practices. Subsequently, the Food and Agriculture Organization (FAO) produced guidelines for identification of VME indicator species/taxa to assist in the implementation of the resolution, but recommended the development of case-specific operational definitions for their application. We applied kernel density estimation (KDE) to research vessel trawl survey data from inside the fishing footprint of the Northwest Atlantic Fisheries Organization (NAFO) Regulatory Area in the high seas of the northwest Atlantic to create biomass density surfaces for four VME indicator taxa: large-sized sponges, sea pens, small and large gorgonian corals. These VME indicator taxa were identified previously by NAFO using the fragility, life history characteristics and structural complexity criteria presented by FAO, along with an evaluation of their recovery trajectories. KDE, a non-parametric neighbour-based smoothing function, has been used previously in ecology to identify hotspots, that is, areas of relatively high biomass/abundance. We present a novel approach of examining relative changes in area under polygons created from encircling successive biomass categories on the KDE surface to identify "significant concentrations" of biomass, which we equate to VMEs. This allows identification of the VMEs from the broader distribution of the species in the study area. We provide independent assessments of the VMEs so identified using underwater images, benthic sampling with other gear types (dredges, cores), and/or published species distribution models of probability of occurrence, as available. For each VME indicator taxon we provide a brief review of their ecological function which will be important in future assessments of significant adverse impact on these habitats here and elsewhere.

ORF phage display to identify cellular proteins with different functions.

PubMed

Li, Wei

2012-09-01

Open reading frame (ORF) phage display is a new branch of phage display aimed at improving its efficiency to identify cellular proteins with specific binding or functional activities. Despite the success of phage display with antibody libraries and random peptide libraries, phage display with cDNA libraries of cellular proteins identifies a high percentage of non-ORF clones encoding unnatural short peptides with minimal biological implications. This is mainly because of the uncontrollable reading frames of cellular proteins in conventional cDNA libraries. ORF phage display solves this problem by eliminating non-ORF clones to generate ORF cDNA libraries. Here I summarize the procedures of ORF phage display, discuss the factors influencing its efficiency, present examples of its versatile applications, and highlight evidence of its capability of identifying biologically relevant cellular proteins. ORF phage display coupled with different selection strategies is capable of delineating diverse functions of cellular proteins with unique advantages. Copyright © 2012 Elsevier Inc. All rights reserved.

Genome-wide association study identifies TF as a significant modifier gene of iron metabolism in HFE hemochromatosis.

PubMed

de Tayrac, Marie; Roth, Marie-Paule; Jouanolle, Anne-Marie; Coppin, Hélène; le Gac, Gérald; Piperno, Alberto; Férec, Claude; Pelucchi, Sara; Scotet, Virginie; Bardou-Jacquet, Edouard; Ropert, Martine; Bouvet, Régis; Génin, Emmanuelle; Mosser, Jean; Deugnier, Yves

2015-03-01

Hereditary hemochromatosis (HH) is the most common form of genetic iron loading disease. It is mainly related to the homozygous C282Y/C282Y mutation in the HFE gene that is, however, a necessary but not a sufficient condition to develop clinical and even biochemical HH. This suggests that modifier genes are likely involved in the expressivity of the disease. Our aim was to identify such modifier genes. We performed a genome-wide association study (GWAS) using DNA collected from 474 unrelated C282Y homozygotes. Associations were examined for both quantitative iron burden indices and clinical outcomes with 534,213 single nucleotide polymorphisms (SNP) genotypes, with replication analyses in an independent sample of 748 C282Y homozygotes from four different European centres. One SNP met genome-wide statistical significance for association with transferrin concentration (rs3811647, GWAS p value of 7×10(-9) and replication p value of 5×10(-13)). This SNP, located within intron 11 of the TF gene, had a pleiotropic effect on serum iron (GWAS p value of 4.9×10(-6) and replication p value of 3.2×10(-6)). Both serum transferrin and iron levels were associated with serum ferritin levels, amount of iron removed and global clinical stage (p<0.01). Serum iron levels were also associated with fibrosis stage (p<0.0001). This GWAS, the largest one performed so far in unselected HFE-associated HH (HFE-HH) patients, identified the rs3811647 polymorphism in the TF gene as the only SNP significantly associated with iron metabolism through serum transferrin and iron levels. Because these two outcomes were clearly associated with the biochemical and clinical expression of the disease, an indirect link between the rs3811647 polymorphism and the phenotypic presentation of HFE-HH is likely. Copyright © 2014 European Association for the Study of the Liver. Published by Elsevier B.V. All rights reserved.

Dynamic connectivity states estimated from resting fMRI Identify differences among Schizophrenia, bipolar disorder, and healthy control subjects.

PubMed

Rashid, Barnaly; Damaraju, Eswar; Pearlson, Godfrey D; Calhoun, Vince D

2014-01-01

Schizophrenia (SZ) and bipolar disorder (BP) share significant overlap in clinical symptoms, brain characteristics, and risk genes, and both are associated with dysconnectivity among large-scale brain networks. Resting state functional magnetic resonance imaging (rsfMRI) data facilitates studying macroscopic connectivity among distant brain regions. Standard approaches to identifying such connectivity include seed-based correlation and data-driven clustering methods such as independent component analysis (ICA) but typically focus on average connectivity. In this study, we utilize ICA on rsfMRI data to obtain intrinsic connectivity networks (ICNs) in cohorts of healthy controls (HCs) and age matched SZ and BP patients. Subsequently, we investigated difference in functional network connectivity, defined as pairwise correlations among the timecourses of ICNs, between HCs and patients. We quantified differences in both static (average) and dynamic (windowed) connectivity during the entire scan duration. Disease-specific differences were identified in connectivity within different dynamic states. Notably, results suggest that patients make fewer transitions to some states (states 1, 2, and 4) compared to HCs, with most such differences confined to a single state. SZ patients showed more differences from healthy subjects than did bipolars, including both hyper and hypo connectivity in one common connectivity state (dynamic state 3). Also group differences between SZ and bipolar patients were identified in patterns (states) of connectivity involving the frontal (dynamic state 1) and frontal-parietal regions (dynamic state 3). Our results provide new information about these illnesses and strongly suggest that state-based analyses are critical to avoid averaging together important factors that can help distinguish these clinical groups.

Elite Junior Australian Football Players Experience Significantly Different Loads Across Levels of Competition and Training Modes.

PubMed

Lathlean, Timothy J H; Gastin, Paul B; Newstead, Stuart; Finch, Caroline F

2018-07-01

Lathlean, TJH, Gastin, PB, Newstead, S, and Finch, CF. Elite junior Australian football players experience significantly different loads across levels of competition and training modes. J Strength Cond Res 32(7): 2031-2038, 2018-Well-developed physical qualities such as high jumping ability, running endurance, acceleration, and speed can help aspiring junior elite Australian football (AF) players transition to the Australian Football League competition. To do so, players need to experience sufficient load to enhance their physical resilience without increasing their risk of negative outcomes in terms of impaired wellness or injury. The aim of this study was to investigate the differences in load for different levels of competition and training modes across one competitive season. Elite junior AF players (n = 562, aged 17.7 ± 0.3, range: 16-18 years) were recruited from 9 teams across the under-18 state league competition in Victoria. All players recorded their training and match intensities according to the session rating of perceived exertion method. Training sessions were categorized according to skills, strength, conditioning, and other activities, whereas matches were identified according to level of competition. The loads in U18 state league matches (656.7 ± 210.9 au) were significantly higher (p = 0.027) than those in school matches (643.3 ± 260.9 au) and those in U18 representative matches (617.2 ± 175.4). Players, who undertook more than one match per week, experienced significantly less load in subsequent matches (p < 0.001). Furthermore, U18 state league training sessions carried the most load when compared with other training modes. This article highlights that different combinations of training and match involvement affect overall player load, which may predispose players to negative outcomes such as impaired wellness or increased injury risk.

A Comparison of Athletic Movement Among Talent-Identified Juniors From Different Football Codes in Australia: Implications for Talent Development.

PubMed

Woods, Carl T; Keller, Brad S; McKeown, Ian; Robertson, Sam

2016-09-01

Woods, CT, Keller, BS, McKeown, I, and Robertson, S. A comparison of athletic movement among talent-identified juniors from different football codes in Australia: implications for talent development. J Strength Cond Res 30(9): 2440-2445, 2016-This study aimed to compare the athletic movement skill of talent-identified (TID) junior Australian Rules football (ARF) and soccer players. The athletic movement skill of 17 TID junior ARF players (17.5-18.3 years) was compared against 17 TID junior soccer players (17.9-18.7 years). Players in both groups were members of an elite junior talent development program within their respective football codes. All players performed an athletic movement assessment that included an overhead squat, double lunge, single-leg Romanian deadlift (both movements performed on right and left legs), a push-up, and a chin-up. Each movement was scored across 3 essential assessment criteria using a 3-point scale. The total score for each movement (maximum of 9) and the overall total score (maximum of 63) were used as the criterion variables for analysis. A multivariate analysis of variance tested the main effect of football code (2 levels) on the criterion variables, whereas a 1-way analysis of variance identified where differences occurred. A significant effect was noted, with the TID junior ARF players outscoring their soccer counterparts when performing the overhead squat and push-up. No other criterions significantly differed according to the main effect. Practitioners should be aware that specific sporting requirements may incur slight differences in athletic movement skill among TID juniors from different football codes. However, given the low athletic movement skill noted in both football codes, developmental coaches should address the underlying movement skill capabilities of juniors when prescribing physical training in both codes.

DNA entropy reveals a significant difference in complexity between housekeeping and tissue specific gene promoters.

PubMed

Thomas, David; Finan, Chris; Newport, Melanie J; Jones, Susan

2015-10-01

The complexity of DNA can be quantified using estimates of entropy. Variation in DNA complexity is expected between the promoters of genes with different transcriptional mechanisms; namely housekeeping (HK) and tissue specific (TS). The former are transcribed constitutively to maintain general cellular functions, and the latter are transcribed in restricted tissue and cells types for specific molecular events. It is known that promoter features in the human genome are related to tissue specificity, but this has been difficult to quantify on a genomic scale. If entropy effectively quantifies DNA complexity, calculating the entropies of HK and TS gene promoters as profiles may reveal significant differences. Entropy profiles were calculated for a total dataset of 12,003 human gene promoters and for 501 housekeeping (HK) and 587 tissue specific (TS) human gene promoters. The mean profiles show the TS promoters have a significantly lower entropy (p<2.2e-16) than HK gene promoters. The entropy distributions for the 3 datasets show that promoter entropies could be used to identify novel HK genes. Functional features comprise DNA sequence patterns that are non-random and hence they have lower entropies. The lower entropy of TS gene promoters can be explained by a higher density of positive and negative regulatory elements, required for genes with complex spatial and temporary expression. Copyright © 2015 Elsevier Ltd. All rights reserved.

Human papillomavirus detection with genotyping by the cobas and Aptima assays: Significant differences in HPV 16 detection?

PubMed

Chorny, Joseph A; Frye, Teresa C; Fisher, Beth L; Remmers, Carol L

2018-03-23

The primary high-risk human papillomavirus (hrHPV) assays in the United States are the cobas (Roche) and the Aptima (Hologic). The cobas assay detects hrHPV by DNA analysis while the Aptima detects messenger RNA (mRNA) oncogenic transcripts. As the Aptima assay identifies oncogenic expression, it should have a lower rate of hrHPV and genotype detection. The Kaiser Permanente Regional Reference Laboratory in Denver, Colorado changed its hrHPV assay from the cobas to the Aptima assay. The rates of hrHPV detection and genotyping were compared over successive six-month periods. The overall hrHPV detection rates by the two platforms were similar (9.5% versus 9.1%) and not statistically different. For genotyping, the HPV 16 rate by the cobas was 1.6% and by the Aptima it was 1.1%. These differences were statistically different with the Aptima detecting nearly one-third less HPV 16 infections. With the HPV 18 and HPV 18/45, there was a slightly higher detection rate of HPV 18/45 by the Aptima platform (0.5% versus 0.9%) and this was statistically significant. While HPV 16 represents a low percentage of hrHPV infections, it was detected significantly less by the Aptima assay compared to the cobas assay. This has been previously reported, although not highlighted. Given the test methodologies, one would expect the Aptima to detect less HPV 16. This difference appears to be mainly due to a significantly increased number of non-oncogenic HPV 16 infections detected by the cobas test as there were no differences in HPV 16 detection rates in the high-grade squamous intraepithelial lesions indicating that the two tests have similar sensitivities for oncogenic HPV 16. © 2018 Wiley Periodicals, Inc.

No significant difference between chiari malformation type 1.5 and type I.

PubMed

Liu, Wei; Wu, Hongxing; Aikebaier, Yalikun; Wulabieke, Maoliti; Paerhati, Rexiti; Yang, Xiaopeng

2017-06-01

Chiari malformation Type 1.5 (CM 1.5) was defined as the association of Chiari malformation Type I (CM I) and brainstem herniation. The objective was to demonstrate the difference of clinical features and surgical outcomes between CM 1.5 and CM I. All CM 1.5 and CM I adult patients who underwent posterior fossa decompression with duraplasty at our institution between 2006 and 2010 were retrospectively reviewed. Clinical characteristics, imaging features, and long-term outcomes were compared between CM 1.5 and CM I patients. A total of 142 adult patients were enrolled, including 27 CM 1.5 and 115 CM I patients. The average follow-up period was 102 months. Age at diagnosis was significantly younger in CM 1.5 group than CM I group (p=0.039). And the degree of tonsillar herniation was significantly more severe in CM 1.5 group than CM I group (p<0.001). There was no significant difference in other clinical and imaging characteristics. Moreover, improvement of symptoms was observed in 21 CM 1.5 patients (77.8%) and 94 CM I patients (81.7%), and no significant difference was detected (p=0.637). There was no significant difference in the resolution of syringomyelia between CM 1.5 (72.7%) and CM I (76.5%) patients, either (p=0. 710). Although CM 1.5 patients presented with brainstem herniation and more severe tonsillar herniation, other clinical and imaging features and surgical outcomes were similar with CM I patients. We think CM 1.5 is just a subtype of CM I, rather than a unique type of Chiari malformations. Copyright © 2017 Elsevier B.V. All rights reserved.

Global genomic analysis of intraductal papillary mucinous neoplasms of the pancreas reveals significant molecular differences compared to ductal adenocarcinoma.

PubMed

Fritz, Stefan; Fernandez-del Castillo, Carlos; Mino-Kenudson, Mari; Crippa, Stefano; Deshpande, Vikram; Lauwers, Gregory Y; Warshaw, Andrew L; Thayer, Sarah P; Iafrate, A John

2009-03-01

To determine whether intraductal papillary mucinous neoplasms of the pancreas (IPMNs) have a different genetic background compared with ductal adenocarcinoma (PDAC). The biologic and clinical behavior of IPMNs and IPMN-associated adenocarcinomas is different from PDAC in having a less aggressive tumor growth and significantly improved survival. Up to date, the molecular mechanisms underlying the clinical behavior of IPMNs are incompletely understood. 128 cystic pancreatic lesions were prospectively identified during the course of 2 years. From the corresponding surgical specimens, 57 IPMNs were separated and subdivided by histologic criteria into those with low-grade dysplasia, moderate dysplasia, high-grade dysplasia, and invasive cancer. Twenty specimens were suitable for DNA isolation and subsequent performance of array CGH. While none of the IPMNs with low-grade dysplasia displayed detectable chromosomal aberrations, IPMNs with moderate and high-grade dysplasia showed frequent copy number alterations. Commonly lost regions were located on chromosome 5q, 6q, 10q, 11q, 13q, 18q, and 22q. The incidence of loss of chromosome 5q, 6q, and 11q was significantly higher in IPMNs with high-grade dysplasia or invasion compared with PDAC. Ten of 13 IPMNs with moderate dysplasia or malignancy had loss of part or all of chromosome 6q, with a minimal deleted region between linear positions 78.0 and 130.0. This study is the first to use array CGH to characterize IPMNs. Recurrent cytogenetic alterations were identified and were different than those described in PDAC. Array CGH may help distinguish between these 2 entities and give insight into the differences in their biology and prognosis.

Targeted Resequencing and Functional Testing Identifies Low-Frequency Missense Variants in the Gene Encoding GARP as Significant Contributors to Atopic Dermatitis Risk.

PubMed

Manz, Judith; Rodríguez, Elke; ElSharawy, Abdou; Oesau, Eva-Maria; Petersen, Britt-Sabina; Baurecht, Hansjörg; Mayr, Gabriele; Weber, Susanne; Harder, Jürgen; Reischl, Eva; Schwarz, Agatha; Novak, Natalija; Franke, Andre; Weidinger, Stephan

2016-12-01

Gene-mapping studies have consistently identified a susceptibility locus for atopic dermatitis and other inflammatory diseases on chromosome band 11q13.5, with the strongest association observed for a common variant located in an intergenic region between the two annotated genes C11orf30 and LRRC32. Using a targeted resequencing approach we identified low-frequency and rare missense mutations within the LRRC32 gene encoding the protein GARP, a receptor on activated regulatory T cells that binds latent transforming growth factor-β. Subsequent association testing in more than 2,000 atopic dermatitis patients and 2,000 control subjects showed a significant excess of these LRRC32 variants in individuals with atopic dermatitis. Structural protein modeling and bioinformatic analysis predicted a disruption of protein transport upon these variants, and overexpression assays in CD4 + CD25 - T cells showed a significant reduction in surface expression of the mutated protein. Consistently, flow cytometric (FACS) analyses of different T-cell subtypes obtained from atopic dermatitis patients showed a significantly reduced surface expression of GARP and a reduced conversion of CD4 + CD25 - T cells into regulatory T cells, along with lower expression of latency-associated protein upon stimulation in carriers of the LRRC32 A407T variant. These results link inherited disturbances of transforming growth factor-β signaling with atopic dermatitis risk. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Development of a model system to identify differences in spring and winter oat.

PubMed

Chawade, Aakash; Lindén, Pernilla; Bräutigam, Marcus; Jonsson, Rickard; Jonsson, Anders; Moritz, Thomas; Olsson, Olof

2012-01-01

Our long-term goal is to develop a Swedish winter oat (Avena sativa). To identify molecular differences that correlate with winter hardiness, a winter oat model comprising of both non-hardy spring lines and winter hardy lines is needed. To achieve this, we selected 294 oat breeding lines, originating from various Russian, German, and American winter oat breeding programs and tested them in the field in south- and western Sweden. By assaying for winter survival and agricultural properties during four consecutive seasons, we identified 14 breeding lines of different origins that not only survived the winter but also were agronomically better than the rest. Laboratory tests including electrolytic leakage, controlled crown freezing assay, expression analysis of the AsVrn1 gene and monitoring of flowering time suggested that the American lines had the highest freezing tolerance, although the German lines performed better in the field. Finally, six lines constituting the two most freezing tolerant lines, two intermediate lines and two spring cultivars were chosen to build a winter oat model system. Metabolic profiling of non-acclimated and cold acclimated leaf tissue samples isolated from the six selected lines revealed differential expression patterns of 245 metabolites including several sugars, amino acids, organic acids and 181 hitherto unknown metabolites. The expression patterns of 107 metabolites showed significant interactions with either a cultivar or a time-point. Further identification, characterisation and validation of these metabolites will lead to an increased understanding of the cold acclimation process in oats. Furthermore, by using the winter oat model system, differential sequencing of crown mRNA populations would lead to identification of various biomarkers to facilitate winter oat breeding.

Significant interarm blood pressure difference predicts cardiovascular risk in hypertensive patients

PubMed Central

Kim, Su-A; Kim, Jang Young; Park, Jeong Bae

2016-01-01

Abstract There has been a rising interest in interarm blood pressure difference (IAD), due to its relationship with peripheral arterial disease and its possible relationship with cardiovascular disease. This study aimed to characterize hypertensive patients with a significant IAD in relation to cardiovascular risk. A total of 3699 patients (mean age, 61 ± 11 years) were prospectively enrolled in the study. Blood pressure (BP) was measured simultaneously in both arms 3 times using an automated cuff-oscillometric device. IAD was defined as the absolute difference in averaged BPs between the left and right arm, and an IAD ≥ 10 mm Hg was considered to be significant. The Framingham risk score was used to calculate the 10-year cardiovascular risk. The mean systolic IAD (sIAD) was 4.3 ± 4.1 mm Hg, and 285 (7.7%) patients showed significant sIAD. Patients with significant sIAD showed larger body mass index (P < 0.001), greater systolic BP (P = 0.050), more coronary artery disease (relative risk = 1.356, P = 0.034), and more cerebrovascular disease (relative risk = 1.521, P = 0.072). The mean 10-year cardiovascular risk was 9.3 ± 7.7%. By multiple regression, sIAD was significantly but weakly correlated with the 10-year cardiovascular risk (β = 0.135, P = 0.008). Patients with significant sIAD showed a higher prevalence of coronary artery disease, as well as an increase in 10-year cardiovascular risk. Therefore, accurate measurements of sIAD may serve as a simple and cost-effective tool for predicting cardiovascular risk in clinical settings. PMID:27310982

Spore populations among bulk tank raw milk and dairy powders are significantly different.

PubMed

Miller, Rachel A; Kent, David J; Watterson, Matthew J; Boor, Kathryn J; Martin, Nicole H; Wiedmann, Martin

2015-12-01

To accommodate stringent spore limits mandated for the export of dairy powders, a more thorough understanding of the spore species present will be necessary to develop prospective strategies to identify and reduce sources (i.e., raw materials or in-plant) of contamination. We characterized 1,523 spore isolates obtained from bulk tank raw milk (n=33 farms) and samples collected from 4 different dairy powder-processing plants producing acid whey, nonfat dry milk, sweet whey, or whey protein concentrate 80. The spores isolated comprised 12 genera, at least 44 species, and 216 rpoB allelic types. Bacillus and Geobacillus represented the most commonly isolated spore genera (approximately 68.9 and 12.1%, respectively, of all spore isolates). Whereas Bacillus licheniformis was isolated from samples collected from all plants and farms, Geobacillus spp. were isolated from samples from 3 out of 4 plants and just 1 out of 33 farms. We found significant differences between the spore population isolated from bulk tank raw milk and those isolated from dairy powder plant samples, except samples from the plant producing acid whey. A comparison of spore species isolated from raw materials and finished powders showed that although certain species, such as B. licheniformis, were found in both raw and finished product samples, other species, such as Geobacillus spp. and Anoxybacillus spp., were more frequently isolated from finished powders. Importantly, we found that 8 out of 12 genera were isolated from at least 2 different spore count methods, suggesting that some spore count methods may provide redundant information if used in parallel. Together, our results suggest that (1) Bacillus and Geobacillus are the predominant spore contaminants in a variety of dairy powders, implying that future research efforts targeted at elucidating approaches to reduce levels of spores in dairy powders should focus on controlling levels of spore isolates from these genera; and (2) the spore

Identifying the ideal profile of French yogurts for different clusters of consumers.

PubMed

Masson, M; Saint-Eve, A; Delarue, J; Blumenthal, D

2016-05-01

Identifying the sensory properties that affect consumer preferences for food products is an important feature of product development. Different methods, such as external preference mapping or partial least squares regression, are used to establish relationships between sensory data and consumer preferences and to identify sensory attributes that drive consumer preferences, by highlighting optimum products. Plain French yogurts were evaluated by a sensory profiling method performed by 12 trained judges. In parallel, 180 consumers were asked to score their overall liking and complete a cognitive restraint questionnaire. After hierarchical cluster analysis on the liking scores, preference mapping using a quadratic regression model was performed. Five clusters of consumers were identified as a function of different preference patterns. Contrary to our expectations, fat levels were not discriminating. For each cluster, the results of preference mapping enabled the identification of optimum products. A comparison of the 5 sensory profiles revealed numerous differences between key sensory attributes. For example, one consumer cluster had a strong preference for products perceived as very thick, grainy, but with a less flowing texture, less sticky, whey presence and color, in contrast to other clusters. In addition, each segment of consumers was characterized according to the results of the cognitive restraint questionnaire. Copyright © 2016 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Statistical Parametric Mapping to Identify Differences between Consensus-Based Joint Patterns during Gait in Children with Cerebral Palsy.

PubMed

Nieuwenhuys, Angela; Papageorgiou, Eirini; Desloovere, Kaat; Molenaers, Guy; De Laet, Tinne

2017-01-01

Experts recently identified 49 joint motion patterns in children with cerebral palsy during a Delphi consensus study. Pattern definitions were therefore the result of subjective expert opinion. The present study aims to provide objective, quantitative data supporting the identification of these consensus-based patterns. To do so, statistical parametric mapping was used to compare the mean kinematic waveforms of 154 trials of typically developing children (n = 56) to the mean kinematic waveforms of 1719 trials of children with cerebral palsy (n = 356), which were classified following the classification rules of the Delphi study. Three hypotheses stated that: (a) joint motion patterns with 'no or minor gait deviations' (n = 11 patterns) do not differ significantly from the gait pattern of typically developing children; (b) all other pathological joint motion patterns (n = 38 patterns) differ from typically developing gait and the locations of difference within the gait cycle, highlighted by statistical parametric mapping, concur with the consensus-based classification rules. (c) all joint motion patterns at the level of each joint (n = 49 patterns) differ from each other during at least one phase of the gait cycle. Results showed that: (a) ten patterns with 'no or minor gait deviations' differed somewhat unexpectedly from typically developing gait, but these differences were generally small (≤3°); (b) all other joint motion patterns (n = 38) differed from typically developing gait and the significant locations within the gait cycle that were indicated by the statistical analyses, coincided well with the classification rules; (c) joint motion patterns at the level of each joint significantly differed from each other, apart from two sagittal plane pelvic patterns. In addition to these results, for several joints, statistical analyses indicated other significant areas during the gait cycle that were not included in the pattern definitions of the consensus study

Genome-wide significant localization for working and spatial memory: Identifying genes for psychosis using models of cognition.

PubMed

Knowles, Emma E M; Carless, Melanie A; de Almeida, Marcio A A; Curran, Joanne E; McKay, D Reese; Sprooten, Emma; Dyer, Thomas D; Göring, Harald H; Olvera, Rene; Fox, Peter; Almasy, Laura; Duggirala, Ravi; Kent, Jack W; Blangero, John; Glahn, David C

2014-01-01

It is well established that risk for developing psychosis is largely mediated by the influence of genes, but identifying precisely which genes underlie that risk has been problematic. Focusing on endophenotypes, rather than illness risk, is one solution to this problem. Impaired cognition is a well-established endophenotype of psychosis. Here we aimed to characterize the genetic architecture of cognition using phenotypically detailed models as opposed to relying on general IQ or individual neuropsychological measures. In so doing we hoped to identify genes that mediate cognitive ability, which might also contribute to psychosis risk. Hierarchical factor models of genetically clustered cognitive traits were subjected to linkage analysis followed by QTL region-specific association analyses in a sample of 1,269 Mexican American individuals from extended pedigrees. We identified four genome wide significant QTLs, two for working and two for spatial memory, and a number of plausible and interesting candidate genes. The creation of detailed models of cognition seemingly enhanced the power to detect genetic effects on cognition and provided a number of possible candidate genes for psychosis. © 2013 Wiley Periodicals, Inc.

[Clinical significance of Q-angle under different conditions in recurrent patellar dislocation].

PubMed

Wang, Zhijie; Chen, You; Li, Anping; Long, Yi

2014-01-01

To investigate the clinical significance of Q-angle measuring under different conditions in female recurrent patellar dislocation female patients. Between August 2012 and March 2013, 10 female patients (11 knees) with recurrent patellar dislocation were collected as trial group; 20 female patients (20 knees) with simple meniscus injury were collected as control group at the same time. Q-angle was measured in extension, 30 degrees flexion, 30 degrees flexion with manual correction, and surgical correction in the trial group, and only in extension and 30 degrees flexion in the control group. Then the difference value of Q-angle between extension and 30 degrees flexion (Q-angle in extension subtracts Q-angle in 30 flexion) were calculated. Independent sample t-test was used to analyze Q-angle degrees in extension, 30 degrees flexion, and the changed degrees of 2 groups. The Q-angle between manual correction and surgical correction of the trial group was analyzed by paired t-test. The Q-angle in extension, Q-angle in 30 degrees flexion, and difference value of Q-angle between extension and 30 degrees flexion were (17.2 +/- 3.6), (14.3 +/- 3.0), and (2.9 +/- 1.9) degrees in the trial group and were (15.2 +/- 3.4), (14.4 +/- 3.5), and (0.8 +/- 1.7) degrees in the control group. No significant difference was found in Q-angle of extension or Q-angle of 30 degrees flexion between 2 groups (P > 0.05), but the difference value of Q-angle between extension and 30 degrees flexion in the trial group was significantly larger than that in the control group (t = 3.253, P = 0.003). The Q-angle in 30 degrees flexion with manual correction and surgical correction in the trial group was (19.8 +/- 3.4) degrees and (18.9 +/- 3.8) degrees respectively, showing no significant difference (t = 2.193, P = 0.053). When a female patient's Q-angle in 30 degrees flexion knee changes obviously compared with Q-angle in extension position, recurrent patellar dislocation should be considered. For

Conventions of Courtship: Gender and Race Differences in the Significance of Dating Rituals

ERIC Educational Resources Information Center

Jackson, Pamela Braboy; Kleiner, Sibyl; Geist, Claudia; Cebulko, Kara

2011-01-01

Dating rituals include dating--courtship methods that are regularly enacted. This study explores gender and race differences in the relative importance placed on certain symbolic activities previously identified by the dating literature as constituting such rituals. Using information collected from a racially diverse sample of college students (N…

A quantitative telomeric chromatin isolation protocol identifies different telomeric states

NASA Astrophysics Data System (ADS)

Grolimund, Larissa; Aeby, Eric; Hamelin, Romain; Armand, Florence; Chiappe, Diego; Moniatte, Marc; Lingner, Joachim

2013-11-01

Telomere composition changes during tumourigenesis, aging and in telomere syndromes in a poorly defined manner. Here we develop a quantitative telomeric chromatin isolation protocol (QTIP) for human cells, in which chromatin is cross-linked, immunopurified and analysed by mass spectrometry. QTIP involves stable isotope labelling by amino acids in cell culture (SILAC) to compare and identify quantitative differences in telomere protein composition of cells from various states. With QTIP, we specifically enrich telomeric DNA and all shelterin components. We validate the method characterizing changes at dysfunctional telomeres, and identify and validate known, as well as novel telomere-associated polypeptides including all THO subunits, SMCHD1 and LRIF1. We apply QTIP to long and short telomeres and detect increased density of SMCHD1 and LRIF1 and increased association of the shelterins TRF1, TIN2, TPP1 and POT1 with long telomeres. Our results validate QTIP to study telomeric states during normal development and in disease.

The connectomes of males and females with autism spectrum disorder have significantly different white matter connectivity densities

PubMed Central

Irimia, Andrei; Torgerson, Carinna M.; Jacokes, Zachary J.; Van Horn, John D.

2017-01-01

Autism spectrum disorder (ASD) encompasses a set of neurodevelopmental conditions whose striking sex-related disparity (with an estimated male-to-female ratio of 4:1) remains unknown. Here we use magnetic resonance imaging (MRI) and diffusion weighted imaging (DWI) to identify the brain structure correlates of the sex-by-ASD diagnosis interaction in a carefully selected cohort of 110 ASD patients (55 females) and 83 typically-developing (TD) subjects (40 females). The interaction was found to be predicated primarily upon white matter connectivity density innervating, bilaterally, the lateral aspect of the temporal lobe, the temporo-parieto-occipital junction and the medial parietal lobe. By contrast, regional gray matter (GM) thickness and volume are not found to modulate this interaction significantly. When interpreted in the context of previous studies, our findings add considerable weight to three long-standing hypotheses according to which the sex disparity of ASD incidence is (A) due to WM connectivity rather than to GM differences, (B) modulated to a large extent by temporoparietal connectivity, and (C) accompanied by brain function differences driven by these effects. Our results contribute substantially to the task of unraveling the biological mechanisms giving rise to the sex disparity in ASD incidence, whose clinical implications are significant. PMID:28397802

Identifying cases of undiagnosed, clinically significant COPD in primary care: qualitative insight from patients in the target population

PubMed Central

Leidy, Nancy K; Kim, Katherine; Bacci, Elizabeth D; Yawn, Barbara P; Mannino, David M; Thomashow, Byron M; Barr, R Graham; Rennard, Stephen I; Houfek, Julia F; Han, Meilan K; Meldrum, Catherine A; Make, Barry J; Bowler, Russ P; Steenrod, Anna W; Murray, Lindsey T; Walsh, John W; Martinez, Fernando

2015-01-01

Background: Many cases of chronic obstructive pulmonary disease (COPD) are diagnosed only after significant loss of lung function or during exacerbations. Aims: This study is part of a multi-method approach to develop a new screening instrument for identifying undiagnosed, clinically significant COPD in primary care. Methods: Subjects with varied histories of COPD diagnosis, risk factors and history of exacerbations were recruited through five US clinics (four pulmonary, one primary care). Phase I: Eight focus groups and six telephone interviews were conducted to elicit descriptions of risk factors for COPD, recent or historical acute respiratory events, and symptoms to inform the development of candidate items for the new questionnaire. Phase II: A new cohort of subjects participated in cognitive interviews to assess and modify candidate items. Two peak expiratory flow (PEF) devices (electronic, manual) were assessed for use in screening. Results: Of 77 subjects, 50 participated in Phase I and 27 in Phase II. Six themes informed item development: exposure (smoking, second-hand smoke); health history (family history of lung problems, recurrent chest infections); recent history of respiratory events (clinic visits, hospitalisations); symptoms (respiratory, non-respiratory); impact (activity limitations); and attribution (age, obesity). PEF devices were rated easy to use; electronic values were significantly higher than manual (P<0.0001). Revisions were made to the draft items on the basis of cognitive interviews. Conclusions: Forty-eight candidate items are ready for quantitative testing to select the best, smallest set of questions that, together with PEF, can efficiently identify patients in need of diagnostic evaluation for clinically significant COPD. PMID:26028486

Statistical Parametric Mapping to Identify Differences between Consensus-Based Joint Patterns during Gait in Children with Cerebral Palsy

PubMed Central

Papageorgiou, Eirini; Desloovere, Kaat; Molenaers, Guy; De Laet, Tinne

2017-01-01

Experts recently identified 49 joint motion patterns in children with cerebral palsy during a Delphi consensus study. Pattern definitions were therefore the result of subjective expert opinion. The present study aims to provide objective, quantitative data supporting the identification of these consensus-based patterns. To do so, statistical parametric mapping was used to compare the mean kinematic waveforms of 154 trials of typically developing children (n = 56) to the mean kinematic waveforms of 1719 trials of children with cerebral palsy (n = 356), which were classified following the classification rules of the Delphi study. Three hypotheses stated that: (a) joint motion patterns with ‘no or minor gait deviations’ (n = 11 patterns) do not differ significantly from the gait pattern of typically developing children; (b) all other pathological joint motion patterns (n = 38 patterns) differ from typically developing gait and the locations of difference within the gait cycle, highlighted by statistical parametric mapping, concur with the consensus-based classification rules. (c) all joint motion patterns at the level of each joint (n = 49 patterns) differ from each other during at least one phase of the gait cycle. Results showed that: (a) ten patterns with ‘no or minor gait deviations’ differed somewhat unexpectedly from typically developing gait, but these differences were generally small (≤3°); (b) all other joint motion patterns (n = 38) differed from typically developing gait and the significant locations within the gait cycle that were indicated by the statistical analyses, coincided well with the classification rules; (c) joint motion patterns at the level of each joint significantly differed from each other, apart from two sagittal plane pelvic patterns. In addition to these results, for several joints, statistical analyses indicated other significant areas during the gait cycle that were not included in the pattern definitions of the consensus

Identifying the Culturally Different Gifted Student.

ERIC Educational Resources Information Center

Chambers, Jack A.; Barron, Frank

The study was designed to provide a relatively simple method of identifying gifted Mexican-American elementary school children, using as Ss approximately 298 Mexican-Americans (in grades 3-6) from both urban and rural schools. Ss were rated by present and former teachers on traits found to be characteristic of highly creative and talented…

Identifying the metabolic differences of a fast-growth phenotype in Synechococcus UTEX 2973

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

Mueller, Thomas J.; Ungerer, Justin L.; Pakrasi, Himadri B.

The photosynthetic capabilities of cyanobacteria make them interesting candidates for industrial bioproduction. One obstacle to large-scale implementation of cyanobacteria is their limited growth rates as compared to industrial mainstays. Synechococcus UTEX 2973, a strain closely related to Synechococcus PCC 7942, was recently identified as having the fastest measured growth rate among cyanobacteria. To facilitate the development of 2973 as a model organism we developed in this study the genome-scale metabolic model iSyu683. Experimental data were used to define CO 2 uptake rates as well as the biomass compositions for each strain. The inclusion of constraints based on experimental measurements ofmore » CO 2 uptake resulted in a ratio of the growth rates of Synechococcus 2973 to Synechococcus 7942 of 2.03, which nearly recapitulates the in vivo growth rate ratio of 2.13. This identified the difference in carbon uptake rate as the main factor contributing to the divergent growth rates. Additionally four SNPs were identified as possible contributors to modified kinetic parameters of metabolic enzymes and candidates for further study. As a result, comparisons against more established cyanobacterial strains identified a number of differences between the strains along with a correlation between the number of cytochrome c oxidase operons and heterotrophic or diazotrophic capabilities.« less

Identifying the metabolic differences of a fast-growth phenotype in Synechococcus UTEX 2973

DOE PAGES

Mueller, Thomas J.; Ungerer, Justin L.; Pakrasi, Himadri B.; ...

2017-01-31

The photosynthetic capabilities of cyanobacteria make them interesting candidates for industrial bioproduction. One obstacle to large-scale implementation of cyanobacteria is their limited growth rates as compared to industrial mainstays. Synechococcus UTEX 2973, a strain closely related to Synechococcus PCC 7942, was recently identified as having the fastest measured growth rate among cyanobacteria. To facilitate the development of 2973 as a model organism we developed in this study the genome-scale metabolic model iSyu683. Experimental data were used to define CO 2 uptake rates as well as the biomass compositions for each strain. The inclusion of constraints based on experimental measurements ofmore » CO 2 uptake resulted in a ratio of the growth rates of Synechococcus 2973 to Synechococcus 7942 of 2.03, which nearly recapitulates the in vivo growth rate ratio of 2.13. This identified the difference in carbon uptake rate as the main factor contributing to the divergent growth rates. Additionally four SNPs were identified as possible contributors to modified kinetic parameters of metabolic enzymes and candidates for further study. As a result, comparisons against more established cyanobacterial strains identified a number of differences between the strains along with a correlation between the number of cytochrome c oxidase operons and heterotrophic or diazotrophic capabilities.« less

Different Volumetric Measurement Methods for Pituitary Adenomas and Their Crucial Clinical Significance

PubMed Central

Chuang, Chi-Cheng; Lin, Shinn-Yn; Pai, Ping-Ching; Yan, Jiun-Lin; Toh, Cheng-Hong; Lee, Shih-Tseng; Wei, Kuo-Chen; Liu, Zhuo-Hao; Chen, Chung-Ming; Wang, Yu-Chi; Lee, Cheng-Chi

2017-01-01

Confirming the status of residual tumors is crucial. In stationary or spontaneous regression cases, early treatments are inappropriate. The long-used geometric calculation formula is 1/2 (length × width × height). However, it yields only rough estimates and is particularly unreliable for irregularly shaped masses. In our study, we attempted to propose a more accurate method. Between 2004 and 2014, 94 patients with pituitary tumors were enrolled in this retrospective study. All patients underwent transsphenoidal surgery and received magnetic resonance imaging (MRI). The pre- and postoperative volumes calculated using the traditional formula were termed A1 and A2, and those calculated using the proposed method were termed O1 and O2, respectively. Wilcoxon signed rank test revealed no significant difference between the A1 and O1 groups (P = 0.1810) but a significant difference between the A2 and O2 groups (P < 0.0001). Significant differences were present in the extent of resection (P < 0.0001), high-grade cavernous sinus invasion (P = 0.0312), and irregular shape (P = 0.0116). Volume is crucial in evaluating tumor status and determining treatment. Therefore, a more scientific method is especially useful when lesions are irregularly shaped or when treatment is determined exclusively based on the tumor volume. PMID:28098212

Consequential Validity Impact of Choosing Different Aptitude-Achievement Discrepancy Models in Identifying Students with Learning Disabilities.

ERIC Educational Resources Information Center

Glasnapp, Douglas R.; Poggio, John P.

This study used computer simulation to provide information on the percentage of students with learning disabilities expected to be identified under different aptitude-achievement discrepancy eligibility models and criteria and to demonstrate the consequential effects in terms of the extent to which the different models identify students of…

The significance of spatial resolution: Identifying forest cover from satellite data

Treesearch

Dumitru Salajanu; Charles E. Olson

2001-01-01

Twenty-five years ago, a National Academy of Sciences report identified species identification as a requirement if satellite data are to reach their full potential in forest inventory and monitoring; the report suggested that improving spatial resolution to 10 meters would probably be required (Committee on Remote Sensing Programs for Earth Resource Surveys [CORSPERS]...

Previously identified patellar tendinopathy risk factors differ between elite and sub-elite volleyball players.

PubMed

Janssen, I; Steele, J R; Munro, B J; Brown, N A T

2015-06-01

Patellar tendinopathy is the most common knee injury incurred in volleyball, with its prevalence in elite athletes more than three times that of their sub-elite counterparts. The purpose of this study was to determine whether patellar tendinopathy risk factors differed between elite and sub-elite male volleyball players. Nine elite and nine sub-elite male volleyball players performed a lateral stop-jump block movement. Maximum vertical jump, training history, muscle extensibility and strength, three-dimensional landing kinematics (250 Hz), along with lower limb neuromuscular activation patterns (1500 Hz), and patellar tendon loading were collected during each trial. Multivariate analyses of variance (P < 0.05) assessed for between-group differences in risk factors or patellar tendon loading. Significant interaction effects were further evaluated using post-hoc univariate analysis of variance tests. Landing kinematics, neuromuscular activation patterns, patellar tendon loading, and most of the previously identified risk factors did not differ between the elite and sub-elite players. However, elite players participated in a higher training volume and had less quadriceps extensibility than sub-elite players. Therefore, high training volume is likely the primary contributor to the injury discrepancy between elite and sub-elite volleyball players. Interventions designed to reduce landing frequency and improve quadriceps extensibility are recommended to reduce patellar tendinopathy prevalence in volleyball players. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Ethnic and Gender Differences in Identifying Gifted Students: A Multi-Cultural Analysis

ERIC Educational Resources Information Center

Sarouphim, Ketty M.; Maker, C. June

2010-01-01

The purpose of this study was to examine ethnic and gender differences in using DISCOVER, a performance-based assessment, for identifying gifted students. The sample consisted of 941 students from grades K-5 belonging to six ethnicities: White Americans, African-Americans, Hispanics, Native-Americans, South Pacific/Pacific Islanders, and Arabs.…

Association analysis of bitter receptor genes in five isolated populations identifies a significant correlation between TAS2R43 variants and coffee liking.

PubMed

Pirastu, Nicola; Kooyman, Maarten; Traglia, Michela; Robino, Antonietta; Willems, Sara M; Pistis, Giorgio; d'Adamo, Pio; Amin, Najaf; d'Eustacchio, Angela; Navarini, Luciano; Sala, Cinzia; Karssen, Lennart C; van Duijn, Cornelia; Toniolo, Daniela; Gasparini, Paolo

2014-01-01

Coffee, one of the most popular beverages in the world, contains many different physiologically active compounds with a potential impact on people's health. Despite the recent attention given to the genetic basis of its consumption, very little has been done in understanding genes influencing coffee preference among different individuals. Given its markedly bitter taste, we decided to verify if bitter receptor genes (TAS2Rs) variants affect coffee liking. In this light, 4066 people from different parts of Europe and Central Asia filled in a field questionnaire on coffee liking. They have been consequently recruited and included in the study. Eighty-eight SNPs covering the 25 TAS2R genes were selected from the available imputed ones and used to run association analysis for coffee liking. A significant association was detected with three SNP: one synonymous and two functional variants (W35S and H212R) on the TAS2R43 gene. Both variants have been shown to greatly reduce in vitro protein activity. Surprisingly the wild type allele, which corresponds to the functional form of the protein, is associated to higher liking of coffee. Since the hTAS2R43 receptor is sensible to caffeine, we verified if the detected variants produced differences in caffeine bitter perception on a subsample of people coming from the FVG cohort. We found a significant association between differences in caffeine perception and the H212R variant but not with the W35S, which suggests that the effect of the TAS2R43 gene on coffee liking is mediated by caffeine and in particular by the H212R variant. No other significant association was found with other TAS2R genes. In conclusion, the present study opens new perspectives in the understanding of coffee liking. Further studies are needed to clarify the role of the TAS2R43 gene in coffee hedonics and to identify which other genes and pathways are involved in its genetics.

Association Analysis of Bitter Receptor Genes in Five Isolated Populations Identifies a Significant Correlation between TAS2R43 Variants and Coffee Liking

PubMed Central

Pirastu, Nicola; Kooyman, Maarten; Traglia, Michela; Robino, Antonietta; Willems, Sara M.; Pistis, Giorgio; d’Adamo, Pio; Amin, Najaf; d’Eustacchio, Angela; Navarini, Luciano; Sala, Cinzia; Karssen, Lennart C.; van Duijn, Cornelia; Toniolo, Daniela; Gasparini, Paolo

2014-01-01

Coffee, one of the most popular beverages in the world, contains many different physiologically active compounds with a potential impact on people’s health. Despite the recent attention given to the genetic basis of its consumption, very little has been done in understanding genes influencing coffee preference among different individuals. Given its markedly bitter taste, we decided to verify if bitter receptor genes (TAS2Rs) variants affect coffee liking. In this light, 4066 people from different parts of Europe and Central Asia filled in a field questionnaire on coffee liking. They have been consequently recruited and included in the study. Eighty-eight SNPs covering the 25 TAS2R genes were selected from the available imputed ones and used to run association analysis for coffee liking. A significant association was detected with three SNP: one synonymous and two functional variants (W35S and H212R) on the TAS2R43 gene. Both variants have been shown to greatly reduce in vitro protein activity. Surprisingly the wild type allele, which corresponds to the functional form of the protein, is associated to higher liking of coffee. Since the hTAS2R43 receptor is sensible to caffeine, we verified if the detected variants produced differences in caffeine bitter perception on a subsample of people coming from the FVG cohort. We found a significant association between differences in caffeine perception and the H212R variant but not with the W35S, which suggests that the effect of the TAS2R43 gene on coffee liking is mediated by caffeine and in particular by the H212R variant. No other significant association was found with other TAS2R genes. In conclusion, the present study opens new perspectives in the understanding of coffee liking. Further studies are needed to clarify the role of the TAS2R43 gene in coffee hedonics and to identify which other genes and pathways are involved in its genetics. PMID:24647340

De Novo Regulatory Motif Discovery Identifies Significant Motifs in Promoters of Five Classes of Plant Dehydrin Genes.

PubMed

Zolotarov, Yevgen; Strömvik, Martina

2015-01-01

Plants accumulate dehydrins in response to osmotic stresses. Dehydrins are divided into five different classes, which are thought to be regulated in different manners. To better understand differences in transcriptional regulation of the five dehydrin classes, de novo motif discovery was performed on 350 dehydrin promoter sequences from a total of 51 plant genomes. Overrepresented motifs were identified in the promoters of five dehydrin classes. The Kn dehydrin promoters contain motifs linked with meristem specific expression, as well as motifs linked with cold/dehydration and abscisic acid response. KS dehydrin promoters contain a motif with a GATA core. SKn and YnSKn dehydrin promoters contain motifs that match elements connected with cold/dehydration, abscisic acid and light response. YnKn dehydrin promoters contain motifs that match abscisic acid and light response elements, but not cold/dehydration response elements. Conserved promoter motifs are present in the dehydrin classes and across different plant lineages, indicating that dehydrin gene regulation is likely also conserved.

QM/MM simulations identify the determinants of catalytic activity differences between type II dehydroquinase enzymes.

PubMed

Lence, Emilio; van der Kamp, Marc W; González-Bello, Concepción; Mulholland, Adrian J

2018-05-16

Type II dehydroquinase enzymes (DHQ2), recognized targets for antibiotic drug discovery, show significantly different activities dependent on the species: DHQ2 from Mycobacterium tuberculosis (MtDHQ2) and Helicobacter pylori (HpDHQ2) show a 50-fold difference in catalytic efficiency. Revealing the determinants of this activity difference is important for our understanding of biological catalysis and further offers the potential to contribute to tailoring specificity in drug design. Molecular dynamics simulations using a quantum mechanics/molecular mechanics potential, with correlated ab initio single point corrections, identify and quantify the subtle determinants of the experimentally observed difference in efficiency. The rate-determining step involves the formation of an enolate intermediate: more efficient stabilization of the enolate and transition state of the key step in MtDHQ2, mainly by the essential residues Tyr24 and Arg19, makes it more efficient than HpDHQ2. Further, a water molecule, which is absent in MtDHQ2 but involved in generation of the catalytic Tyr22 tyrosinate in HpDHQ2, was found to destabilize both the transition state and the enolate intermediate. The quantification of the contribution of key residues and water molecules in the rate-determining step of the mechanism also leads to improved understanding of higher potencies and specificity of known inhibitors, which should aid ongoing inhibitor design.

Gene Network for Identifying the Entropy Changes of Different Modules in Pediatric Sepsis.

PubMed

Yang, Jing; Zhang, Pingli; Wang, Lumin

2016-01-01

Pediatric sepsis is a disease that threatens life of children. The incidence of pediatric sepsis is higher in developing countries due to various reasons, such as insufficient immunization and nutrition, water and air pollution, etc. Exploring the potential genes via different methods is of significance for the prevention and treatment of pediatric sepsis. This study aimed to identify potential genes associated with pediatric sepsis utilizing analysis of gene network and entropy. The mRNA expression in the blood samples collected from 20 septic children and 30 healthy controls was quantified by using Affymetrix HG-U133A microarray. Two condition-specific protein-protein interaction networks (PINs), one for the healthy control and the other one for the children with sepsis, were deduced by combining the fundamental human PINs with gene expression profiles in the two phenotypes. Subsequently, distinct modules from the two conditional networks were extracted by adopting a maximal clique-merging approach. Delta entropy (ΔS) was calculated between sepsis and control modules. Then, key genes displaying changes in gene composition were identified by matching the control and sepsis modules. Two objective modules were obtained, in which ribosomal protein RPL4 and RPL9 as well as TOP2A were probably considered as the key genes differentiating sepsis from healthy controls. According to previous reports and this work, TOP2A is the potential gene therapy target for pediatric sepsis. The relationship between pediatric sepsis and RPL4 and RPL9 needs further investigation. © 2016 The Author(s) Published by S. Karger AG, Basel.

Efficiency of different techniques to identify changes in land use

NASA Astrophysics Data System (ADS)

Zornoza, Raúl; Mateix-Solera, Jorge; Gerrero, César

2013-04-01

The need for the development of sensitive and efficient methodologies for soil quality evaluation is increasing. The ability to assess soil quality and identify key soil properties that serve as indicators of soil function is complicated by the multiplicity of physical, chemical and biological factors that control soil processes. In the mountain region of the Mediterranean Basin of Spain, almond trees have been cultivated in terraced orchards for centuries. These crops are immersed in the Mediterranean forest scenery, configuring a mosaic landscape where orchards are integrated in the forest masses. In the last decades, almond orchards are being abandoned, leading to an increase in vegetation cover, since abandoned fields are naturally colonized by the surrounded natural vegetation. Soil processes and properties are expected to be associated with vegetation successional dynamics. Thus, the establishment of suitable parameters to monitor soil quality related to land use changes is particularly important to guarantee the regeneration of the mature community. In this study, we selected three land uses, constituted by forest, almond trees orchards, and orchards abandoned between 10 and 15 years previously to sampling. Sampling was carried out in four different locations in SE Spain. The main purpose was to evaluate if changes in management have significantly influenced different sets of soil characteristics. For this purpose, we used a discriminant analysis (DA). The different sets of soil characteristics tested in this study were 1: physical, chemical and biochemical properties; 2: soil near infrared (NIR) spectra; and 3: phospholipid fatty acids (PLFAs). After the DA performed with the sets 1 and 2, the three land uses were clearly separated by the two first discriminant functions, and more than 85 % of the samples were correctly classified (grouped). Using the sets 3 and 4 for DA resulted in a slightly better separation of land uses, being more than 85% of the

Significant differences in ion and electron guiding through highly insulating capillaries

NASA Astrophysics Data System (ADS)

Stolterfoht, N.; Tanis, J.

2018-04-01

Outstanding phenomena of capillary guiding are discussed in accordance with a recent review in the field. Experiments concerning highly charged ions of a few keV energy guided through insulating nanocapillaries are shown. Studies of the temporal evolution of ion transmission are presented. Attention is focused on oscillatory structures in the ion emission and the independence of the ion guiding on the beam intensity. A few experiments of electron guiding are presented showing a significantly different temporal evolution of the transmitted intensity. The onset of the electron transmission is very sudden accompanied by a considerable energy loss within the capillary. To achieve more insight into the different guiding mechanisms, theoretical aspects of the capillary guiding are analyzed. A scenario is offered to explain the abrupt rise of transmitted electrons. Altogether, these studies show that ion and electron guiding are accomplished through different manifestations of the charge build up that underlies both.

Self- and Peer-Identified Victims in Late Childhood: Differences in Perceptions of the School Ecology.

PubMed

Dawes, Molly; Chen, Chin-Chih; Farmer, Thomas W; Hamm, Jill V

2017-11-01

Patterns of adjustment for youth victimized by peers vary depending on whether youth are identified as victims through self-reports, peer-reports, or both. In order to provide more targeted strategies that may help mitigate negative consequences associated with specific victimization groups, more information is needed about how these youth perceive their school ecology (bullying and academic ecology), their feelings of school belonging, and their valuing of school. Based on the convergence of self- and peer-reports of victimization, we identified four victim groups from a sample of students in 5th grade classrooms (N = 1360; 52.8% girls, 53.1% White, 34.6% Black or Hispanic, 12.2% Native American, Asian, or other) using Latent Profile Analysis (LPA): convergent victims (high self- and peer-reports), self-identified victims (high self-, low peer-reports), peer-identified victims (low self-, high peer-reports), and nonvictims (low self- and peer-reports). Convergent victims' perceptions were similar to nonvictims with key differences being convergent victims' greater willingness to protect peers being bullied but lower feelings of school belonging compared to nonvictims. Peer-identified and self-identified victims perceived differences in the bullying and academic ecology including peer-identified victims' greater willingness to protect peers and expectations for more peers to encourage bulling against them compared to self-identified victims. However, both peer- and self-identified victims perceived greater emotional risk of participating in class and had lower feelings of school belonging compared to nonvictims. Implications for supporting youth with divergent self- and peer-reported victimization status as they transition to middle school are discussed.

Microarray analysis to identify the similarities and differences of pathogenesis between aortic occlusive disease and abdominal aortic aneurysm.

PubMed

Wang, Guofu; Bi, Lechang; Wang, Gaofeng; Huang, Feilai; Lu, Mingjing; Zhu, Kai

2018-06-01

Objectives Expression profile of GSE57691 was analyzed to identify the similarities and differences between aortic occlusive disease and abdominal aortic aneurysm. Methods The expression profile of GSE57691 was downloaded from Gene Expression Omnibus database, including 20 small abdominal aortic aneurysm samples, 29 large abdominal aortic aneurysm samples, 9 aortic occlusive disease samples, and 10 control samples. Using the limma package in R, the differentially expressed genes were screened. Followed by enrichment analysis was performed for the differentially expressed genes using database for annotation, visualization, and integrated discovery online tool. Based on string online tool and Cytoscape software, protein-protein interaction network and module analyses were carried out. Moreover, integrated TF platform database and Cytoscape software were used for constructing transcriptional regulatory networks. Results As a result, 1757, 354, and 396 differentially expressed genes separately were identified in aortic occlusive disease, large abdominal aortic aneurysm, and small abdominal aortic aneurysm samples. UBB was significantly enriched in proteolysis related pathways with a high degree in three groups. SPARCL1 was another gene shared by these groups and regulated by NFIA, which had a high degree in transcriptional regulatory network. ACTB, a significant upregulated gene in abdominal aortic aneurysm samples, could be regulated by CLIC4, which was significantly enriched in cell motions. ACLY and NFIB were separately identified in aortic occlusive disease and small abdominal aortic aneurysm samples, and separately enriched in lipid metabolism and negative regulation of cell proliferation. Conclusions The downregulated UBB, NFIA, and SPARCL1 might play key roles in both aortic occlusive disease and abdominal aortic aneurysm, while the upregulated ACTB might only involve in abdominal aortic aneurysm. ACLY and NFIB were specifically involved in aortic occlusive

Identifying behavioural differences in working donkeys in response to analgesic administration.

PubMed

Regan, F H; Hockenhull, J; Pritchard, J C; Waterman-Pearson, A E; Whay, H R

2016-01-01

To identify pain-related behaviour in working donkeys in order to assist their owners and veterinarians to recognise and manage pain. To identify general and specific behaviours associated with pain or its relief using a trial with the nonsteroidal anti-inflammatory drug meloxicam (Metacam). Observer-blinded, placebo-controlled trial. Forty adult male working donkeys with common clinical abnormalities were randomly assigned to receive either a single loading dose of meloxicam (1.2 mg/kg bwt per os; n = 20) or a placebo (30 mg honey/250 ml water per os; n = 20). Observation of postural and event behaviours was undertaken at 2 pretreatment time points followed by 4 post treatment time points, using scan (instantaneous) and focal sampling. In comparison to pretreatment baselines, donkeys receiving meloxicam were more alert post treatment than the placebo group. They were observed lying down less frequently (P = 0.007), with their eyes closed less frequently (P = 0.04) and having a high head carriage more frequently (P = 0.02). Dozing behaviour decreased after meloxicam compared with the pretreatment baseline (P = 0.03). Donkeys given meloxicam also showed more interest in their environment, turning to look at environmental stimuli more frequently (P = 0.05) than those in the placebo group post treatment. Neither the meloxicam nor the placebo group showed a significant post treatment improvement in lameness scores. Working donkeys receiving meloxicam were more active and alert compared with their pretreatment behaviour, confirming the potential value of nonsteroidal anti-inflammatory drugs in identifying behaviours indicative of pain in working donkeys. Behavioural assessment of pain in working donkeys in field clinic conditions will enable veterinary staff and owners to identify welfare issues promptly and monitor response to analgesia. The Summary is available in Chinese--see Supporting information. © 2015 EVJ Ltd.

Methodology to identify risk-significant components for inservice inspection and testing

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

Anderson, M.T.; Hartley, R.S.; Jones, J.L. Jr.

1992-08-01

Periodic inspection and testing of vital system components should be performed to ensure the safe and reliable operation of Department of Energy (DOE) nuclear processing facilities. Probabilistic techniques may be used to help identify and rank components by their relative risk. A risk-based ranking would allow varied DOE sites to implement inspection and testing programs in an effective and cost-efficient manner. This report describes a methodology that can be used to rank components, while addressing multiple risk issues.

Parallel RNAi screens across different cell lines identify generic and cell type-specific regulators of actin organization and cell morphology.

PubMed

Liu, Tao; Sims, David; Baum, Buzz

2009-01-01

In recent years RNAi screening has proven a powerful tool for dissecting gene functions in animal cells in culture. However, to date, most RNAi screens have been performed in a single cell line, and results then extrapolated across cell types and systems. Here, to dissect generic and cell type-specific mechanisms underlying cell morphology, we have performed identical kinome RNAi screens in six different Drosophila cell lines, derived from two distinct tissues of origin. This analysis identified a core set of kinases required for normal cell morphology in all lines tested, together with a number of kinases with cell type-specific functions. Most significantly, the screen identified a role for minibrain (mnb/DYRK1A), a kinase associated with Down's syndrome, in the regulation of actin-based protrusions in CNS-derived cell lines. This cell type-specific requirement was not due to the peculiarities in the morphology of CNS-derived cells and could not be attributed to differences in mnb expression. Instead, it likely reflects differences in gene expression that constitute the cell type-specific functional context in which mnb/DYRK1A acts. Using parallel RNAi screens and gene expression analyses across cell types we have identified generic and cell type-specific regulators of cell morphology, which include mnb/DYRK1A in the regulation of protrusion morphology in CNS-derived cell lines. This analysis reveals the importance of using different cell types to gain a thorough understanding of gene function across the genome and, in the case of kinases, the difficulties of using the differential gene expression to predict function.

Identifying the most significant indicators of the total road safety performance index.

PubMed

Tešić, Milan; Hermans, Elke; Lipovac, Krsto; Pešić, Dalibor

2018-04-01

The review of the national and international literature dealing with the assessment of the road safety level has shown great efforts of the authors who tried to define the methodology for calculating the composite road safety index on a territory (region, state, etc.). The procedure for obtaining a road safety composite index of an area has been largely harmonized. The question that has not been fully resolved yet concerns the selection of indicators. There is a wide range of road safety indicators used to show a road safety situation on a territory. Road safety performance index (RSPI) obtained on the basis of a larger number of safety performance indicators (SPIs) enable decision makers to more precisely define the earlier goal- oriented actions. However, recording a broader comprehensive set of SPIs helps identify the strengths and weaknesses of a country's road safety system. Providing high quality national and international databases that would include comparable SPIs seems to be difficult since a larger number of countries dispose of a small number of identical indicators available for use. Therefore, there is a need for calculating a road safety performance index with a limited number of indicators (RSPI ln n ) which will provide a comparison of a sufficient quality, of as many countries as possible. The application of the Data Envelopment Analysis (DEA) method and correlative analysis has helped to check if the RSPI ln n is likely to be of sufficient quality. A strong correlation between the RSPI ln n and the RSPI has been identified using the proposed methodology. Based on this, the most contributing indicators and methodologies for gradual monitoring of SPIs, have been defined for each country analyzed. The indicator monitoring phases in the analyzed countries have been defined in the following way: Phase 1- the indicators relating to alcohol, speed and protective systems; Phase 2- the indicators relating to roads and Phase 3- the indicators relating to

The significance of intrauterine growth restriction is different from prematurity for the outcome of infants with gastroschisis.

PubMed

Puligandla, Pramod S; Janvier, Annie; Flageole, Hélène; Bouchard, Sarah; Mok, Elise; Laberge, Jean-Martin

2004-08-01

Recent reviews of gastroschisis identify prematurity and low birth weight as predictors of morbidity and mortality. The authors compared the outcomes of intrauterine growth-restricted infants (IUGR) with gastroschisis to those without growth restriction because IUGR is different from prematurity. A retrospective analysis was performed for infants born with gastroschisis between 1990 and 2000 at 2 pediatric hospitals. Patients were segregated into 3 groups based on birth weight corrected for gestational age: group 1 (IUGR, 25th percentile). Patient demographics, method of closure, number of surgeries, presence of atresia, and time to full enteral feedings (FPO days) were assessed. Mortality rate, length of stay (LOS), and readmission rates were also compared. Analysis of variance (ANOVA)/Student's t test and Fisher's. Exact tests were used for statistical analysis (P <.05 significant). Regression analysis was also performed. One hundred thirteen patients were included (group 1 = 17; group 2 = 43; group 3 = 53). Overall, infants with IUGR had similar outcomes to non-IUGR infants, including FPO and total parenteral nutrition (TPN) days, LOS, readmission, and mortality rates. The method of closure did not affect outcome. Infants with atresia had significantly increased times to full feeding (95 v 34 days; P =.034), more surgeries (2.7 v 1.4; P =.002), and longer LOS (106 v 48 days; P =.011). Infants born at less than 37 weeks' gestation had significantly increased fasting (NPO) days (28 v 18 days; P =.005) and longer LOS (65 v 37 days; P =.006) when compared with infants born at greater than 37 weeks. Logistic regression analysis identified the presence of atresia as an independent risk factor for gastrointestinal dysfunction and the need for prolonged TPN. Prematurity also adversely affected these same parameters, although it did not reach statistical significance. Although infants with

The Ability of Different Imputation Methods to Preserve the Significant Genes and Pathways in Cancer.

PubMed

Aghdam, Rosa; Baghfalaki, Taban; Khosravi, Pegah; Saberi Ansari, Elnaz

2017-12-01

Deciphering important genes and pathways from incomplete gene expression data could facilitate a better understanding of cancer. Different imputation methods can be applied to estimate the missing values. In our study, we evaluated various imputation methods for their performance in preserving significant genes and pathways. In the first step, 5% genes are considered in random for two types of ignorable and non-ignorable missingness mechanisms with various missing rates. Next, 10 well-known imputation methods were applied to the complete datasets. The significance analysis of microarrays (SAM) method was applied to detect the significant genes in rectal and lung cancers to showcase the utility of imputation approaches in preserving significant genes. To determine the impact of different imputation methods on the identification of important genes, the chi-squared test was used to compare the proportions of overlaps between significant genes detected from original data and those detected from the imputed datasets. Additionally, the significant genes are tested for their enrichment in important pathways, using the ConsensusPathDB. Our results showed that almost all the significant genes and pathways of the original dataset can be detected in all imputed datasets, indicating that there is no significant difference in the performance of various imputation methods tested. The source code and selected datasets are available on http://profiles.bs.ipm.ir/softwares/imputation_methods/. Copyright © 2017. Production and hosting by Elsevier B.V.

Identifying different transcribed proteins in the newly described Theraphosidae Pamphobeteus verdolaga.

PubMed

Estrada-Gómez, Sebastian; Vargas-Muñoz, Leidy Johana; Saldarriaga-Córdoba, Mónica; Cifuentes, Yeimy; Perafan, Carlos

2017-04-01

Theraphosidae spider venoms are well known for possess a complex mixture of protein and non-protein compounds in their venom. The objective of this study was to report and identify different proteins translated from the venom gland DNA information of the recently described Theraphosidae spider Pamphobeteus verdolaga. Using a venom gland transcriptomic analysis, we reported a set of the first complete sequences of seven different proteins of the recenlty described Theraphosidae spider P. verdolaga. Protein analysis indicates the presence of different proteins on the venom composition of this new spider, some of them uncommon in the Theraphosidae family. MS/MS analysis of P. verdolaga showed different fragments matching sphingomyelinases (sicaritoxin), barytoxins, hexatoxins, latroinsectotoxins, and linear (zadotoxins) peptides. Only four of the MS/MS fragments showed 100% sequence similarity with one of the transcribed proteins. Transcriptomic analysis showed the presence of different groups of proteins like phospholipases, hyaluronidases, inhibitory cysteine knots (ICK) peptides among others. The three database of protein domains used in this study (Pfam, SMART and CDD) showed congruency in the search of unique conserved protein domain for only four of the translated proteins. Those proteins matched with EF-hand proteins, cysteine rich secretory proteins, jingzhaotoxins, theraphotoxins and hexatoxins, from different Mygalomorphae spiders belonging to the families Theraphosidae, Barychelidae and Hexathelidae. None of the analyzed sequences showed a complete 100% similarity. Copyright © 2017 Elsevier Ltd. All rights reserved.

Sex-role ideology among self-identified psychotherapists.

PubMed

Harper, D W; Leichner, P P; McCrimmon, E

1985-10-01

Analysis of the sex-role ideology of 1,258 self-identified psychotherapists from nine occupations indicated that: the sample was representative; as a group, self-identified psychotherapists were moderately feminist; there were significant differences among occupations; and results were not due solely to the effects of age or sex distributions among occupations.

Integrated genomic and transcriptomic analysis of human brain metastases identifies alterations of potential clinical significance.

PubMed

Saunus, Jodi M; Quinn, Michael C J; Patch, Ann-Marie; Pearson, John V; Bailey, Peter J; Nones, Katia; McCart Reed, Amy E; Miller, David; Wilson, Peter J; Al-Ejeh, Fares; Mariasegaram, Mythily; Lau, Queenie; Withers, Teresa; Jeffree, Rosalind L; Reid, Lynne E; Da Silva, Leonard; Matsika, Admire; Niland, Colleen M; Cummings, Margaret C; Bruxner, Timothy J C; Christ, Angelika N; Harliwong, Ivon; Idrisoglu, Senel; Manning, Suzanne; Nourse, Craig; Nourbakhsh, Ehsan; Wani, Shivangi; Anderson, Matthew J; Fink, J Lynn; Holmes, Oliver; Kazakoff, Stephen; Leonard, Conrad; Newell, Felicity; Taylor, Darrin; Waddell, Nick; Wood, Scott; Xu, Qinying; Kassahn, Karin S; Narayanan, Vairavan; Taib, Nur Aishah; Teo, Soo-Hwang; Chow, Yock Ping; kConFab; Jat, Parmjit S; Brandner, Sebastian; Flanagan, Adrienne M; Khanna, Kum Kum; Chenevix-Trench, Georgia; Grimmond, Sean M; Simpson, Peter T; Waddell, Nicola; Lakhani, Sunil R

2015-11-01

Treatment options for patients with brain metastases (BMs) have limited efficacy and the mortality rate is virtually 100%. Targeted therapy is critically under-utilized, and our understanding of mechanisms underpinning metastatic outgrowth in the brain is limited. To address these deficiencies, we investigated the genomic and transcriptomic landscapes of 36 BMs from breast, lung, melanoma and oesophageal cancers, using DNA copy-number analysis and exome- and RNA-sequencing. The key findings were as follows. (a) Identification of novel candidates with possible roles in BM development, including the significantly mutated genes DSC2, ST7, PIK3R1 and SMC5, and the DNA repair, ERBB-HER signalling, axon guidance and protein kinase-A signalling pathways. (b) Mutational signature analysis was applied to successfully identify the primary cancer type for two BMs with unknown origins. (c) Actionable genomic alterations were identified in 31/36 BMs (86%); in one case we retrospectively identified ERBB2 amplification representing apparent HER2 status conversion, then confirmed progressive enrichment for HER2-positivity across four consecutive metastatic deposits by IHC and SISH, resulting in the deployment of HER2-targeted therapy for the patient. (d) In the ERBB/HER pathway, ERBB2 expression correlated with ERBB3 (r(2)  = 0.496; p < 0.0001) and HER3 and HER4 were frequently activated in an independent cohort of 167 archival BM from seven primary cancer types: 57.6% and 52.6% of cases were phospho-HER3(Y1222) or phospho-HER4(Y1162) membrane-positive, respectively. The HER3 ligands NRG1/2 were barely detectable by RNAseq, with NRG1 (8p12) genomic loss in 63.6% breast cancer-BMs, suggesting a microenvironmental source of ligand. In summary, this is the first study to characterize the genomic landscapes of BM. The data revealed novel candidates, potential clinical applications for genomic profiling of resectable BMs, and highlighted the possibility of therapeutically targeting

Comparison of a video-based assessment and a multiple stimulus assessment to identify preferred jobs for individuals with significant intellectual disabilities.

PubMed

Horrocks, Erin L; Morgan, Robert L

2009-01-01

The authors compare two methods of identifying job preferences for individuals with significant intellectual disabilities. Three individuals with intellectual disabilities between the ages of 19 and 21 participated in a video-based preference assessment and a multiple stimulus without replacement (MSWO) assessment. Stimulus preference assessment procedures typically involve giving participants access to the selected stimuli to increase the probability that participants will associate the selected choice with the actual stimuli. Although individuals did not have access to the selected stimuli in the video-based assessment, results indicated that both assessments identified the same highest preference job for all participants. Results are discussed in terms of using a video-based assessment to accurately identify job preferences for individuals with developmental disabilities.

Using the 3-Sigma Limit to Identify Significantly Long Pauses during Composing.

ERIC Educational Resources Information Center

Kelly, Leonard P.; Nolan, Thomas W.

Ten deaf college freshmen and a comparison group of five hearing students participated in a study of a method to identify long pauses in written composition that have important statistical properties. Subjects first wrote two initial drafts of short stories they had viewed on video tape. Later, they revised and recopied their two originals and one…

Identifying medical students at risk of underperformance from significant stressors.

PubMed

Wilkinson, Tim J; McKenzie, Jan M; Ali, Anthony N; Rudland, Joy; Carter, Frances A; Bell, Caroline J

2016-02-02

Stress is associated with poorer academic performance but identifying vulnerable students is less clear. A series of earthquakes and disrupted learning environments created an opportunity to explore the relationships among stress, student factors, support and academic performance within a medical course. The outcomes were deviations from expected performances on end of year written and clinical examinations. The predictors were questionnaire-based measures of connectedness/support, impact of the earthquakes, safety, depression, anxiety, stress, resilience and personality. The response rate was 77%. Poorer than expected performance on all examinations was associated with greater disruptions to living arrangements and fewer years in the country; on the written examination with not having a place to study; and on the clinical examination with relationship status, not having the support of others, less extroversion, and feeling less safe. There was a suggestion of a beneficial association with some markers of stress. We show that academic performance is assisted by students having a secure physical and emotional base. The students who are most vulnerable are those with fewer social networks, and those who are recent immigrants.

Significant Adverse Events and Outcomes After Medical Abortion

PubMed Central

Cleland, Kelly; Creinin, Mitchell D.; Nucatola, Deborah; Nshom, Montsine; Trussell, James

2013-01-01

Objective To analyze rates of significant adverse events and outcomes in women having a medical abortion at Planned Parenthood health centers in 2009 and 2010, and to identify changes in the rates of adverse events and outcomes between the 2 years. Methods In this database review we analyzed data from Planned Parenthood affiliates that provided medical abortion in 2009 and 2010, almost exclusively using an evidence-based buccal misoprostol regimen. We evaluated the incidence of six clinically significant adverse events (hospital admission, blood transfusion, emergency room treatment, intravenous antibiotics administration, infection, and death) and two significant outcomes (ongoing pregnancy and ectopic pregnancy diagnosed after medical abortion treatment was initiated). We calculated an overall rate as well as rates for each event and identified changes between the 2 years. Results Amongst 233,805 medical abortions provided in 2009 and 2010, significant adverse events or outcomes were reported in 1,530 cases (0.65%). There was no statistically significant difference in overall rates between years. The most common significant outcome was ongoing intrauterine pregnancy (0.50%); significant adverse events occurred in 0.16% of cases. One patient death occurred due to an undiagnosed ectopic pregnancy. Only rates for emergency room treatment and blood transfusion differed by year, and were slightly higher in 2010. Conclusion Review of this large dataset reinforces the safety of the evidence-based medical abortion regimen. PMID:23262942

No smile like another: adult age differences in identifying emotions that accompany smiles.

PubMed

Riediger, Michaela; Studtmann, Markus; Westphal, Andrea; Rauers, Antje; Weber, Hannelore

2014-01-01

People smile in various emotional contexts, for example, when they are amused or angry or simply being polite. We investigated whether younger and older adults differ in how well they are able to identify the emotional experiences accompanying smile expressions, and whether the age of the smiling person plays a role in this respect. With this aim, we produced 80 video episodes of three types of smile expressions: positive-affect smiles had been spontaneously displayed by target persons as they were watching amusing film clips and cartoons. Negative-affect smiles had been displayed spontaneously by target persons during an interaction in which they were being unfairly accused. Affectively neutral smiles were posed upon request. Differences in the accompanying emotional experiences were validated by target persons' self-reports. These smile videos served as experimental stimuli in two studies with younger and older adult participants. In Study 1, older participants were less likely to attribute positive emotions to smiles, and more likely to assume that a smile was posed. Furthermore, younger participants were more accurate than older adults at identifying emotional experiences accompanying smiles. In Study 2, both younger and older participants attributed positive emotions more frequently to smiles shown by older as compared to younger target persons, but older participants did so less frequently than younger participants. Again, younger participants were more accurate than older participants in identifying emotional experiences accompanying smiles, but this effect was attenuated for older target persons. Older participants could better identify the emotional state accompanying smiles shown by older than by younger target persons. Taken together, these findings indicate that there is an age-related decline in the ability to decipher the emotional meaning of smiles presented without context, which, however, is attenuated when the smiling person is also an older adult.

No smile like another: adult age differences in identifying emotions that accompany smiles

PubMed Central

Riediger, Michaela; Studtmann, Markus; Westphal, Andrea; Rauers, Antje; Weber, Hannelore

2014-01-01

People smile in various emotional contexts, for example, when they are amused or angry or simply being polite. We investigated whether younger and older adults differ in how well they are able to identify the emotional experiences accompanying smile expressions, and whether the age of the smiling person plays a role in this respect. With this aim, we produced 80 video episodes of three types of smile expressions: positive-affect smiles had been spontaneously displayed by target persons as they were watching amusing film clips and cartoons. Negative-affect smiles had been displayed spontaneously by target persons during an interaction in which they were being unfairly accused. Affectively neutral smiles were posed upon request. Differences in the accompanying emotional experiences were validated by target persons' self-reports. These smile videos served as experimental stimuli in two studies with younger and older adult participants. In Study 1, older participants were less likely to attribute positive emotions to smiles, and more likely to assume that a smile was posed. Furthermore, younger participants were more accurate than older adults at identifying emotional experiences accompanying smiles. In Study 2, both younger and older participants attributed positive emotions more frequently to smiles shown by older as compared to younger target persons, but older participants did so less frequently than younger participants. Again, younger participants were more accurate than older participants in identifying emotional experiences accompanying smiles, but this effect was attenuated for older target persons. Older participants could better identify the emotional state accompanying smiles shown by older than by younger target persons. Taken together, these findings indicate that there is an age-related decline in the ability to decipher the emotional meaning of smiles presented without context, which, however, is attenuated when the smiling person is also an older adult

Age-Related Differences in Diagnostic Accuracy of Plasma GFAP and Tau For Identifying Acute Intracranial Trauma on CT: A TRACK-TBI Study.

PubMed

Gardner, Raquel C; Rubenstein, Richard; Wang, Kevin K W; Korley, Frederick Kofi; Yue, John K; Yuh, Esther Lim; Mukherjee, Pratik; Valadka, Alex; Okonkwo, David O; Diaz-Arrastia, Ramon; Manley, Geoffrey

2018-05-02

Plasma tau and glial fibrillary acidic protein (GFAP) are promising biomarkers for identifying traumatic brain injury (TBI) patients with intracranial trauma on CT. Accuracy in older adults with mild TBI (mTBI), the fastest growing TBI population, is unknown. Our aim was to assess for age-related differences in diagnostic accuracy of plasma tau and GFAP for identifying intracranial trauma on CT. Samples from 169 patients (age <40y [n=79], age 40-59y [n=60], age 60y+ [n=30]), a subset of patients from the TRACK-TBI Pilot study, who presented with mTBI (GCS 13-15), received head CT, and consented to blood-draw within 24h of injury were assayed for hyperphosphorylated-tau (P-tau), total-tau (T-tau; both via amplification-linked enhanced immunoassay using multi-arrayed fiberoptics), and GFAP (via sandwich enzyme-linked immunosorbent assay). P-tau, T-tau, P-tau:T-tau ratio, and GFAP concentration were significantly associated with CT findings. Overall, discriminative ability declined with increasing age for all assays, but this decline was only statistically significant for GFAP (area under the receiver operating characteristic curve [AUC]: old 0.73[ref] vs. young 0.93[p=0.037] or middle-aged 0.92[p<0.050]). P-tau concentration showed consistently highest diagnostic accuracy across all age-groups (AUC: old 0.84[ref] vs. young 0.95[p=0.274] or middle-aged 0.93[p=0.367]). Comparison of models including P-tau alone versus P-tau plus GFAP revealed significant added value of GFAP. In conclusion, the GFAP assay was less accurate for identifying intracranial trauma on CT among older versus younger mTBI patients. Mechanisms of this age-related difference, including role of assay methodology, specific TBI neuroanatomy, pre-existing conditions, and anti-thrombotic use warrant further study.

Identifying significant predictors of head-on conflicts on two-lane rural roads using inductive loop detectors data.

PubMed

Shariat-Mohaymany, Afshin; Tavakoli-Kashani, Ali; Nosrati, Hadi; Ranjbari, Andisheh

2011-12-01

To identify the significant factors that influence head-on conflicts resulting from dangerous overtaking maneuvers on 2-lane rural roads in Iran. A traffic conflict technique was applied to 12 two-lane rural roads in order to investigate the potential situations for accidents to occur and thus to identify the geometric and traffic factors affecting traffic conflicts. Traffic data were collected via the inductive loop detectors installed on these roads, and geometric characteristics were obtained through field observations. Two groups of data were then analyzed independently by Pearson's chi-square test to evaluate their relationship to traffic conflicts. The independent variables were percentage of time spent following (PTSF), percentage of heavy vehicles, directional distribution of traffic (DDT), mean speed, speed standard deviation, section type, road width, longitudinal slope, holiday or workday, and lighting condition. It was indicated that increasing the PTSF, decreasing the percentage of heavy vehicles, increasing the mean speed (up to 75 km/h), increasing DDT in the range of 0 to 60 percent, and decreasing the standard deviation of speed significantly increased the occurrence of traffic conflicts. It was also revealed that traffic conflicts occur more frequently on curve sections and on workdays. The variables road width, slope, and lighting condition were found to have a minor effect on conflict occurrence. To reduce the number of head-on conflicts on the aforementioned roads, some remedial measures are suggested, such as not constructing long "No Passing" zones and constructing passing lanes where necessary; keeping road width at the standard value; constructing roads with horizontal curves and a high radius and using appropriate road markings and overtaking-forbidden signs where it is impossible to modify the radius; providing enough light and installing caution signs/devices on the roads; and intensifying police control and supervision on workdays

A strategy to identify linker-based modules for the allosteric regulation of antibody-antigen binding affinities of different scFvs

PubMed Central

Thie, Holger

2017-01-01

ABSTRACT Antibody single-chain variable fragments (scFvs) are used in a variety of applications, such as for research, diagnosis and therapy. Essential for these applications is the extraordinary specificity, selectivity and affinity of antibody paratopes, which can also be used for efficient protein purification. However, this use is hampered by the high affinity for the protein to be purified because harsh elution conditions, which may impair folding, integrity or viability of the eluted biomaterials, are typically required. In this study, we developed a strategy to obtain structural elements that provide allosteric modulation of the affinities of different antibody scFvs for their antigen. To identify suitable allosteric modules, a complete set of cyclic permutations of calmodulin variants was generated and tested for modulation of the affinity when substituting the linker between VH and VL. Modulation of affinity induced by addition of different calmodulin-binding peptides at physiologic conditions was demonstrated for 5 of 6 tested scFvs of different specificities and antigens ranging from cell surface proteins to haptens. In addition, a variety of different modulator peptides were tested. Different structural solutions were found in respect of the optimal calmodulin permutation, the optimal peptide and the allosteric effect for scFvs binding to different antigen structures. Significantly, effective linker modules were identified for scFvs with both VH-VL and VL-VH architecture. The results suggest that this approach may offer a rapid, paratope-independent strategy to provide allosteric regulation of affinity for many other antibody scFvs. PMID:28055297

Biographical Narratives of Encounter: The Significance of Mobility and Emplacement in Shaping Attitudes towards Difference

PubMed Central

Sadgrove, Joanna

2014-01-01

This paper is located within work in urban studies about the significance of contact with difference as a means for reducing prejudice and achieving social change. Recent approaches, influenced by theories of affect, have emphasised non-conscious everyday negotiations of difference in the city. In this paper it is argued that such approaches lose sight of the significance of the subject: of the reflective judgements of ‘others’ made by individuals; of our ability to make decisions around the control of our feelings and identifications; and of the significance of personal pasts and collective histories in shaping the ways we perceive and react to encounters. Rather, this paper uses a biographical approach focusing on interviewees’ narratives of encounter. Through its attention to processes of mobility and emplacement, it contributes to debates about when contact with difference matters by highlighting the importance of everyday social normativities in the production of moral dispositions. PMID:26300566

Significant difference in the dynamics between strong and fragile glass formers.

PubMed

Furukawa, Akira; Tanaka, Hajime

2016-11-01

Glass-forming liquids are often classified into strong glass formers with nearly Arrhenius behavior and fragile ones with super-Arrhenius behavior. We reveal a significant difference in the dynamics between these two types of glass formers through molecular dynamics simulations: In strong glass formers, the relaxation dynamics of density fluctuations is nondiffusive, whereas in fragile glass formers it exhibits diffusive behavior. We demonstrate that this distinction is a direct consequence of the fundamental difference in the underlying elementary relaxation process between these two dynamical classes of glass formers. For fragile glass formers, a density-exchange process proceeds the density relaxation, which takes place locally at the particle level in normal states but is increasingly cooperative and nonlocal as the temperature is lowered in supercooled states. On the other hand, in strong glass formers, such an exchange process is not necessary for density relaxation due to the presence of other local relaxation channels. Our finding provides a novel insight into Angell's classification scheme from a hydrodynamic perspective.

Identifying determinants of care for tailoring implementation in chronic diseases: an evaluation of different methods.

PubMed

Krause, Jane; Van Lieshout, Jan; Klomp, Rien; Huntink, Elke; Aakhus, Eivind; Flottorp, Signe; Jaeger, Cornelia; Steinhaeuser, Jost; Godycki-Cwirko, Maciek; Kowalczyk, Anna; Agarwal, Shona; Wensing, Michel; Baker, Richard

2014-08-12

The tailoring of implementation interventions includes the identification of the determinants of, or barriers to, healthcare practice. Different methods for identifying determinants have been used in implementation projects, but which methods are most appropriate to use is unknown. The study was undertaken in five European countries, recommendations for a different chronic condition being addressed in each country: Germany (polypharmacy in multimorbid patients); the Netherlands (cardiovascular risk management); Norway (depression in the elderly); Poland (chronic obstructive pulmonary disease--COPD); and the United Kingdom (UK) (obesity). Using samples of professionals and patients in each country, three methods were compared directly: brainstorming amongst health professionals, interviews of health professionals, and interviews of patients. The additional value of discussion structured through reference to a checklist of determinants in addition to brainstorming, and determinants identified by open questions in a questionnaire survey, were investigated separately. The questionnaire, which included closed questions derived from a checklist of determinants, was administered to samples of health professionals in each country. Determinants were classified according to whether it was likely that they would inform the design of an implementation intervention (defined as plausibly important determinants). A total of 601 determinants judged to be plausibly important were identified. An additional 609 determinants were judged to be unlikely to inform an implementation intervention, and were classified as not plausibly important. Brainstorming identified 194 of the plausibly important determinants, health professional interviews 152, patient interviews 63, and open questions 48. Structured group discussion identified 144 plausibly important determinants in addition to those already identified by brainstorming. Systematic methods can lead to the identification of large

Sex differences in the significance of isolated reactive treponemal chemiluminescence immunoassay results.

PubMed

Bopage, Rohan I; Vollmer-Conna, Ute; Shand, Antonia W; Post, Jeffrey John

2018-05-01

The significance of sera with isolated reactive treponemal chemiluminescence immunoassay (IRTCIA) results is unclear. Women have this phenotype more commonly than men. Most cohorts examining this phenotype have included predominantly men and have demonstrated evidence of past or subsequently confirmed syphilis infection in a significant proportion of cases. We hypothesised that a proportion of sera with IRTCIA results would be positive on immunoblot testing and that sera from women with IRTCIA would have different results in immunoblot testing than men. IRTCIA sera from a tertiary referral serology laboratory serving multiple clinical sites were analysed with a syphilis line immunoblot assay (LIA) and analysed by sex. Logistic regression was undertaken to assess factors associated with LIA status. Medical record review and descriptive analysis of a separate cohort of women with the IRTCIA phenotype from a single campus was also undertaken. Overall, 19/63 (30.1%) subjects with the IRTCIA phenotype were positive in the LIA, including 13 men and 6 women. Women were significantly less likely to have definitive results (positive or negative) than men (p=0.015). Pregnant women were less likely than non-pregnant women to have a negative LIA result (OR 0.57; p=0.03). Record review of 22 different women with IRTCIA reactivity showed that 2/22 (9.1%) had HIV and previous syphilis infection, 15/22 (68.2%) were pregnant and 3 (13.6%) had autoimmune disease. A significant proportion of sera with IRTCIA results on serological tests are reactive on LIA testing and some may not be false positive results. The interpretation of IRTCIA results should be undertaken in conjunction with an assessment of factors such as sex, pregnancy, a history of syphilis and other STIs and syphilis risk. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Different Combinations of Perceived Autonomy Support and Control: Identifying the Most Optimal Motivating Style

ERIC Educational Resources Information Center

Haerens, L.; Vansteenkiste, M.; De Meester, A.; Delrue, J.; Tallir, I.; Vande Broek, G.; Goris, W.; Aelterman, N.

2018-01-01

Background: According to Self-Determination Theory, teachers and sport coaches can differ in the motivating style they rely upon to motivate young people. When endorsing an autonomy-supportive motivating style, instructors try to identify, vitalize, and nurture youngsters' inner motivational resources. In contrast, instructors with a dominant…

No Differences Identified in Transverse Plane Biomechanics Between Medial Pivot and Rotating Platform Total Knee Implant Designs.

PubMed

Papagiannis, Georgios I; Roumpelakis, Ilias M; Triantafyllou, Athanasios I; Makris, Ioannis N; Babis, George C

2016-08-01

Total knee arthroplasties (TKAs) using well-designed, fixed bearing prostheses, such as medial pivot (MP), have produced good long-term results. Rotating-platform, posterior-stabilized (RP-PS) mobile bearing implants were designed to decrease polyethylene wear. Sagittal and coronal plane TKA biomechanics are well examined and correlated to polyethylene wear. However, limited research findings describe this relationship in transverse plane. We assumed that although axial plane biomechanics might not be the most destructive parameters on polyethylene wear, it is important to clarify their role because both joint kinematics and kinetics in all 3 planes are important input parameters for TKA wear testing (International Organization for Standardization 14243-1 and 14343-3). Our hypothesis was that transverse plane overall range of motion (ROM) and/or peak moment show differences that reflect on wear advantages when compared RP-PS implants to MP designs. Two groups (MPs = 24 and RP-PSs = 22 subjects) were examined by using 3D gait analysis. The variables were total internal-external rotation (IER) ROM and peak IER moments. No statistically significant difference was demonstrated between the 2 groups in kinetics (P = .389) or kinematics (P = .275). In the present study, no wear advantages were found between 2 TKAs. Both designs showed identical kinetics at the transverse plane in level-ground walking. Kinematic analysis could not illustrate any statistically significant difference in terms of overall IER ROM. Nevertheless, kinematic gait pattern differences observed possibly reflect different patterns of joint surface motion or abnormal gait patterns. Thus, wear testing with various input waveforms combined with functional data analysis will be necessary to identify the actual effects of gait variability on polyethylene wear. Copyright © 2016 Elsevier Inc. All rights reserved.

49 CFR 520.5 - Guidelines for identifying major actions significantly affecting the environment.

Code of Federal Regulations, 2011 CFR

2011-10-01

... impact but which have a potential for significantly affecting the environment; (2) Any proposed action... relating to the environment; (ii) has a significantly detrimental impact on air or water quality or on... vehicles or motor vehicle equipment; and (13) Any other action that causes significant environment impact...

49 CFR 520.5 - Guidelines for identifying major actions significantly affecting the environment.

Code of Federal Regulations, 2010 CFR

2010-10-01

... significantly affecting the environment. 520.5 Section 520.5 Transportation Other Regulations Relating to... significantly affecting the environment. (a) General guidelines. The phrase, “major Federal actions significantly affecting the quality of the human environment,” as used in this part, shall be construed with a...

Differences in Alcohol Use and Alcohol-Related Problems between Transgender- and Nontransgender-identified Young Adults

PubMed Central

Coulter, Robert W.S.; Blosnich, John R.; Bukowski, Leigh A.; Herrick, A. L.; Siconolfi, Daniel E.; Stall, Ron D.

2015-01-01

Background Little is known about differences in alcohol use and alcohol-related problems between transgender- and nontransgender-identified populations. Using data from a large-scale health survey, we compare the drinking patterns and prevalence of alcohol-related problems of transgender-identified individuals to nontransgender-identified males and females. For transgender-identified people, we examine how various forms of victimization relate to heavy episodic drinking (HED). Methods Cross-sectional surveys were completed by 75,192 students aged 18–29 years attending 120 post-secondary educational institutions in the United States from 2011–2013. Self-reported measures included alcohol use, alcohol-related problems, victimization, and sociodemographics, including 3 gender-identity groups: transgender-identified individuals; nontransgender-identified males; and nontransgender-identified females. Results Compared to transgender-identified individuals, nontransgender-identified males were more likely to report HED in the past 2 weeks (relative risk=1.42; p=0.006); however, nontransgender-identified males and females reported HED on fewer days than transgender-identified people (incidence-rate ratios [IRRs] ranged from 0.28–0.43; p-values<0.001). Compared to transgender-identified people, nontransgender-identified males and females had lower odds of past-year alcohol-related sexual assault and suicidal ideation (odds ratios ranged from 0.24–0.45; p-values<0.05). Among transgender-identified people, individuals who were sexually assaulted (IRR=3.21, p=0.011) or verbally threatened (IRR=2.42, p=0.021) in the past year had greater HED days than those who did not experience those forms of victimization. Conclusions Compared to transgender-identified people, nontransgender-identified males and females: have fewer HED occasions (despite nontransgender-identified males having greater prevalence of HED); and are at lower risk for alcohol-related sexual assaults and

49 CFR 520.5 - Guidelines for identifying major actions significantly affecting the environment.

Code of Federal Regulations, 2012 CFR

2012-10-01

... indirectly result in a significant increase in the problem of solid waste, as in the disposal of motor... directly or indirectly result in a significant increase in noise levels, either within a motor vehicle's... significant increase in the energy or fuel necessary to operate a motor vehicle, including but not limited to...

49 CFR 520.5 - Guidelines for identifying major actions significantly affecting the environment.

Code of Federal Regulations, 2014 CFR

2014-10-01

... indirectly result in a significant increase in the problem of solid waste, as in the disposal of motor... directly or indirectly result in a significant increase in noise levels, either within a motor vehicle's... significant increase in the energy or fuel necessary to operate a motor vehicle, including but not limited to...

49 CFR 520.5 - Guidelines for identifying major actions significantly affecting the environment.

Code of Federal Regulations, 2013 CFR

2013-10-01

... indirectly result in a significant increase in the problem of solid waste, as in the disposal of motor... directly or indirectly result in a significant increase in noise levels, either within a motor vehicle's... significant increase in the energy or fuel necessary to operate a motor vehicle, including but not limited to...

Identifying seismic electirc signals upon significant periodic data loss. The case of Japan

NASA Astrophysics Data System (ADS)

Varotsos, P.; Skordas, E. S.; Sarlis, N. V.; Lazaridou, M. S.

2011-12-01

In many cases of geophysical interest, it happens that for substantial parts of the time of data collection, high noise prevents any attempt for extracting a useful signal. Data for such time segments are removed from further analysis. This is the case, for example, in the geoelectrical field measurements at some sites in Japan, where high noise - due mainly to leakage currents from DC driven trains - prevails almost during 70% of the 24 hour operational time. In particular, the low noise time occurs from 00:00 to 06:00 and from 22:00 to 24:00 local time (LT) when nearby DC driven trains cease service, i.e., almost only 30% of the 24 h. Thus, the question arises whether it is still possible to identify seismic electric signals [P. Varotsos and K. Alexopoulos, Tectonophysics 110 (1984) 73-98; 99-125] upon removing the noisy data segments lasting for the period 06:00 to 22:00 every day. We show that even in such a case, the identification of seismic electric signals, which are long-range correlated signals [PA Varotsos, NV Sarlis and ES Skordas, Phys. Rev. E 66 (2002), 011902], may be possible[PA Varotsos, NV Sarlis and ES Skordas, Tectonophysics 503 (2011) 189-194]. The key point is the use of the following two modern methods: The natural time analysis [PA Varotsos, NV Sarlis and ES Skordas, Natural Time Analysis: The new view of time (2011) Springer-Verlag Berlin-Heidelberg] of the remaining data and the Detrended Fluctuation Analysis (DFA). Our main conclusion states that the distinction between seismic electric signal activities (critical dynamics) and artificial noise becomes possible even after removing periodically a significant portion of the data.

Urinary metabolomics analysis identifies key biomarkers of different stages of nonalcoholic fatty liver disease

PubMed Central

Dong, Shu; Zhan, Zong-Ying; Cao, Hong-Yan; Wu, Chao; Bian, Yan-Qin; Li, Jian-Yuan; Cheng, Gen-Hong; Liu, Ping; Sun, Ming-Yu

2017-01-01

AIM To identify a panel of biomarkers that can distinguish between non-alcoholic fatty liver disease (NAFLD) and non-alcoholic steatohepatitis (NASH), and explore molecular mechanism involved in the process of developing NASH from NAFLD. METHODS Biomarkers may differ during stages of NAFLD. Urine and blood were obtained from non-diabetic subjects with NAFLD and steatosis, with normal liver function (n = 33), from patients with NASH, with abnormal liver function (n = 45), and from healthy age and sex-matched controls (n = 30). Samples were subjected to metabolomic analysis to identify potential non-invasive biomarkers. Differences in urinary metabolic profiles were analyzed using liquid chromatography tandem mass spectrometry with principal component analysis and partial least squares-discriminate analysis. RESULTS Compared with NAFLD patients, patients with NASH had abnormal liver function and high serum lipid concentrations. Urinary metabonomics found differences in 31 metabolites between these two groups, including differences in nucleic acids and amino acids. Pathway analysis based on overlapping metabolites showed that pathways of energy and amino acid metabolism, as well as the pentose phosphate pathway, were closely associated with pathological processes in NAFLD and NASH. CONCLUSION These findings suggested that a panel of biomarkers could distinguish between NAFLD and NASH, and could help to determine the molecular mechanism involved in the process of developing NASH from NAFLD. Urinary biomarkers may be diagnostic in these patients and could be used to assess responses to therapeutic interventions. PMID:28487615

Risk of Clinically Significant Prostate Cancer Associated With Prostate Imaging Reporting and Data System Category 3 (Equivocal) Lesions Identified on Multiparametric Prostate MRI.

PubMed

Sheridan, Alison D; Nath, Sameer K; Syed, Jamil S; Aneja, Sanjay; Sprenkle, Preston C; Weinreb, Jeffrey C; Spektor, Michael

2018-02-01

The objective of this study is to determine the frequency of clinically significant cancer (CSC) in Prostate Imaging Reporting and Data System (PI-RADS) category 3 (equivocal) lesions prospectively identified on multiparametric prostate MRI and to identify risk factors (RFs) for CSC that may aid in decision making. Between January 2015 and July 2016, a total of 977 consecutively seen men underwent multiparametric prostate MRI, and 342 underwent MRI-ultrasound (US) fusion targeted biopsy. A total of 474 lesions were retrospectively reviewed, and 111 were scored as PI-RADS category 3 and were visualized using a 3-T MRI scanner. Multiparametric prostate MR images were prospectively interpreted by body subspecialty radiologists trained to use PI-RADS version 2. CSC was defined as a Gleason score of at least 7 on targeted biopsy. A multivariate logistic regression model was constructed to identify the RFs associated with CSC. Of the 111 PI-RADS category 3 lesions, 81 (73.0%) were benign, 11 (9.9%) were clinically insignificant (Gleason score, 6), and 19 (17.1%) were clinically significant. On multivariate analysis, three RFs were identified as significant predictors of CSC: older patient age (odds ratio [OR], 1.13; p = 0.002), smaller prostate volume (OR, 0.94; p = 0.008), and abnormal digital rectal examination (DRE) findings (OR, 3.92; p = 0.03). For PI-RADS category 3 lesions associated with zero, one, two, or three RFs, the risk of CSC was 4%, 16%, 62%, and 100%, respectively. PI-RADS category 3 lesions for which two or more RFs were noted (e.g., age ≥ 70 years, gland size ≤ 36 mL, or abnormal DRE findings) had a CSC detection rate of 67% with a sensitivity of 53%, a specificity of 95%, a positive predictive value of 67%, and a negative predictive value of 91%. Incorporating clinical parameters into risk stratification algorithms may improve the ability to detect clinically significant disease among PI-RADS category 3 lesions and may aid in the decision to

Ethnic differences in the ability of triglyceride levels to identify insulin resistance.

PubMed

Sumner, Anne E; Cowie, Catherine C

2008-02-01

-resistant NHB, NHW and MA with TG<130mg/dL were: 64, 31 and 36. The percents of insulin-resistant NHB, NHW and MA with TG<150mg/dL were: 75, 46 and 47. The percents of insulin-resistant NHB, NHW and MA with TG<176 mg/dL were: 81, 58 and 59. Significance was P<0.001 for each comparison to NHB. In conclusion, the prevalence of syndromes that use TG as a diagnostic criterion is lower in NHB than NHW or MA. NHB are more likely than NHW or MA to be insulin-resistant and have TG levels below threshold values. As syndromes are formulated to identify individuals at high risk for conditions such as cardiovascular disease and Type 2 diabetes, ethnic differences in TG levels should be considered.

Liver stiffness identifies two different patterns of fibrosis progression in patients with hepatitis C virus recurrence after liver transplantation.

PubMed

Carrión, José A; Torres, Ferran; Crespo, Gonzalo; Miquel, Rosa; García-Valdecasas, Juan-Carlos; Navasa, Miquel; Forns, Xavier

2010-01-01

Significant liver fibrosis (F >or= 2) and portal hypertension (hepatic venous pressure gradient [HVPG] >or= 6 mmHg) at 1 year after liver transplantation (LT) identify patients with severe hepatitis C recurrence. We evaluated whether repeated liver stiffness measurements (LSM) following LT can discriminate between slow and rapid "fibrosers" (fibrosis stage F2-F4 at 1 year after LT). Eighty-four patients who had undergone LT and who were infected with hepatitis C virus (HCV) and 19 LT controls who were not infected with HCV underwent LSM at 3, 6, 9, and 12 months after LT. All HCV-infected patients underwent liver biopsy 12 months after LT (paired HVPG measurements in 74); 31 (37%) were rapid fibrosers. Median LSM (in kilopascal) at months 6, 9, and 12 were significantly higher in rapid fibrosers (9.9, 9.5, 12.1) than in slow fibrosers (6.9, 7.5, 6.6) (P < 0.01 all time points). The slope of liver stiffness progression (kPa x month) in rapid fibrosers (0.42) was significantly greater than in slow fibrosers (0.05) (P < 0.001), suggesting two different speeds of liver fibrosis progression. Figures were almost identical for patients with HVPG >or= 6 mmHg or HVPG < 6 mmHg at 1 year after LT. Multivariate analysis identified donor age, bilirubin level, and LSM as independent predictors of fibrosis progression and portal hypertension in the estimation group (n = 50) and were validated in a second group of 34 patients. The areas under the receiver operating characteristic curve that could identify rapid fibrosers and patients with portal hypertension as early as 6 months after LT were 0.83 and 0.87, respectively, in the estimation group and 0.75 and 0.80, respectively, in the validation group. Early and repeated LSM following hepatitis C recurrence in combination with clinical variables discriminates between rapid and slow fibrosers after LT.

Comparing identified and statistically significant lipids and polar metabolites in 15-year old serum and dried blood spot samples for longitudinal studies: Comparing lipids and metabolites in serum and DBS samples

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

Kyle, Jennifer E.; Casey, Cameron P.; Stratton, Kelly G.

The use of dried blood spots (DBS) has many advantages over traditional plasma and serum samples such as smaller blood volume required, storage at room temperature, and ability for sampling in remote locations. However, understanding the robustness of different analytes in DBS samples is essential, especially in older samples collected for longitudinal studies. Here we analyzed DBS samples collected in 2000-2001 and stored at room temperature and compared them to matched serum samples stored at -80°C to determine if they could be effectively used as specific time points in a longitudinal study following metabolic disease. Four hundred small molecules weremore » identified in both the serum and DBS samples using gas chromatograph-mass spectrometry (GC-MS), liquid chromatography-MS (LC-MS) and LC-ion mobility spectrometry-MS (LC-IMS-MS). The identified polar metabolites overlapped well between the sample types, though only one statistically significant polar metabolite in a case-control study was conserved, indicating degradation occurs in the DBS samples affecting quantitation. Differences in the lipid identifications indicated that some oxidation occurs in the DBS samples. However, thirty-six statistically significant lipids correlated in both sample types indicating that lipid quantitation was more stable across the sample types.« less

Metabolomic biomarkers identify differences in milk produced by Holstein cows and other minor dairy animals.

PubMed

Yang, Yongxin; Zheng, Nan; Zhao, Xiaowei; Zhang, Yangdong; Han, Rongwei; Yang, Jinhui; Zhao, Shengguo; Li, Songli; Guo, Tongjun; Zang, Changjiang; Wang, Jiaqi

2016-03-16

Several milk metabolites are associated with breeds or species of dairy animals. A better understanding of milk metabolites from different dairy animals would advance their use in evaluating milk traits and detecting milk adulteration. The objective of this study was to characterize the milk metabolite profiles of Chinese Holstein, Jersey, yak, buffalo, goat, camel, and horse and identify any differences using non-targeted metabolomic approaches. Milk samples were tested using nuclear magnetic resonance (NMR) spectroscopy and liquid chromatography-tandem mass spectrometry (LC-MS). Data were analyzed using a multivariate analysis of variance and differences in milk metabolites between Holstein and the other dairy animals were assessed using orthogonal partial least-squares discriminant analysis. Differential metabolites were identified and some metabolites, such as choline and succinic acid, were used to distinguish Holstein milk from that of the other studied animals. Metabolic pathway analysis of different metabolites revealed that glycerophospholipid metabolism as well as valine, leucine, and isoleucine biosynthesis were shared in the other ruminant animals (Jersey, buffalo, yak, and goat), and biosynthesis of unsaturated fatty acids was shared in the non-ruminant animals (camel and horse). These results can be useful for gaining a better understanding of the differences in milk synthesis between Holstein and the other dairy animals. Copyright © 2016. Published by Elsevier B.V.

Testing for significance of phase synchronisation dynamics in the EEG.

PubMed

Daly, Ian; Sweeney-Reed, Catherine M; Nasuto, Slawomir J

2013-06-01

A number of tests exist to check for statistical significance of phase synchronisation within the Electroencephalogram (EEG); however, the majority suffer from a lack of generality and applicability. They may also fail to account for temporal dynamics in the phase synchronisation, regarding synchronisation as a constant state instead of a dynamical process. Therefore, a novel test is developed for identifying the statistical significance of phase synchronisation based upon a combination of work characterising temporal dynamics of multivariate time-series and Markov modelling. We show how this method is better able to assess the significance of phase synchronisation than a range of commonly used significance tests. We also show how the method may be applied to identify and classify significantly different phase synchronisation dynamics in both univariate and multivariate datasets.

Identifying crash-prone traffic conditions under different weather on freeways.

PubMed

Xu, Chengcheng; Wang, Wei; Liu, Pan

2013-09-01

Understanding the relationships between traffic flow characteristics and crash risk under adverse weather conditions will help highway agencies develop proactive safety management strategies to improve traffic safety in adverse weather conditions. The primary objective is to develop separate crash risk prediction models for different weather conditions. The crash data, weather data, and traffic data used in this study were collected on the I-880N freeway in California in 2008 and 2010. This study considered three different weather conditions: clear weather, rainy weather, and reduced visibility weather. The preliminary analysis showed that there was some heterogeneity in the risk estimates for traffic flow characteristics by weather conditions, and that the crash risk prediction model for all weather conditions cannot capture the impacts of the traffic flow variables on crash risk under adverse weather conditions. The Bayesian random intercept logistic regression models were applied to link the likelihood of crash occurrence with various traffic flow characteristics under different weather conditions. The crash risk prediction models were compared to their corresponding logistic regression model. It was found that the random intercept model improved the goodness-of-fit of the crash risk prediction models. The model estimation results showed that the traffic flow characteristics contributing to crash risk were different across different weather conditions. The speed difference between upstream and downstream stations was found to be significant in each crash risk prediction model. Speed difference between upstream and downstream stations had the largest impact on crash risk in reduced visibility weather, followed by that in rainy weather. The ROC curves were further developed to evaluate the predictive performance of the crash risk prediction models under different weather conditions. The predictive performance of the crash risk model for clear weather was better

Prognostic significance of between-arm blood pressure differences.

PubMed

Agarwal, Rajiv; Bunaye, Zerihun; Bekele, Dagim M

2008-03-01

Blood pressure (BP) recordings often differ between arms, but the extent to which these differences are reproducible and whether the differences have prognostic importance is unknown. We enrolled 421 consecutive patients from a medicine and a renal clinic at a veterans' hospital. Three BP recordings were obtained in each arm using an oscillometric device in a sequential manner and repeated in 1 week. Patients were followed for all-cause mortality difference in systolic BP between the arms conferred a mortality hazard of 1.24 (95% CI: 1.01 to 1.52) after adjusting for average systolic BP and chronic kidney disease. BP differences between arms are reproducible and carry prognostic information. Patients should have evaluation of BP in both arms at the screening visit.

How powerful are summary-based methods for identifying expression-trait associations under different genetic architectures?

PubMed

Veturi, Yogasudha; Ritchie, Marylyn D

2018-01-01

Transcriptome-wide association studies (TWAS) have recently been employed as an approach that can draw upon the advantages of genome-wide association studies (GWAS) and gene expression studies to identify genes associated with complex traits. Unlike standard GWAS, summary level data suffices for TWAS and offers improved statistical power. Two popular TWAS methods include either (a) imputing the cis genetic component of gene expression from smaller sized studies (using multi-SNP prediction or MP) into much larger effective sample sizes afforded by GWAS - TWAS-MP or (b) using summary-based Mendelian randomization - TWAS-SMR. Although these methods have been effective at detecting functional variants, it remains unclear how extensive variability in the genetic architecture of complex traits and diseases impacts TWAS results. Our goal was to investigate the different scenarios under which these methods yielded enough power to detect significant expression-trait associations. In this study, we conducted extensive simulations based on 6000 randomly chosen, unrelated Caucasian males from Geisinger's MyCode population to compare the power to detect cis expression-trait associations (within 500 kb of a gene) using the above-described approaches. To test TWAS across varying genetic backgrounds we simulated gene expression and phenotype using different quantitative trait loci per gene and cis-expression /trait heritability under genetic models that differentiate the effect of causality from that of pleiotropy. For each gene, on a training set ranging from 100 to 1000 individuals, we either (a) estimated regression coefficients with gene expression as the response using five different methods: LASSO, elastic net, Bayesian LASSO, Bayesian spike-slab, and Bayesian ridge regression or (b) performed eQTL analysis. We then sampled with replacement 50,000, 150,000, and 300,000 individuals respectively from the testing set of the remaining 5000 individuals and conducted GWAS on each

Identifying different learning styles to enhance the learning experience.

PubMed

Anderson, Irene

2016-10-12

Identifying your preferred learning style can be a useful way to optimise learning opportunities, and can help learners to recognise their strengths and areas for development in the way that learning takes place. It can also help teachers (educators) to recognise where additional activities are required to ensure the learning experience is robust and effective. There are several models available that may be used to identify learning styles. This article discusses these models and considers their usefulness in healthcare education. Models of teaching styles are also considered.

Using benchmarking to identify inter-centre differences in persistent ductus arteriosus treatment: can we improve outcome?

PubMed

Jansen, Esther J S; Dijkman, Koen P; van Lingen, Richard A; de Vries, Willem B; Vijlbrief, Daniel C; de Boode, Willem P; Andriessen, Peter

2017-10-01

The aim of this study was to identify inter-centre differences in persistent ductus arteriosus treatment and their related outcomes. Materials and methods We carried out a retrospective, multicentre study including infants between 24+0 and 27+6 weeks of gestation in the period between 2010 and 2011. In all centres, echocardiography was used as the standard procedure to diagnose a patent ductus arteriosus and to document ductal closure. In total, 367 preterm infants were included. All four participating neonatal ICU had a comparable number of preterm infants; however, differences were observed in the incidence of treatment (33-63%), choice and dosing of medication (ibuprofen or indomethacin), number of pharmacological courses (1-4), and the need for surgical ligation after failure of pharmacological treatment (8-52%). Despite the differences in treatment, we found no difference in short-term morbidity between the centres. Adjusted mortality showed independent risk contribution of gestational age, birth weight, ductal ligation, and perinatal centre. Using benchmarking as a tool identified inter-centre differences. In these four perinatal centres, the factors that explained the differences in patent ductus arteriosus treatment are quite complex. Timing, choice of medication, and dosing are probably important determinants for successful patent ductus arteriosus closure.

Criterion Predictability: Identifying Differences Between [r-squares

ERIC Educational Resources Information Center

Malgady, Robert G.

1976-01-01

An analysis of variance procedure for testing differences in r-squared, the coefficient of determination, across independent samples is proposed and briefly discussed. The principal advantage of the procedure is to minimize Type I error for follow-up tests of pairwise differences. (Author/JKS)

Cutpoints for Low Appendicular Lean Mass That Identify Older Adults With Clinically Significant Weakness

PubMed Central

Peters, Katherine W.; Shardell, Michelle D.; McLean, Robert R.; Dam, Thuy-Tien L.; Kenny, Anne M.; Fragala, Maren S.; Harris, Tamara B.; Kiel, Douglas P.; Guralnik, Jack M.; Ferrucci, Luigi; Kritchevsky, Stephen B.; Vassileva, Maria T.; Studenski, Stephanie A.; Alley, Dawn E.

2014-01-01

Background. Low lean mass is potentially clinically important in older persons, but criteria have not been empirically validated. As part of the FNIH (Foundation for the National Institutes of Health) Sarcopenia Project, this analysis sought to identify cutpoints in lean mass by dual-energy x-ray absorptiometry that discriminate the presence or absence of weakness (defined in a previous report in the series as grip strength <26kg in men and <16kg in women). Methods. In pooled cross-sectional data stratified by sex (7,582 men and 3,688 women), classification and regression tree (CART) analysis was used to derive cutpoints for appendicular lean body mass (ALM) that best discriminated the presence or absence of weakness. Mixed-effects logistic regression was used to quantify the strength of the association between lean mass category and weakness. Results. In primary analyses, CART models identified cutpoints for low lean mass (ALM <19.75kg in men and <15.02kg in women). Sensitivity analyses using ALM divided by body mass index (BMI: ALMBMI) identified a secondary definition (ALMBMI <0.789 in men and ALMBMI <0.512 in women). As expected, after accounting for study and age, low lean mass (compared with higher lean mass) was associated with weakness by both the primary (men, odds ratio [OR]: 6.9 [95% CI: 5.4, 8.9]; women, OR: 3.6 [95% CI: 2.9, 4.3]) and secondary definitions (men, OR: 4.3 [95% CI: 3.4, 5.5]; women, OR: 2.2 [95% CI: 1.8, 2.8]). Conclusions. ALM cutpoints derived from a large, diverse sample of older adults identified lean mass thresholds below which older adults had a higher likelihood of weakness. PMID:24737559

Identifying dietary differences between Scotland and England: a rapid review of the literature.

PubMed

Chambers, Stephanie; Barton, Karen L; Albani, Viviana; Anderson, Annie S; Wrieden, Wendy L

2017-10-01

Rates of premature mortality have been higher in Scotland than in England since the 1970s. Given the known association of diet with chronic disease, the study objective was to identify and synthesise evidence on current and historical differences in food and nutrient intakes in Scotland and England. A rapid review of the peer-reviewed and grey literature was carried out. After an initial scoping search, Medline, CINAHL, Embase and Web of Science were searched. Relevant grey literature was also included. Inclusion criteria were: any date; measures of dietary intake; representative populations; cross-sectional or observational cohort studies; and English-language publications. Study quality was assessed using the Quality Assessment Tool for Observational Cohort and Cross-sectional Studies. A narrative synthesis of extracted information was conducted. Fifty publications and reports were included in the review. Results indicated that children and adults in Scotland had lower intakes of vegetables and vitamins compared with those living in England. Higher intakes of salt in Scotland were also identified. Data were limited by small Scottish samples, difficulty in finding England-level data, lack of statistical testing and adjustment for key confounders. Further investigation of adequately powered and analysed surveys is required to examine more fully dietary differences between Scotland and England. This would provide greater insight into potential causes of excess mortality in Scotland compared with England and suitable policy recommendations to address these inequalities.

Differences in handgrip strength protocols to identify sarcopenia and frailty - a systematic review.

PubMed

Sousa-Santos, A R; Amaral, T F

2017-10-16

Hand grip strength (HGS) is used for the diagnosis of sarcopenia and frailty. Several factors have been shown to influence HGS values during measurement. Therefore, variations in the protocols used to assess HGS, as part of the diagnosis of sarcopenia and frailty, may lead to the identification of different individuals with low HGS, introducing bias. The aim of this systematic review is to gather all the relevant studies that measured HGS to diagnose sarcopenia and frailty and to identify the differences between the protocols used. A systematic review was carried out following the recommendations of The Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) Statement. PubMed and Web of Science were systematically searched, until August 16, 2016. The evidence regarding HGS measurement protocols used to diagnose sarcopenia and frailty was summarised and the most recent protocols regarding the procedure were compared. From the described search 4393 articles were identified. Seventy-two studies were included in this systematic review, in which 37 referred to sarcopenia articles, 33 to frailty and two evaluated both conditions. Most studies presented limited information regarding the protocols used. The majority of the studies included did not describe a complete procedure of HGS measurement. The high heterogeneity between the protocols used, in sarcopenia and frailty studies, create an enormous difficulty in drawing comparative conclusions among them.

Violence-related Versus Terror-related Stabbings: Significant Differences in Injury Characteristics.

PubMed

Rozenfeld, Michael; Givon, Adi; Peleg, Kobi

2018-05-01

To demonstrate the gap between injury epidemiology of terror-related stabbings (TRS) and non-terror-related intentional stabbings. Terror attacks with sharp instruments have multiplied recently, with many victims of these incidents presented to hospitals with penetrating injuries. Because most practical experience of surgeons with intentional stabbing injuries comes from treating victims of interpersonal violence, potential gaps in knowledge may exist if injuries from TRS significantly differ from interpersonal stabbings (IPS). A retrospective study of 1615 patients from intentional stabbing events recorded in the Israeli National Trauma Registry during the period of "Knife Intifada" (January 2013-March 2016). All stabbings were divided into TRS and IPS. The 2 categories were compared in terms of sustained injuries, utilization of hospital resources, and clinical outcomes. TRS patients were older, comprised more females and were ethnically homogenous. Most IPS incidents happened on weekdays and at night hours, whereas TRS events peaked midweek during morning and afternoon hours. TRS patients had more injuries of head, face, and neck, and severe head and neck injuries. IPS patients had more abdomen injuries; however, respective injuries in the TRS group were more severe. Greater injury severity of the TRS patients reflected on their higher hospital resources utilization and greater in-hospital mortality. Victims of terror stabbings are profoundly different in their characteristics, sustain injuries of a different profile and greater severity, require more hospital resources, and have worse off clinical outcomes, emphasizing the need of the healthcare systems to adjust itself appropriately to deal successfully with future terror attacks.

Different approaches for identifying important concepts in probabilistic biomedical text summarization.

PubMed

Moradi, Milad; Ghadiri, Nasser

2018-01-01

Automatic text summarization tools help users in the biomedical domain to acquire their intended information from various textual resources more efficiently. Some of biomedical text summarization systems put the basis of their sentence selection approach on the frequency of concepts extracted from the input text. However, it seems that exploring other measures rather than the raw frequency for identifying valuable contents within an input document, or considering correlations existing between concepts, may be more useful for this type of summarization. In this paper, we describe a Bayesian summarization method for biomedical text documents. The Bayesian summarizer initially maps the input text to the Unified Medical Language System (UMLS) concepts; then it selects the important ones to be used as classification features. We introduce six different feature selection approaches to identify the most important concepts of the text and select the most informative contents according to the distribution of these concepts. We show that with the use of an appropriate feature selection approach, the Bayesian summarizer can improve the performance of biomedical summarization. Using the Recall-Oriented Understudy for Gisting Evaluation (ROUGE) toolkit, we perform extensive evaluations on a corpus of scientific papers in the biomedical domain. The results show that when the Bayesian summarizer utilizes the feature selection methods that do not use the raw frequency, it can outperform the biomedical summarizers that rely on the frequency of concepts, domain-independent and baseline methods. Copyright © 2017 Elsevier B.V. All rights reserved.

Discrimination of germline V genes at different sequencing lengths and mutational burdens: A new tool for identifying and evaluating the reliability of V gene assignment.

PubMed

Zhang, Bochao; Meng, Wenzhao; Prak, Eline T Luning; Hershberg, Uri

2015-12-01

Immune repertoires are collections of lymphocytes that express diverse antigen receptor gene rearrangements consisting of Variable (V), (Diversity (D) in the case of heavy chains) and Joining (J) gene segments. Clonally related cells typically share the same germline gene segments and have highly similar junctional sequences within their third complementarity determining regions. Identifying clonal relatedness of sequences is a key step in the analysis of immune repertoires. The V gene is the most important for clone identification because it has the longest sequence and the greatest number of sequence variants. However, accurate identification of a clone's germline V gene source is challenging because there is a high degree of similarity between different germline V genes. This difficulty is compounded in antibodies, which can undergo somatic hypermutation. Furthermore, high-throughput sequencing experiments often generate partial sequences and have significant error rates. To address these issues, we describe a novel method to estimate which germline V genes (or alleles) cannot be discriminated under different conditions (read lengths, sequencing errors or somatic hypermutation frequencies). Starting with any set of germline V genes, this method measures their similarity using different sequencing lengths and calculates their likelihood of unambiguous assignment under different levels of mutation. Hence, one can identify, under different experimental and biological conditions, the germline V genes (or alleles) that cannot be uniquely identified and bundle them together into groups of specific V genes with highly similar sequences. Copyright © 2015 Elsevier B.V. All rights reserved.

Different Ecological Niches for Ticks of Public Health Significance in Canada

PubMed Central

Gabriele-Rivet, Vanessa; Arsenault, Julie; Badcock, Jacqueline; Cheng, Angela; Edsall, Jim; Goltz, Jim; Kennedy, Joe; Lindsay, L. Robbin; Pelcat, Yann; Ogden, Nicholas H.

2015-01-01

Tick-borne diseases are a growing public health concern as their incidence and range have increased in recent decades. Lyme disease is an emerging infectious disease in Canada due to northward expansion of the geographic range of Ixodes scapularis, the principal tick vector for the Lyme disease agent Borrelia burgdorferi, into central and eastern Canada. In this study the geographical distributions of Ixodid ticks, including I. scapularis, and environmental factors associated with their occurrence were investigated in New Brunswick, Canada, where few I. scapularis populations have been found to date. Density of host-seeking ticks was evaluated by drag sampling of woodland habitats in a total of 159 sites. Ixodes scapularis ticks (n = 5) were found on four sites, Ixodes muris (n = 1) on one site and Haemaphysalis leporispalustris (n = 243) on 41 sites. One of four adult I. scapularis ticks collected was PCR-positive for B. burgdorferi. No environmental variables were significantly associated with the presence of I. scapularis although comparisons with surveillance data in neighbouring provinces (Québec and Nova Scotia) suggested that temperature conditions may be too cold for I. scapularis (< 2800 annual degree days above 0°C [DD > 0°C]) across much of New Brunswick. In contrast, the presence of H. leporispalustris, which is a competent vector of tularaemia, was significantly (P < 0.05) associated with specific ranges of mean DD > 0°C, mean annual precipitation, percentage of clay in site soil, elevation and season in a multivariable logistic regression model. With the exception of some localized areas, temperature conditions and deer density may be too low for the establishment of I. scapularis and Lyme disease risk areas in New Brunswick, while environmental conditions were suitable for H. leporispalustris at many sites. These findings indicate differing ecological niches for two tick species of public health significance. PMID:26131550

Different Ecological Niches for Ticks of Public Health Significance in Canada.

PubMed

Gabriele-Rivet, Vanessa; Arsenault, Julie; Badcock, Jacqueline; Cheng, Angela; Edsall, Jim; Goltz, Jim; Kennedy, Joe; Lindsay, L Robbin; Pelcat, Yann; Ogden, Nicholas H

2015-01-01

Tick-borne diseases are a growing public health concern as their incidence and range have increased in recent decades. Lyme disease is an emerging infectious disease in Canada due to northward expansion of the geographic range of Ixodes scapularis, the principal tick vector for the Lyme disease agent Borrelia burgdorferi, into central and eastern Canada. In this study the geographical distributions of Ixodid ticks, including I. scapularis, and environmental factors associated with their occurrence were investigated in New Brunswick, Canada, where few I. scapularis populations have been found to date. Density of host-seeking ticks was evaluated by drag sampling of woodland habitats in a total of 159 sites. Ixodes scapularis ticks (n = 5) were found on four sites, Ixodes muris (n = 1) on one site and Haemaphysalis leporispalustris (n = 243) on 41 sites. One of four adult I. scapularis ticks collected was PCR-positive for B. burgdorferi. No environmental variables were significantly associated with the presence of I. scapularis although comparisons with surveillance data in neighbouring provinces (Québec and Nova Scotia) suggested that temperature conditions may be too cold for I. scapularis (< 2800 annual degree days above 0°C [DD > 0°C]) across much of New Brunswick. In contrast, the presence of H. leporispalustris, which is a competent vector of tularaemia, was significantly (P < 0.05) associated with specific ranges of mean DD > 0°C, mean annual precipitation, percentage of clay in site soil, elevation and season in a multivariable logistic regression model. With the exception of some localized areas, temperature conditions and deer density may be too low for the establishment of I. scapularis and Lyme disease risk areas in New Brunswick, while environmental conditions were suitable for H. leporispalustris at many sites. These findings indicate differing ecological niches for two tick species of public health significance.

Nonsphericity Index and Size Ratio Identify Morphologic Differences between Growing and Stable Aneurysms in a Longitudinal Study of 93 Cases.

PubMed

Chien, A; Xu, M; Yokota, H; Scalzo, F; Morimoto, E; Salamon, N

2018-01-25

Recent studies have strongly associated intracranial aneurysm growth with increased risk of rupture. Identifying aneurysms that are likely to grow would be beneficial to plan more effective monitoring and intervention strategies. Our hypothesis is that for unruptured intracranial aneurysms of similar size, morphologic characteristics differ between aneurysms that continue to grow and those that do not. From aneurysms in our medical center with follow-up imaging dates in 2015, ninety-three intracranial aneurysms (23 growing, 70 stable) were selected. All CTA images for the aneurysm diagnosis and follow-up were collected, a total of 348 3D imaging studies. Aneurysm 3D geometry for each imaging study was reconstructed, and morphologic characteristics, including volume, surface area, nonsphericity index, aspect ratio, and size ratio were calculated. Morphologic characteristics were found to differ between growing and stable groups. For aneurysms of <3 mm, nonsphericity index ( P < .001); 3-5 mm, nonsphericity index ( P < .001); 5-7 mm, size ratio ( P = .003); >7 mm, volume ( P < .001); surface area ( P < .001); and nonsphericity index ( P = .002) were significant. Within the anterior communicating artery, the nonsphericity index ( P = .008) and, within the posterior communicating artery, size ratio ( P = .004) were significant. The nonsphericity index receiver operating characteristic area under the curve was 0.721 for discriminating growing and stable cases on the basis of initial images. Among aneurysms with similar sizes, morphologic characteristics appear to differ between those that are growing and those that are stable. The nonsphericity index, in particular, was found to be higher among growing aneurysms. The size ratio was found to be the second most significant parameter associated with growth. © 2018 by American Journal of Neuroradiology.

Advance to and Persistence in Graduate School: Identifying the Influential Factors and Major-Based Differences

ERIC Educational Resources Information Center

Xu, Yonghong Jade

2014-01-01

Structured within an expanded econometric theoretical framework, this study uses national data sources to identify the critical factors that influence college graduates' advance to and persistence in graduate education and to compare the systematic differences between students in the STEM and non-STEM majors. The findings indicate that there is a…

A large-scale RNA interference screen identifies genes that regulate autophagy at different stages.

PubMed

Guo, Sujuan; Pridham, Kevin J; Virbasius, Ching-Man; He, Bin; Zhang, Liqing; Varmark, Hanne; Green, Michael R; Sheng, Zhi

2018-02-12

Dysregulated autophagy is central to the pathogenesis and therapeutic development of cancer. However, how autophagy is regulated in cancer is not well understood and genes that modulate cancer autophagy are not fully defined. To gain more insights into autophagy regulation in cancer, we performed a large-scale RNA interference screen in K562 human chronic myeloid leukemia cells using monodansylcadaverine staining, an autophagy-detecting approach equivalent to immunoblotting of the autophagy marker LC3B or fluorescence microscopy of GFP-LC3B. By coupling monodansylcadaverine staining with fluorescence-activated cell sorting, we successfully isolated autophagic K562 cells where we identified 336 short hairpin RNAs. After candidate validation using Cyto-ID fluorescence spectrophotometry, LC3B immunoblotting, and quantitative RT-PCR, 82 genes were identified as autophagy-regulating genes. 20 genes have been reported previously and the remaining 62 candidates are novel autophagy mediators. Bioinformatic analyses revealed that most candidate genes were involved in molecular pathways regulating autophagy, rather than directly participating in the autophagy process. Further autophagy flux assays revealed that 57 autophagy-regulating genes suppressed autophagy initiation, whereas 21 candidates promoted autophagy maturation. Our RNA interference screen identifies identified genes that regulate autophagy at different stages, which helps decode autophagy regulation in cancer and offers novel avenues to develop autophagy-related therapies for cancer.

Significant interarm blood pressure difference predicts cardiovascular risk in hypertensive patients: CoCoNet study.

PubMed

Kim, Su-A; Kim, Jang Young; Park, Jeong Bae

2016-06-01

There has been a rising interest in interarm blood pressure difference (IAD), due to its relationship with peripheral arterial disease and its possible relationship with cardiovascular disease. This study aimed to characterize hypertensive patients with a significant IAD in relation to cardiovascular risk. A total of 3699 patients (mean age, 61 ± 11 years) were prospectively enrolled in the study. Blood pressure (BP) was measured simultaneously in both arms 3 times using an automated cuff-oscillometric device. IAD was defined as the absolute difference in averaged BPs between the left and right arm, and an IAD ≥ 10 mm Hg was considered to be significant. The Framingham risk score was used to calculate the 10-year cardiovascular risk. The mean systolic IAD (sIAD) was 4.3 ± 4.1 mm Hg, and 285 (7.7%) patients showed significant sIAD. Patients with significant sIAD showed larger body mass index (P < 0.001), greater systolic BP (P = 0.050), more coronary artery disease (relative risk = 1.356, P = 0.034), and more cerebrovascular disease (relative risk = 1.521, P = 0.072). The mean 10-year cardiovascular risk was 9.3 ± 7.7%. By multiple regression, sIAD was significantly but weakly correlated with the 10-year cardiovascular risk (β = 0.135, P = 0.008). Patients with significant sIAD showed a higher prevalence of coronary artery disease, as well as an increase in 10-year cardiovascular risk. Therefore, accurate measurements of sIAD may serve as a simple and cost-effective tool for predicting cardiovascular risk in clinical settings.

[Expression of ATAD2 in different liver lesions and its clinical significance].

PubMed

Liu, F; Zhou, X; Ji, H H; Li, H; Xiang, F G

2017-05-20

Objective: To examine the expression of ATAD2 in different liver lesions and its clinical significance. Methods: ATAD2 expression in 60 hepatocellular carcinoma (HCC) surgical specimens (49 of which have concurrent liver cirrhosis), 43 HCC biopsy specimens, 2 high-grade liver dysplastic nodule specimens, 3 low-grade liver dysplastic nodule specimens, 50 liver cirrhosis tissue samples, and 20 normal liver tissue samples were measured using immunohistochemistry. The F-test, q-test, t-test, and chi-square test were used for statistical analysis of data. Results: ATAD2 was expressed in 56 HCC surgical specimens (93.33%), 35 HCC biopsy specimens (81.40%), and 2 high-grade liver dysplastic nodule specimens (2/2), but not in the low-grade liver dysplastic nodule, liver cirrhosis tissue, and normal liver tissue samples. The mean expression of ATAD2 was significantly higher in HCC tissues than in high-grade and low-grade liver dysplastic nodule tissues, liver cirrhosis tissue, and normal liver tissue ( F = 22.96, q = 3.138, 3.972, 12.272, and 9.101, respectively, all P < 0.01). There were no significant differences in the mean expression and positive expression rate of ATAD2 between HCC surgical and biopsy specimens ( t = 1.40, P > 0.05; χ ² = 3.47, P >0.05). Of the 35 HCC biopsy specimens that expressed ATAD2, the mean ATAD2 expression was ≥1% in 35 specimens (100%), ≥3% in 27 specimens (77.14%), and ≥5 % in 23 specimens (65.71%). In addition, among the pathological grade I-II HCC biopsy specimens, the mean ATAD2 expression was ≥1% in 28 specimens (100%), ≥3% in 22 specimens (62.86%), and ≥5% in 19 specimens (54.29%). Moreover, ATAD2 expression in HCC was associated with serum alpha-fetoprotein level, presence of hepatitis B virus surface antigen (HBsAg), and presence of concurrent liver cirrhosis ( t = 2.09, 2.30, and 2.18, respectively, all P < 0.05). Conclusion: ATAD2 may play an important role in HCC tumorigenesis, and may be involved in malignant

Increased frequency of retinopathy of prematurity over the last decade and significant regional differences.

PubMed

Holmström, Gerd; Tornqvist, Kristina; Al-Hawasi, Abbas; Nilsson, Åsa; Wallin, Agneta; Hellström, Ann

2018-03-01

Retinopathy of prematurity (ROP) causes childhood blindness globally in prematurely born infants. Although increased levels of oxygen supply lead to increased survival and reduced frequency of cerebral palsy, increased incidence of ROP is reported. With the help of a Swedish register for ROP, SWEDROP, national and regional incidences of ROP and frequencies of treatment were evaluated from 2008 to 2015 (n = 5734), as well as before and after targets of provided oxygen changed from 85-89% to 91-95% in 2014. Retinopathy of prematurity (ROP) was found in 31.9% (1829/5734) of all infants with a gestational age (GA) of <31 weeks at birth and 5.7% of the infants (329/5734) had been treated for ROP. Analyses of the national data revealed an increased incidence of ROP during the 8-year study period (p = 0.003), but there was no significant increase in the frequency of treatment. There were significant differences between the seven health regions of Sweden, regarding both incidence of ROP and frequency of treatment (p < 0.001). Comparison of regional data before and after the new oxygen targets revealed a significant increase in treated ROP in one region [OR: 2.24 (CI: 1.11-4.49), p = 0.024] and a borderline increase in one other [OR: 3.08 (CI: 0.99-9.60), p = 0.052]. The Swedish national ROP register revealed an increased incidence of ROP during an 8-year period and significant regional differences regarding the incidence of ROP and frequency of treatment. © 2017 Acta Ophthalmologica Scandinavica Foundation. Published by John Wiley & Sons Ltd.

Poly-victimization from different methodological approaches using the juvenile victimization questionnaire: Are we identifying the same victims?

PubMed

Segura, Anna; Pereda, Noemí; Guilera, Georgina

2018-01-01

This study aims to determine whether three different methodological approaches used to assess poly-victimization that apply the Juvenile Victimization Questionnaire (JVQ; Finkelhor, Hamby, Ormrod, & Turner, 2005) identify the same group of adolescent poly-victims. The sample consisted of 1,105 adolescents (590 males and 515 females), aged 12-17 years old (M = 14.52, SD = 1.76) and recruited from seven secondary schools in Spain. The JVQ was used to assess lifetime and past-year experiences of victimization. Poly-victims were more likely to experience all types of victimization than victims, regardless of the method used. The degree of agreement between the methods for identifying poly-victimization was moderate for both timeframes, with the highest agreements being recorded between the one-above-the-mean number of victimizations and Latent Class Analysis (LCA) for lifetime, and between the top 10% and LCA for past-year victimization. Researchers and clinicians should be aware that the use of different methods to define poly-victimization may mean that different victims are identified. The choice of one method or another may have important implications. In consequence, focusing on how we operationalize poly-victimization should be a priority in the near future.

Gender differences and regionalization of the cultural significance of wild mushrooms around La Malinche volcano, Tlaxcala, Mexico.

PubMed

Montoya, A; Torres-García, E A; Kong, A; Estrada-Torres, A; Caballero, J

2012-01-01

The purpose of this study was to determine the cultural significance of wild mushrooms in 10 communities on the slopes of La Malinche volcano, Tlaxcala. The frequency and order of mention of each mushroom species in interviews of 200 individuals were used as indicators of the relative cultural significance of each species. A X(2) analysis was used to compare the frequency of mention of each species between males and females, and a Mann-Whitney U test was used to compare the difference in the total number of fungi mentioned by either gender. Traditional names for mushroom species were documented and frequency of mention assessed through multivariate statistics. The fungi with highest frequency of mention were Amanita basii, Lyophyllum decastes, Boletus pinophilus, Gomphus floccosus and Cantharellus cibarius complex. We found significant differences in the frequency of mention of different fungi by males and females but no significant difference was found for the total number of fungi mentioned by either gender. Principal component analysis suggested a cultural regionalization of La Malinche volcano communities based on preferences for consumption and use of traditional names. We observed two groups: one formed by communities on the eastern part of the volcano (with mixed cultures) and the other including communities on the western slope (ethnic Nahua towns). San Isidro Buensuceso is the most distinct community, according to the criteria in this study.

Full investigation of patients with polycystic ovary syndrome (PCOS) presenting to four different clinical specialties reveals significant differences and undiagnosed morbidity.

PubMed

Sivayoganathan, Dhakshana; Maruthini, Deivanayagam; Glanville, Julie M; Balen, Adam H

2011-12-01

This study aimed to compare the spectrum of polycystic ovary syndrome (PCOS) symptoms in patients from four different specialist clinics. A prospective cross-sectional observational study. The study was conducted at the infertility, gynaecology, endocrine and dermatology clinics at Leeds General Infirmary, U.K. Seventy women presenting with features of PCOS: 20 from infertility, 17 from gynaecology, 17 from dermatology and 16 from endocrine clinics. Participants were assessed for symptoms and signs of PCOS and underwent a full endocrine and metabolic profile and a pelvic ultrasound scan. All subjects had experienced menstrual problems, 81% were overweight, 86% had polycystic ovaries on ultrasound, 56% had hirsutism, 53% had acne, 23% had acanthosis nigricans, 16% had alopecia and 38% had previously undiagnosed impaired glucose tolerance (IGT) or diabetes. A significant difference between the four clinic groups existed with regard to menstrual patterns (p = 0.0234), frequency distribution of presenting symptoms and the percentages of patients with PCOS who had already been diagnosed as having PCOS (p = 0.0088). This study emphasizes the importance of understanding the full spectrum of PCOS as presented to different specialty clinics. Not only is the syndrome under diagnosed but also are the significant associated morbidities such as IGT and type 2 diabetes. Different specialists need to appreciate the spectrum of health problems for women with PCOS that may extend beyond the specific symptoms that precipitated the initial referral.

Imaging Flow Cytometry Analysis to Identify Differences of Survival Motor Neuron Protein Expression in Patients With Spinal Muscular Atrophy.

PubMed

Arakawa, Reiko; Arakawa, Masayuki; Kaneko, Kaori; Otsuki, Noriko; Aoki, Ryoko; Saito, Kayoko

2016-08-01

Spinal muscular atrophy is a neurodegenerative disorder caused by the deficient expression of survival motor neuron protein in motor neurons. A major goal of disease-modifying therapy is to increase survival motor neuron expression. Changes in survival motor neuron protein expression can be monitored via peripheral blood cells in patients; therefore we tested the sensitivity and utility of imaging flow cytometry for this purpose. After the immortalization of peripheral blood lymphocytes from a human healthy control subject and two patients with spinal muscular atrophy type 1 with two and three copies of SMN2 gene, respectively, we used imaging flow cytometry analysis to identify significant differences in survival motor neuron expression. A bright detail intensity analysis was used to investigate differences in the cellular localization of survival motor neuron protein. Survival motor neuron expression was significantly decreased in cells derived from patients with spinal muscular atrophy relative to those derived from a healthy control subject. Moreover, survival motor neuron expression correlated with the clinical severity of spinal muscular atrophy according to SMN2 copy number. The cellular accumulation of survival motor neuron protein was also significantly decreased in cells derived from patients with spinal muscular atrophy relative to those derived from a healthy control subject. The benefits of imaging flow cytometry for peripheral blood analysis include its capacities for analyzing heterogeneous cell populations; visualizing cell morphology; and evaluating the accumulation, localization, and expression of a target protein. Imaging flow cytometry analysis should be implemented in future studies to optimize its application as a tool for spinal muscular atrophy clinical trials. Copyright © 2016 Elsevier Inc. All rights reserved.

Onset dynamics of action potentials in rat neocortical neurons and identified snail neurons: quantification of the difference.

PubMed

Volgushev, Maxim; Malyshev, Aleksey; Balaban, Pavel; Chistiakova, Marina; Volgushev, Stanislav; Wolf, Fred

2008-04-09

The generation of action potentials (APs) is a key process in the operation of nerve cells and the communication between neurons. Action potentials in mammalian central neurons are characterized by an exceptionally fast onset dynamics, which differs from the typically slow and gradual onset dynamics seen in identified snail neurons. Here we describe a novel method of analysis which provides a quantitative measure of the onset dynamics of action potentials. This method captures the difference between the fast, step-like onset of APs in rat neocortical neurons and the gradual, exponential-like AP onset in identified snail neurons. The quantitative measure of the AP onset dynamics, provided by the method, allows us to perform quantitative analyses of factors influencing the dynamics.

Onset Dynamics of Action Potentials in Rat Neocortical Neurons and Identified Snail Neurons: Quantification of the Difference

PubMed Central

Volgushev, Maxim; Malyshev, Aleksey; Balaban, Pavel; Chistiakova, Marina; Volgushev, Stanislav; Wolf, Fred

2008-01-01

The generation of action potentials (APs) is a key process in the operation of nerve cells and the communication between neurons. Action potentials in mammalian central neurons are characterized by an exceptionally fast onset dynamics, which differs from the typically slow and gradual onset dynamics seen in identified snail neurons. Here we describe a novel method of analysis which provides a quantitative measure of the onset dynamics of action potentials. This method captures the difference between the fast, step-like onset of APs in rat neocortical neurons and the gradual, exponential-like AP onset in identified snail neurons. The quantitative measure of the AP onset dynamics, provided by the method, allows us to perform quantitative analyses of factors influencing the dynamics. PMID:18398478

The significance of Antarctica for studies of global geodynamics

USGS Publications Warehouse

Sutherland, R.

2007-01-01

Antarctica has geometric significance for global plate kinematic studies, because it links seafloor spreading systems of the African hemisphere (Indian and Atlantic Oceans) with those of the Pacific. Inferences of plate motions back to 44 Ma, around the onset of rapid spreading south of Australia and formation of a new boundary through New Zealand, are consistent with Antarctic rifting and formation of the Adare Basin during 44-26 Ma (i.e., no additional plate motions are required in the South Pacific). The time period 52-44 Ma represents a profound global and South Pacific tectonic change, and significant details remain unresolved. For 74 Ma a significant nonclosure of the South Pacific plate-motion circuit is identified if Antarctic motion is not included. Alternate inferences of motion through Antarctica during the interval 74-44 Ma imply significantly different subduction volumes and directions around the Pacific, and imply different relative motions between hotspots

Identifying significant genetic regulatory networks in the prostate cancer from microarray data based on transcription factor analysis and conditional independency.

PubMed

Yeh, Hsiang-Yuan; Cheng, Shih-Wu; Lin, Yu-Chun; Yeh, Cheng-Yu; Lin, Shih-Fang; Soo, Von-Wun

2009-12-21

Prostate cancer is a world wide leading cancer and it is characterized by its aggressive metastasis. According to the clinical heterogeneity, prostate cancer displays different stages and grades related to the aggressive metastasis disease. Although numerous studies used microarray analysis and traditional clustering method to identify the individual genes during the disease processes, the important gene regulations remain unclear. We present a computational method for inferring genetic regulatory networks from micorarray data automatically with transcription factor analysis and conditional independence testing to explore the potential significant gene regulatory networks that are correlated with cancer, tumor grade and stage in the prostate cancer. To deal with missing values in microarray data, we used a K-nearest-neighbors (KNN) algorithm to determine the precise expression values. We applied web services technology to wrap the bioinformatics toolkits and databases to automatically extract the promoter regions of DNA sequences and predicted the transcription factors that regulate the gene expressions. We adopt the microarray datasets consists of 62 primary tumors, 41 normal prostate tissues from Stanford Microarray Database (SMD) as a target dataset to evaluate our method. The predicted results showed that the possible biomarker genes related to cancer and denoted the androgen functions and processes may be in the development of the prostate cancer and promote the cell death in cell cycle. Our predicted results showed that sub-networks of genes SREBF1, STAT6 and PBX1 are strongly related to a high extent while ETS transcription factors ELK1, JUN and EGR2 are related to a low extent. Gene SLC22A3 may explain clinically the differentiation associated with the high grade cancer compared with low grade cancer. Enhancer of Zeste Homolg 2 (EZH2) regulated by RUNX1 and STAT3 is correlated to the pathological stage. We provide a computational framework to reconstruct

Identifying significant genetic regulatory networks in the prostate cancer from microarray data based on transcription factor analysis and conditional independency

PubMed Central

2009-01-01

Background Prostate cancer is a world wide leading cancer and it is characterized by its aggressive metastasis. According to the clinical heterogeneity, prostate cancer displays different stages and grades related to the aggressive metastasis disease. Although numerous studies used microarray analysis and traditional clustering method to identify the individual genes during the disease processes, the important gene regulations remain unclear. We present a computational method for inferring genetic regulatory networks from micorarray data automatically with transcription factor analysis and conditional independence testing to explore the potential significant gene regulatory networks that are correlated with cancer, tumor grade and stage in the prostate cancer. Results To deal with missing values in microarray data, we used a K-nearest-neighbors (KNN) algorithm to determine the precise expression values. We applied web services technology to wrap the bioinformatics toolkits and databases to automatically extract the promoter regions of DNA sequences and predicted the transcription factors that regulate the gene expressions. We adopt the microarray datasets consists of 62 primary tumors, 41 normal prostate tissues from Stanford Microarray Database (SMD) as a target dataset to evaluate our method. The predicted results showed that the possible biomarker genes related to cancer and denoted the androgen functions and processes may be in the development of the prostate cancer and promote the cell death in cell cycle. Our predicted results showed that sub-networks of genes SREBF1, STAT6 and PBX1 are strongly related to a high extent while ETS transcription factors ELK1, JUN and EGR2 are related to a low extent. Gene SLC22A3 may explain clinically the differentiation associated with the high grade cancer compared with low grade cancer. Enhancer of Zeste Homolg 2 (EZH2) regulated by RUNX1 and STAT3 is correlated to the pathological stage. Conclusions We provide a

Using the Bootstrap Method for a Statistical Significance Test of Differences between Summary Histograms

NASA Technical Reports Server (NTRS)

Xu, Kuan-Man

2006-01-01

A new method is proposed to compare statistical differences between summary histograms, which are the histograms summed over a large ensemble of individual histograms. It consists of choosing a distance statistic for measuring the difference between summary histograms and using a bootstrap procedure to calculate the statistical significance level. Bootstrapping is an approach to statistical inference that makes few assumptions about the underlying probability distribution that describes the data. Three distance statistics are compared in this study. They are the Euclidean distance, the Jeffries-Matusita distance and the Kuiper distance. The data used in testing the bootstrap method are satellite measurements of cloud systems called cloud objects. Each cloud object is defined as a contiguous region/patch composed of individual footprints or fields of view. A histogram of measured values over footprints is generated for each parameter of each cloud object and then summary histograms are accumulated over all individual histograms in a given cloud-object size category. The results of statistical hypothesis tests using all three distances as test statistics are generally similar, indicating the validity of the proposed method. The Euclidean distance is determined to be most suitable after comparing the statistical tests of several parameters with distinct probability distributions among three cloud-object size categories. Impacts on the statistical significance levels resulting from differences in the total lengths of satellite footprint data between two size categories are also discussed.

Significant Coronary Stenosis in Asymptomatic Chinese With Different Glycemic Status

PubMed Central

Xu, Yu; Bi, Yufang; Li, Mian; Wang, Tiange; Sun, Kun; Xu, Min; Lu, Jieli; Yu, Yi; Li, Xiaoying; Lai, Shenghan; Wang, Weiqing; Ning, Guang

2013-01-01

OBJECTIVE To evaluate coronary artery stenosis in early diabetes or prediabetes asymptomatic of myocardial ischemia in community-dwelling Chinese adults. RESEARCH DESIGN AND METHODS Age- and sex-matched participants with normal glucose regulation (NGR), prediabetes, or diabetes diagnosed within 5 years, asymptomatic of coronary artery disease (CAD), were randomly selected from a community-dwelling Chinese population aged 40–60 years. Dual-source computed tomography coronary angiography was used to evaluate the existence and extent of coronary stenosis, which was considered significant if >50% narrowing of vessel lumen was detected. RESULTS After excluding uninterpretable segments attributable to motion artifacts, a total of 135 participants with NGR, 132 with prediabetes, and 134 with diabetes participated in data analysis. Significant coronary stenosis was detected in 10 (7.4%), 10 (7.6%), and 22 (16.4%) individuals with NGR, prediabetes, and diabetes, respectively (P for trend = 0.029). Diabetes, rather than prediabetes, was associated with a significant 2.34-fold elevated risk [odds ratio (OR) 2.34 (95% CI 1.01–5.43); P = 0.047] of significant coronary stenosis as compared with that associated with NGR. Levels of glucose evaluation were independently and significantly associated with risks of significant coronary stenosis in diabetes. Each 1-SD increase in fasting plasma glucose, 2-h postload plasma glucose, and HbA1c conveyed 2.11-fold, 1.73-fold, and 1.81-fold higher risks of significant coronary stenosis, respectively, after adjustment for other conventional cardiovascular risk factors. CONCLUSIONS Using a noninvasive CAD diagnostic modality such as dual-source computed tomography coronary angiography, we detected a markedly elevated risk of significant coronary stenosis with early diabetes in asymptomatic Chinese adults. PMID:23462666

Clinically significant and practical! Enhancing precision does make a difference. Reply to McGlinchey and Jacobson, Hsu, and Speer.

PubMed

Hageman, W J; Arrindell, W A

1999-12-01

Based on a secondary analysis of the Jacobson and Truax [Jacobson, N.S. & Truax, P. (1991). a statistical approach to defining meaningful change in psychotherapy research. Journal of Consulting and Clinical Psychology, 59, 12-19.] data using both their own traditional approach and the refined method advanced by Hageman and Arrindell [Hageman, W.J.J.M., & Arrindell, W.A. (1999). Establishing clinically significant change: increment of precision and the distinction between individual and group level of analysis. Behaviour Research and Therapy, 37, 1169-1193], McGlinchey and Jacobson [McGlinchey, J. B., & Jacobson, N. S. (1999). Clinically significant but impractical? A response to Hageman and Arrindell. Behaviour Research and Therapy, 37, 1211-1217.] reported practically identical findings on reliable and clinically significant change across the two approaches. This led McGlinchey and Jacobson to conclude that there is little practical gain in utilizing the refined method over the traditional approach. Close inspection of the data used by McGlinchey and Jacobson however revealed a serious mistake with respect to the value of the standard error of measurement that was employed in their calculations. When the proper index value was utilised, further re-analysis by the present authors disclosed clear differences (i.e. different classifications of S's) across the two approaches. Importantly, these differences followed exactly the same pattern as depicted in Table 2 in Hageman and Arrindell (1999). The theoretical advantages of the refined method, i.e. enhanced precision, appropriate distinction between analysis at the individual and group levels, and maximal comparability of findings across studies, exceed those of the traditional method. Application of the refined method may be carried out within approximately half an hour, which not only supports its practical manageability, but also challenges the suggestion of McGlinchey and Jacobson (1999) that the relevant method

Identifying Differences between Depressed Adolescent Suicide Ideators and Attempters

PubMed Central

Auerbach, Randy P.; Millner, Alexander J.; Stewart, Jeremy G.; Esposito, Erika

2015-01-01

Background Adolescent depression and suicide are pressing public health concerns, and identifying key differences among suicide ideators and attempters is critical. The goal of the current study is to test whether depressed adolescent suicide attempters report greater anhedonia severity and exhibit aberrant effort-cost computations in the face of uncertainty. Methods Depressed adolescents (n = 101) ages 13–19 years were administered structured clinical interviews to assess current mental health disorders and a history of suicidality (suicide ideators = 55, suicide attempters = 46). Then, participants completed self-report instruments assessing symptoms of suicidal ideation, depression, anhedonia, and anxiety as well as a computerized effort-cost computation task. Results Compared with depressed adolescent suicide ideators, attempters report greater anhedonia severity, even after concurrently controlling for symptoms of suicidal ideation, depression, and anxiety. Additionally, when completing the effort-cost computation task, suicide attempters are less likely to pursue the difficult, high value option when outcomes are uncertain. Follow-up, trial-level analyses of effort-cost computations suggest that receipt of reward does not influence future decision-making among suicide attempters, however, suicide ideators exhibit a win-stay approach when receiving rewards on previous trials. Limitations Findings should be considered in light of limitations including a modest sample size, which limits generalizability, and the cross-sectional design. Conclusions Depressed adolescent suicide attempters are characterized by greater anhedonia severity, which may impair the ability to integrate previous rewarding experiences to inform future decisions. Taken together, this may generate a feeling of powerlessness that contributes to increased suicidality and a needless loss of life. PMID:26233323

Significant events in psychotherapy: An update of research findings.

PubMed

Timulak, Ladislav

2010-11-01

Significant events research represents a specific approach to studying client-identified important moments in the therapy process. The current study provides an overview of the significant events research conducted, the methodology used together with findings and implications. PsychInfo database was searched with keywords such as significant events, important events, significant moments, important moments, and counselling or psychotherapy. The references of the selected studies were also searched. This process led to the identification of 41 primary studies that used client-identified significant event(s) as a main or secondary focus of the study. These were consequently reviewed with regard to their methodology and findings. The findings are presented according to type of study conducted. The impacts of helpful events reported by clients are focused on contributions to therapeutic relationship and to in-session outcomes. Hindering events focus on some client disappointment with the therapist or therapy. The group therapy modality highlighted additional helpful impacts (like learning from others). Perspectives on what is significant in therapy differ between clients and therapists. The intensive qualitative studies reviewed confirm that the processes involved in significant events are complex and ambiguous. Studies show that the helpful events may also contain many hindering elements and that specific events are deeply contextually embedded in the preceding events of therapy. Some studies suggest that helpful significant events are therapeutically productive although this may need to be established further. Specific intensive studies show that the clients' perceptions in therapy may differ dramatically from that of the therapist. Furthermore, the relational and emotional aspects of significant moments may be more important for the clients than the cognitive aspects of therapy which are frequently stressed by therapists. 2010 The British Psychological Society.

An integrative transcriptomic approach to identify depot differences in genes and microRNAs in adipose tissues from high fat fed mice.

PubMed

Wijayatunga, Nadeeja N; Pahlavani, Mandana; Kalupahana, Nishan S; Kottapalli, Kameswara Rao; Gunaratne, Preethi H; Coarfa, Cristian; Ramalingam, Latha; Moustaid-Moussa, Naima

2018-02-06

Obesity contributes to metabolic disorders such as diabetes and cardiovascular disease. Characterization of differences between the main adipose tissue depots, white (WAT) [including subcutaneous (SAT) and visceral adipose tissue (VAT)] and brown adipose tissue (BAT) helps to identify their roles in obesity. Thus, we studied depot-specific differences in whole transcriptome and miRNA profiles of SAT, VAT and BAT from high fat diet (HFD/45% of calories from fat) fed mice using RNA sequencing and small RNA-Seq. Using quantitative real-time polymerase chain reaction, we validated depot-specific differences in endoplasmic reticulum (ER) stress related genes and miRNAs using mice fed a HFD vs. low fat diet (LFD/10% of calories from fat). According to the transcriptomic analysis, lipogenesis, adipogenesis, inflammation, endoplasmic reticulum (ER) stress and unfolded protein response (UPR) were higher in VAT compared to BAT, whereas energy expenditure, fatty acid oxidation and oxidative phosphorylation were higher in BAT than in VAT of the HFD fed mice. In contrast to BAT, ER stress marker genes were significantly upregulated in VAT of HFD fed mice than the LFD fed mice. For the first time, we report depot specific differences in ER stress related miRNAs including; downregulation of miR-125b-5p, upregulation miR-143-3p, and miR-222-3p in VAT following HFD and upregulation of miR-30c-2-3p only in BAT following a HFD in mice than the LFD mice. In conclusion, HFD differentially regulates miRNAs and genes in different adipose depots with significant induction of genes related to lipogenesis, adipogenesis, inflammation, ER stress, and UPR in WAT compared to BAT.

Identifying high production, low production and degraded rangelands in Senegal with normalized difference vegetation index data

USGS Publications Warehouse

Tappan, G. Gray; Wood, Lynette; Moore, Donald G.

1993-01-01

Seasonal herbaceous vegetation production on Senegal's native rangelands exhibits high spatial and temporal variability. This variability can be monitored using normalized difference vegetation index (NDVI) data computed from 1-km resolution Advanced Very High Resolution Radiometer (AVHRR) image data. Although annual fluctuations in rainfall account for some of the variability, numerous long-term production patterns are evident in the AVHRR time-series data. Different n productivity reflect variations in the region's climate, topography, soils, and land use. Areas of overgrazing and intensive cultivation have caused long-term soil and vegetation degradation. Rangelands of high and low productivity, and degraded rangelands were identified using NDVI. Time-series image data from 1987 though 1992 were used to map relative rangeland productivity. The results were compared to detailed resource maps on soils, vegetation and land use. Much of the variation in rangeland productivity correlated well to the known distribution of resources. The study developed an approach that identified a number of areas of degraded soils and low vegetation production.

Prenatal Particulate Air Pollution and Asthma Onset in Urban Children. Identifying Sensitive Windows and Sex Differences.

PubMed

Hsu, Hsiao-Hsien Leon; Chiu, Yueh-Hsiu Mathilda; Coull, Brent A; Kloog, Itai; Schwartz, Joel; Lee, Alison; Wright, Robert O; Wright, Rosalind J

2015-11-01

The influence of particulate air pollution on respiratory health starts in utero. Fetal lung growth and structural development occurs in stages; thus, effects on postnatal respiratory disorders may differ based on timing of exposure. We implemented an innovative method to identify sensitive windows for effects of prenatal exposure to particulate matter with a diameter less than or equal to 2.5 μm (PM2.5) on children's asthma development in an urban pregnancy cohort. Analyses included 736 full-term (≥37 wk) children. Each mother's daily PM2.5 exposure was estimated over gestation using a validated satellite-based spatiotemporal resolved model. Using distributed lag models, we examined associations between weekly averaged PM2.5 levels over pregnancy and physician-diagnosed asthma in children by age 6 years. Effect modification by sex was also examined. Most mothers were ethnic minorities (54% Hispanic, 30% black), had 12 or fewer years of education (66%), and did not smoke in pregnancy (80%). In the sample as a whole, distributed lag models adjusting for child age, sex, and maternal factors (education, race and ethnicity, smoking, stress, atopy, prepregnancy obesity) showed that increased PM2.5 exposure levels at 16-25 weeks gestation were significantly associated with early childhood asthma development. An interaction between PM2.5 and sex was significant (P = 0.01) with sex-stratified analyses showing that the association exists only for boys. Higher prenatal PM2.5 exposure at midgestation was associated with asthma development by age 6 years in boys. Methods to better characterize vulnerable windows may provide insight into underlying mechanisms.

Significant Differences in Physicochemical Properties of Human Immunoglobulin Kappa and Lambda CDR3 Regions.

PubMed

Townsend, Catherine L; Laffy, Julie M J; Wu, Yu-Chang Bryan; Silva O'Hare, Joselli; Martin, Victoria; Kipling, David; Fraternali, Franca; Dunn-Walters, Deborah K

2016-01-01

Antibody variable regions are composed of a heavy and a light chain, and in humans, there are two light chain isotypes: kappa and lambda. Despite their importance in receptor editing, the light chain is often overlooked in the antibody literature, with the focus being on the heavy chain complementarity-determining region (CDR)-H3 region. In this paper, we set out to investigate the physicochemical and structural differences between human kappa and lambda light chain CDR regions. We constructed a dataset containing over 29,000 light chain variable region sequences from IgM-transcribing, newly formed B cells isolated from human bone marrow and peripheral blood. We also used a published human naïve dataset to investigate the CDR-H3 properties of heavy chains paired with kappa and lambda light chains and probed the Protein Data Bank to investigate the structural differences between kappa and lambda antibody CDR regions. We found that kappa and lambda light chains have very different CDR physicochemical and structural properties, whereas the heavy chains with which they are paired do not differ significantly. We also observed that the mean CDR3 N nucleotide addition in the kappa, lambda, and heavy chain gene rearrangements are correlated within donors but can differ between donors. This indicates that terminal deoxynucleotidyl transferase may work with differing efficiencies between different people but the same efficiency in the different classes of immunoglobulin chain within one person. We have observed large differences in the physicochemical and structural properties of kappa and lambda light chain CDR regions. This may reflect different roles in the humoral immune response.

Significant Differences in Physicochemical Properties of Human Immunoglobulin Kappa and Lambda CDR3 Regions

PubMed Central

Townsend, Catherine L.; Laffy, Julie M. J.; Wu, Yu-Chang Bryan; Silva O’Hare, Joselli; Martin, Victoria; Kipling, David; Fraternali, Franca; Dunn-Walters, Deborah K.

2016-01-01

Antibody variable regions are composed of a heavy and a light chain, and in humans, there are two light chain isotypes: kappa and lambda. Despite their importance in receptor editing, the light chain is often overlooked in the antibody literature, with the focus being on the heavy chain complementarity-determining region (CDR)-H3 region. In this paper, we set out to investigate the physicochemical and structural differences between human kappa and lambda light chain CDR regions. We constructed a dataset containing over 29,000 light chain variable region sequences from IgM-transcribing, newly formed B cells isolated from human bone marrow and peripheral blood. We also used a published human naïve dataset to investigate the CDR-H3 properties of heavy chains paired with kappa and lambda light chains and probed the Protein Data Bank to investigate the structural differences between kappa and lambda antibody CDR regions. We found that kappa and lambda light chains have very different CDR physicochemical and structural properties, whereas the heavy chains with which they are paired do not differ significantly. We also observed that the mean CDR3 N nucleotide addition in the kappa, lambda, and heavy chain gene rearrangements are correlated within donors but can differ between donors. This indicates that terminal deoxynucleotidyl transferase may work with differing efficiencies between different people but the same efficiency in the different classes of immunoglobulin chain within one person. We have observed large differences in the physicochemical and structural properties of kappa and lambda light chain CDR regions. This may reflect different roles in the humoral immune response. PMID:27729912

Flash visual evoked potentials are not specific enough to identify parieto-occipital lobe involvement in term neonates after significant hypoglycaemia.

PubMed

Hu, Liyuan; Gu, Qiufang; Zhu, Zhen; Yang, Chenhao; Chen, Chao; Cao, Yun; Zhou, Wenhao

2014-08-01

Hypoglycaemia is a significant problem in high-risk neonates and predominant parieto-occipital lobe involvement has been observed after severe hypoglycaemic insult. We explored the use of flash visual evoked potentials (FVEP) in detecting parieto-occipital lobe involvement after significant hypoglycaemia. Full-term neonates (n = 15) who underwent FVEP from January 2008 to May 2013 were compared with infants (n = 11) without hypoglycaemia or parietal-occipital lobe injury. Significant hypoglycaemia was defined as being symptomatic or needing steroids, glucagon or a glucose infusion rate of ≥12 mg/kg/min. The hypoglycaemia group exhibited delayed latency of the first positive waveform on FVEP. The initial detected time for hypoglycaemia was later in the eight subjects with seizures (median 51-h-old) than those without (median 22-h-old) (P = 0.003). Magnetic resonance imaging showed that 80% of the hypoglycaemia group exhibited occipital-lobe injuries, and they were more likely to exhibit abnormal FVEP morphology (P = 0.007) than the controls. FVEP exhibited 100% sensitivity, but only 25% specificity, for detecting injuries to the parieto-occipital lobes. Flash visual evoked potential (FVEP) was sensitive, but not sufficiently specific, in identifying parieto-occipital lobe injuries among term neonates exposed to significant hypoglycaemia. Larger studies exploring the potential role of FVEP in neonatal hypoglycaemia are required. ©2014 Foundation Acta Paediatrica. Published by John Wiley & Sons Ltd.

[Integrated DNA barcoding database for identifying Chinese animal medicine].

PubMed

Shi, Lin-Chun; Yao, Hui; Xie, Li-Fang; Zhu, Ying-Jie; Song, Jing-Yuan; Zhang, Hui; Chen, Shi-Lin

2014-06-01

In order to construct an integrated DNA barcoding database for identifying Chinese animal medicine, the authors and their cooperators have completed a lot of researches for identifying Chinese animal medicines using DNA barcoding technology. Sequences from GenBank have been analyzed simultaneously. Three different methods, BLAST, barcoding gap and Tree building, have been used to confirm the reliabilities of barcode records in the database. The integrated DNA barcoding database for identifying Chinese animal medicine has been constructed using three different parts: specimen, sequence and literature information. This database contained about 800 animal medicines and the adulterants and closely related species. Unknown specimens can be identified by pasting their sequence record into the window on the ID page of species identification system for traditional Chinese medicine (www. tcmbarcode. cn). The integrated DNA barcoding database for identifying Chinese animal medicine is significantly important for animal species identification, rare and endangered species conservation and sustainable utilization of animal resources.

Diagnosed, identified, current and complete depression among patients attending primary care in southern Catalonia: different aspects of the same concept.

PubMed

Montesó-Curto, Pilar; Ferré-Grau, Carme; Lleixà-Fortuño, Mar; Albacar-Riobóo, Nuria; Lejeune, Marylene

2014-02-01

The aims of this study were to explore the prevalence and the conceptualizations of depression detected by the healthcare system, identified by the patient or classified/identified in the validated Goldberg's questionnaire in a community. We conducted a cross-sectional evaluation of 317 patients. The different types of depression diagnosed, identified, current or total were stratified by age and gender groups. The difference in the conceptualization of depression from the medical or ordinary people point of view indicate that depression care requires the understanding of the lifestyle, beliefs, attitudes, family and social networks of the people the physicians and nurses care for. © 2014.

Featured Article: Transcriptional landscape analysis identifies differently expressed genes involved in follicle-stimulating hormone induced postmenopausal osteoporosis.

PubMed

Maasalu, Katre; Laius, Ott; Zhytnik, Lidiia; Kõks, Sulev; Prans, Ele; Reimann, Ene; Märtson, Aare

2017-01-01

Osteoporosis is a disorder associated with bone tissue reorganization, bone mass, and mineral density. Osteoporosis can severely affect postmenopausal women, causing bone fragility and osteoporotic fractures. The aim of the current study was to compare blood mRNA profiles of postmenopausal women with and without osteoporosis, with the aim of finding different gene expressions and thus targets for future osteoporosis biomarker studies. Our study consisted of transcriptome analysis of whole blood serum from 12 elderly female osteoporotic patients and 12 non-osteoporotic elderly female controls. The transcriptome analysis was performed with RNA sequencing technology. For data analysis, the edgeR package of R Bioconductor was used. Two hundred and fourteen genes were expressed differently in osteoporotic compared with non-osteoporotic patients. Statistical analysis revealed 20 differently expressed genes with a false discovery rate of less than 1.47 × 10 -4 among osteoporotic patients. The expression of 10 genes were up-regulated and 10 down-regulated. Further statistical analysis identified a potential osteoporosis mRNA biomarker pattern consisting of six genes: CACNA1G, ALG13, SBK1, GGT7, MBNL3, and RIOK3. Functional ingenuity pathway analysis identified the strongest candidate genes with regard to potential involvement in a follicle-stimulating hormone activated network of increased osteoclast activity and hypogonadal bone loss. The differentially expressed genes identified in this study may contribute to future research of postmenopausal osteoporosis blood biomarkers.

Identifying crash contributory factors at urban roundabouts and using association rules to explore their relationships to different crash types.

PubMed

Montella, Alfonso

2011-07-01

The use of roundabouts improves intersection safety by eliminating or altering conflict types, reducing crash severity, and causing drivers to reduce speeds. However, roundabout performances can degrade if precautions are not taken during either the design or the operation phase. Therefore, additional information on the safety of the roundabouts is extremely helpful for planners and designers in identifying existing deficiencies and in refining the design criteria currently being used. The aim of the paper was to investigate the crash contributory factors in 15 urban roundabouts located in Italy and to study the interdependences between these factors. The crash data refer to the period 2003-2008. The identification of the crash contributory factors was based on site inspections and rigorous analyses performed by a team of specialists with a relevant road safety engineering background. Each roundabout was inspected once every year from 2004 to 2009, both in daytime and in nighttime. Overall, 62 different contributory factors and 2156 total contributory factors were identified. In 51 crashes, a single contributory factor was found, whereas in the other 223 crashes, a combination of contributory factors was identified. Given the large amount of data, the interdependences between the contributory factors and between the contributory factors and the different crash types were explored by an association discovery. Association discovery is the identification of sets of items (i.e., crash contributory factors and crash types in our study) that occur together in a given event (i.e., a crash in our study). The rules were filtered by support, confidence, and lift. As a result, 112 association rules were discovered. Overall, numerous contributory factors related to the road and environment deficiencies but not related to the road user or to the vehicle were identified. The most important factors related to geometric design were the radius of deflection and the deviation angle

A new index for identifying different types of El Niño Modoki events

NASA Astrophysics Data System (ADS)

Wang, Xin; Tan, Wei; Wang, Chunzai

2018-04-01

El Niño Modoki events can be further classified into El Niño Modoki I and II in terms of their opposite impacts on southern China rainfall (Wang and Wang, J Clim 26:1322-1338, 2013) and the Indian Ocean dipole mode (Wang and Wang, Clim Dyn 42:991-1005, 2014). The present paper develops an index to identify the types of El Niño events. The El Niño Modoki II (MII) index is defined as the leading principle component of multivariate empirical orthogonal function analysis of the normalized El Niño Modoki index, Niño4 index and 850 hPa relative vorticity anomalies averaged near the Philippine Sea during autumn. The MII index exhibits dominant variations on interannual (2-3 and 4-5 years) and decadal (10-20 years) timescales. El Niño Modoki II events can be well identified by using the MII index value being larger than 1 standard deviation. Further analyses and numerical model experiments confirm that the MII index can portray the major oceanic and atmospheric features of El Niño Modoki II events. The constructed MII index along with previous ENSO indices can be used for classifying and identifying all types of El Niño events. Because of distinct impacts induced by different types of El Niño events, the implication of the present study is that climate prediction and future climate projection under global warming can be improved by using the MII index and other indices to identify the types of El Niño events.

GWAS and admixture mapping identify different asthma-associated loci in Latinos: The GALA II Study

PubMed Central

Galanter, Joshua M; Gignoux, Christopher R; Torgerson, Dara G; Roth, Lindsey A; Eng, Celeste; Oh, Sam S; Nguyen, Elizabeth A; Drake, Katherine A; Huntsman, Scott; Hu, Donglei; Sen, Saunak; Davis, Adam; Farber, Harold J.; Avila, Pedro C.; Brigino-Buenaventura, Emerita; LeNoir, Michael A.; Meade, Kelley; Serebrisky, Denise; Borrell, Luisa N; Rodríguez-Cintrón, William; Estrada, Andres Moreno; Mendoza, Karla Sandoval; Winkler, Cheryl A.; Klitz, William; Romieu, Isabelle; London, Stephanie J.; Gilliland, Frank; Martinez, Fernando; Bustamante, Carlos; Williams, L Keoki; Kumar, Rajesh; Rodríguez-Santana, José R.; Burchard, and Esteban G.

2013-01-01

Background Asthma is a complex disease with both genetic and environmental causes. Genome-wide association studies of asthma have mostly involved European populations and replication of positive associations has been inconsistent. Objective To identify asthma-associated genes in a large Latino population with genome-wide association analysis and admixture mapping. Methods Latino children with asthma (n = 1,893) and healthy controls (n = 1,881) were recruited from five sites in the United States: Puerto Rico, New York, Chicago, Houston, and the San Francisco Bay Area. Subjects were genotyped on an Affymetrix World Array IV chip. We performed genome-wide association and admixture mapping to identify asthma-associated loci. Results We identified a significant association between ancestry and asthma at 6p21 (lowest p-value: rs2523924, p < 5 × 10−6). This association replicates in a meta-analysis of the EVE Asthma Consortium (p = 0.01). Fine mapping of the region in this study and the EVE Asthma Consortium suggests an association between PSORS1C1 and asthma. We confirmed the strong allelic association between the 17q21 asthma in Latinos (IKZF3, lowest p-value: rs90792, OR: 0.67, 95% CI 0.61 – 0.75, p = 6 × 10−13) and replicated associations in several genes that had previously been associated with asthma in genome-wide association studies. Conclusions Admixture mapping and genome-wide association are complementary techniques that provide evidence for multiple asthma-associated loci in Latinos. Admixture mapping identifies a novel locus on 6p21 that replicates in a meta-analysis of several Latino populations, while genome-wide association confirms the previously identified locus on 17q21. PMID:24406073

Understanding identifiability as a crucial step in uncertainty assessment

NASA Astrophysics Data System (ADS)

Jakeman, A. J.; Guillaume, J. H. A.; Hill, M. C.; Seo, L.

2016-12-01

The topic of identifiability analysis offers concepts and approaches to identify why unique model parameter values cannot be identified, and can suggest possible responses that either increase uniqueness or help to understand the effect of non-uniqueness on predictions. Identifiability analysis typically involves evaluation of the model equations and the parameter estimation process. Non-identifiability can have a number of undesirable effects. In terms of model parameters these effects include: parameters not being estimated uniquely even with ideal data; wildly different values being returned for different initialisations of a parameter optimisation algorithm; and parameters not being physically meaningful in a model attempting to represent a process. This presentation illustrates some of the drastic consequences of ignoring model identifiability analysis. It argues for a more cogent framework and use of identifiability analysis as a way of understanding model limitations and systematically learning about sources of uncertainty and their importance. The presentation specifically distinguishes between five sources of parameter non-uniqueness (and hence uncertainty) within the modelling process, pragmatically capturing key distinctions within existing identifiability literature. It enumerates many of the various approaches discussed in the literature. Admittedly, improving identifiability is often non-trivial. It requires thorough understanding of the cause of non-identifiability, and the time, knowledge and resources to collect or select new data, modify model structures or objective functions, or improve conditioning. But ignoring these problems is not a viable solution. Even simple approaches such as fixing parameter values or naively using a different model structure may have significant impacts on results which are too often overlooked because identifiability analysis is neglected.

Statistical Methods for Identifying Sequence Motifs Affecting Point Mutations

PubMed Central

Zhu, Yicheng; Neeman, Teresa; Yap, Von Bing; Huttley, Gavin A.

2017-01-01

Mutation processes differ between types of point mutation, genomic locations, cells, and biological species. For some point mutations, specific neighboring bases are known to be mechanistically influential. Beyond these cases, numerous questions remain unresolved, including: what are the sequence motifs that affect point mutations? How large are the motifs? Are they strand symmetric? And, do they vary between samples? We present new log-linear models that allow explicit examination of these questions, along with sequence logo style visualization to enable identifying specific motifs. We demonstrate the performance of these methods by analyzing mutation processes in human germline and malignant melanoma. We recapitulate the known CpG effect, and identify novel motifs, including a highly significant motif associated with A→G mutations. We show that major effects of neighbors on germline mutation lie within ±2 of the mutating base. Models are also presented for contrasting the entire mutation spectra (the distribution of the different point mutations). We show the spectra vary significantly between autosomes and X-chromosome, with a difference in T→C transition dominating. Analyses of malignant melanoma confirmed reported characteristic features of this cancer, including statistically significant strand asymmetry, and markedly different neighboring influences. The methods we present are made freely available as a Python library https://bitbucket.org/pycogent3/mutationmotif. PMID:27974498

Significance analysis of the regional differences on icing time of water onto fire protective clothing

NASA Astrophysics Data System (ADS)

Zhao, L. Z.; Jing, L. S.; Zhang, X. Z.; Xia, J. J.; Chen, Y.; Chen, T.; Hu, C.; Bao, Z. M.; Fu, X. C.; Wang, R. J.; Wang, Y.; Wang, Y. J.

2017-09-01

The object of this work was to determine the icing temperature in icing experiment. Firstly, a questionnaire investigation was carried out on 38 fire detachments in different regions. These Statistical percentage results were divided into northern east group and northern west group. Secondly, a significance analysis between these two results was made using Mann-Whitney U test. Then the icing temperature was determined in different regions. Thirdly, the icing experiment was made in the environment of -20°C in Daxing’an Mountain. The anti-icing effect of new fire protective clothing was verified in this icing.

System and method employing a self-organizing map load feature database to identify electric load types of different electric loads

DOEpatents

Lu, Bin; Harley, Ronald G.; Du, Liang; Yang, Yi; Sharma, Santosh K.; Zambare, Prachi; Madane, Mayura A.

2014-06-17

A method identifies electric load types of a plurality of different electric loads. The method includes providing a self-organizing map load feature database of a plurality of different electric load types and a plurality of neurons, each of the load types corresponding to a number of the neurons; employing a weight vector for each of the neurons; sensing a voltage signal and a current signal for each of the loads; determining a load feature vector including at least four different load features from the sensed voltage signal and the sensed current signal for a corresponding one of the loads; and identifying by a processor one of the load types by relating the load feature vector to the neurons of the database by identifying the weight vector of one of the neurons corresponding to the one of the load types that is a minimal distance to the load feature vector.

Significant differences in parameters of glucose metabolism in children of hypertensive and normotensive parents.

PubMed

Gryko, Anna; Głowińska-Olszewska, Barbara; Płudowska, Katarzyna; Smithson, W Henry; Owłasiuk, Anna; Żelazowska-Rutkowska, Beata; Wojtkielewicz, Katarzyna; Milewski, Robert; Chlabicz, Sławomir

2017-01-01

In the recent years, alterations in the carbohydrate metabolism, including insulin resistance, are considered as risk factors in the development of hypertension and its complications in young age. Hypertension is associated with significant cardiovascular morbidity and mortality. The onset of pathology responsible for the development of hypertension, as well as levels of biomarkers specific for early stages of atherosclerosis are poorly understood. To compare a group of children whose parents have a history of hypertension (study group) with a group of children with normotensive parents (reference group), with consideration of typical risk factors for atherosclerosis, parameters of lipid and carbohydrate metabolism, anthropometric data and new biomarkers of early cardiovascular disease (hsCRP, adiponectin, sICAM-1). The study population consists of 84 children. Of these, 40 children (mean age 13.6±2.7 years) had a parental history of hypertension, and 44 aged 13.1±3.7 yrs were children of normotensive parents. Anthropometric measurements were taken, and measurements of blood pressure, lipid profile, glucose and insulin levels were carried out. The insulin resistance index (HOMA IR) was calculated. Levels of hsCRP, soluble cell adhesion molecules (sICAM) and adiponectin were measured. There were no statistically significant differences in anthropometric parameters (body mass, SDS BMI, skin folds) between groups. Values of systolic blood pressure were statistically significantly higher in the study group (Me 108 vs. 100 mmHg, p= 0.031), as were glycaemia (Me 80 vs. 67 mg/dl p<0.001) and insulinaemia levels (Me 8.89 vs. 5.34 µIU/ml, p=0.024). Higher, statistically significant values of HOMA IR were found in the study group (children of hypertensive parents) (Me 1.68 vs. 0.80 mmol/l × mU/l, p=0.007). Lower adiponectin levels (Me 13959.45 vs. 16822 ng/ml, p=0.020) were found in children with a family history of hypertension. No significant differences were found in

System and method employing a minimum distance and a load feature database to identify electric load types of different electric loads

DOEpatents

Lu, Bin; Yang, Yi; Sharma, Santosh K; Zambare, Prachi; Madane, Mayura A

2014-12-23

A method identifies electric load types of a plurality of different electric loads. The method includes providing a load feature database of a plurality of different electric load types, each of the different electric load types including a first load feature vector having at least four different load features; sensing a voltage signal and a current signal for each of the different electric loads; determining a second load feature vector comprising at least four different load features from the sensed voltage signal and the sensed current signal for a corresponding one of the different electric loads; and identifying by a processor one of the different electric load types by determining a minimum distance of the second load feature vector to the first load feature vector of the different electric load types of the load feature database.

Understanding cultural significance, the edible mushrooms case

PubMed Central

Garibay-Orijel, Roberto; Caballero, Javier; Estrada-Torres, Arturo; Cifuentes, Joaquín

2007-01-01

Background Cultural significance is a keystone in quantitative ethnobiology, which offers the possibility to make inferences about traditional nomenclature systems, use, appropriation and valuing of natural resources. In the present work, using as model the traditional mycological knowledge of Zapotecs from Oaxaca, Mexico, we analyze the cultural significance of wild edible resources. Methods In 2003 we applied 95 questionnaires to a random sample of informants. With this data we integrated the Edible Mushroom Cultural Significance Index. This index included eight variables: frequency of mention, perceived abundance, use frequency, taste, multifunctional food use, knowledge transmission, health and economy. Data were analyzed in an inductive perspective using ordination and grouping techniques to reveal the behavior of species in a cultural multivariate dimension. Results In each variable the species had different conducts. Cantharellus cibarius s.l. was the species with most frequency of mention. Pleurotus sp. had the highest perceived abundance. C. cibarius s.l. was the most frequently consumed species. Gomphus clavatus was the most palatable species and also ranked highest in the multifunctional food index. Cortinarius secc.Malacii sp. had the highest traditional importance. Only Tricholoma magnivelare was identified as a health enhancer. It also had the most economic importance. According to the compound index, C. cibarius s.l., the Amanita caesarea complex, Ramaria spp. and Neolentinus lepideus were the mushrooms with highest cultural significance. Multivariate analysis showed that interviewees identify three main groups of mushrooms: species with high traditional values, frequent consumption and known by the majority; species that are less known, infrequently consumed and without salient characteristics; and species with low traditional values, with high economic value and health enhancers. Conclusion The compound index divided the cultural significance into

Identifying physical activity gender differences among youth

USDA-ARS?s Scientific Manuscript database

Physical activity (PA) is an important part of a healthy lifestyle and reduces risk of certain chronic diseases. Many youth do not currently meet PA guidelines; evidence suggests that girls are less active than boys are at all ages. PA differences need to be understood, so that gender-specific inter...

Comprehensive molecular profiling of 718 Multiple Myelomas reveals significant differences in mutation frequencies between African and European descent cases

PubMed Central

Christofferson, Austin; Aldrich, Jessica; Jewell, Scott; Kittles, Rick A.; Derome, Mary; Craig, David Wesley; Carpten, John D.

2017-01-01

Multiple Myeloma (MM) is a plasma cell malignancy with significantly greater incidence and mortality rates among African Americans (AA) compared to Caucasians (CA). The overall goal of this study is to elucidate differences in molecular alterations in MM as a function of self-reported race and genetic ancestry. Our study utilized somatic whole exome, RNA-sequencing, and correlated clinical data from 718 MM patients from the Multiple Myeloma Research Foundation CoMMpass study Interim Analysis 9. Somatic mutational analyses based upon self-reported race corrected for ancestry revealed significant differences in mutation frequency between groups. Of interest, BCL7A, BRWD3, and AUTS2 demonstrate significantly higher mutation frequencies among AA cases. These genes are all involved in translocations in B-cell malignancies. Moreover, we detected a significant difference in mutation frequency of TP53 and IRF4 with frequencies higher among CA cases. Our study provides rationale for interrogating diverse tumor cohorts to best understand tumor genomics across populations. PMID:29166413

The focused abdominal sonography for trauma examination can reliably identify patients with significant intra-abdominal hemorrhage in life-threatening pelvic fractures.

PubMed

Christian, Nicole Townsend; Burlew, Clay Cothren; Moore, Ernest E; Geddes, Andrea E; Wagenaar, Amy E; Fox, Charles J; Pieracci, Fredric M

2018-06-01

The focused abdominal sonography for trauma (FAST) examination has been reported to be unreliable in pelvic fracture patients. Additionally, given the advent of new therapeutic interventions, such as resuscitative endovascular balloon occlusion of the aorta (REBOA), rapid identification of intra-abdominal hemorrhage compared with Zone III hemorrhage may guide different therapeutic strategies. We hypothesized that FAST is reliable for detecting clinically significant intra-abdominal hemorrhage in the face of complex pelvic fractures. Our pelvic fracture database of all hemodynamically unstable patients requiring intervention from January 1, 2005, to July 1, 2015, was reviewed. The FAST examination was compared with operative and computed tomography (CT) scan findings. Confirmatory evaluation for FAST(-) patients was considered positive if therapeutic intervention was required. During the study period, 81 patients in refractory shock with FAST imaging in our emergency department (ED) underwent pelvic packing. Mean age was 45 ± 2 years and Injury Severity Score was 50 ± 1.5. The FAST examination was negative in 53 patients; 52 patients did not require operative intervention for abdominal bleeding while one patient required splenectomy. The FAST examination was positive in 28 patients; 26 had findings confirmed by CT or laparotomy while two patients did not have intra-abdominal hemorrhage on further evaluation. The sensitivity and specificity for FAST in this population was 96% and 96%, respectively, positive predictive value was 93%, and negative predictive value was 98%. The false-negative and -positive rates for FAST were 2% and 7%. Focused abdominal sonography for trauma examination reliably identifies clinically significant hemoperitoneum in life-threatening, pelvic fracture related hemorrhage. The incidence of a false-negative FAST in this unstable pelvic fracture population was 2%. FAST results may be used when determining the role of REBOA in these

Application of latent growth modeling to identify different working life trajectories: the case of the Spanish WORKss cohort.

PubMed

Serra, Laura; López Gómez, María Andrée; Sanchez-Niubo, Albert; Delclos, George L; Benavides, Fernando G

2017-01-01

Objective The aim of this study was to describe the application of latent class growth analysis (LCGA) to identify different working life trajectories (WLT) using employed working time by year as a repeated measure. Methods Trajectories are estimated using LCGA, which considers all individuals within a trajectory to be homogeneous. The methodology was applied to a subsample of the Spanish WORKing life Social Security (WORKss) cohort, limited to persons born 1956-1965 (N=247 475). The number of days worked per year is used as a repeated measure across 32 time points (1981-2013). Results According to the model-fit results and further guided by expert knowledge, a four WTL model was selected as the optimal approach: WLT1 or "high labor force participation" (N=99 591; 40.2%); WLT2 or "decreased labor force participation" (N= 22 846; 9.2%); WLT3 or "increased labor force participation" (N=59 213; 23.9%); and WLT4 or "low labor force participation" (N=65 827; 26.6%). WLT1 consisted mainly of men with more years of work experience (>19 years) while WLT4 was mainly composed by women with <9 years. The other two trajectories had opposite trends and no sex differences. The occupational category variable had little influence in the trajectories. Conclusions Longitudinal data that are regularly collected by administrative systems can benefit from LCGA approaches to identify different trajectory patterns that may be associated with an outcome of interest. In occupational epidemiology, this study represents a step forward by using this modeling approach to identify different WLT.

AbsIDconvert: An absolute approach for converting genetic identifiers at different granularities

PubMed Central

2012-01-01

Background High-throughput molecular biology techniques yield vast amounts of data, often by detecting small portions of ribonucleotides corresponding to specific identifiers. Existing bioinformatic methodologies categorize and compare these elements using inferred descriptive annotation given this sequence information irrespective of the fact that it may not be representative of the identifier as a whole. Results All annotations, no matter the granularity, can be aligned to genomic sequences and therefore annotated by genomic intervals. We have developed AbsIDconvert, a methodology for converting between genomic identifiers by first mapping them onto a common universal coordinate system using an interval tree which is subsequently queried for overlapping identifiers. AbsIDconvert has many potential uses, including gene identifier conversion, identification of features within a genomic region, and cross-species comparisons. The utility is demonstrated in three case studies: 1) comparative genomic study mapping plasmodium gene sequences to corresponding human and mosquito transcriptional regions; 2) cross-species study of Incyte clone sequences; and 3) analysis of human Ensembl transcripts mapped by Affymetrix®; and Agilent microarray probes. AbsIDconvert currently supports ID conversion of 53 species for a given list of input identifiers, genomic sequence, or genome intervals. Conclusion AbsIDconvert provides an efficient and reliable mechanism for conversion between identifier domains of interest. The flexibility of this tool allows for custom definition identifier domains contingent upon the availability and determination of a genomic mapping interval. As the genomes and the sequences for genetic elements are further refined, this tool will become increasingly useful and accurate. AbsIDconvert is freely available as a web application or downloadable as a virtual machine at: http://bioinformatics.louisville.edu/abid/. PMID:22967011

[Post-lasik corneal ectasia in patients with significant differences in keratometry readings between both eyes].

PubMed

Ortega-Usobiaga, J; Llovet-Osuna, F; Djodeyre, M R; Llovet-Rausell, A; Beltran-Sanz, J; Baviera-Sabater, J

2014-03-01

A study is made on the incidence of corneal ectasia after laser in situ keratomileusis (LASIK) in patients with large differences in mean keratometry (MK) readings between both eyes (OU). Visual outcomes were also evaluated. The medical records of 164,603 patients (315,259 eyes) who underwent LASIK from January 2003 to December 2011 were reviewed in order to identify patients with a difference in MK of ≥ 1.25 D between OU. The main outcome measures were incidence of ectasia after LASIK, and visual outcome. A total of 35 eyes that met the inclusion criteria were found. Functional and visual results were those expected for myopia studies. After a minimum follow-up of 2 years, no corneal ectasia was found in 3 eyes (2 patients). The possibility of finding a patient with an asymmetry in MK and normal topography is low (0.021%), and it does not seem to be a contraindication of LASIK. Although no corneal ectasia was found in this case series, and as it is a potentially sight-threatening complication, patients with very different MK between OU should be studied carefully before undergoing LASIK. Copyright © 2013 Sociedad Española de Oftalmología. Published by Elsevier Espana. All rights reserved.

Attitudinal and behavioral differences between cigarette users who do and do not identify as "smokers".

PubMed

Berg, Michael B; Lin, Linda; White, Madeleine; Alfonso-Barry, Jacqueline

2017-01-01

The current research aimed to understand differences in smoking-related identity among college students and to illustrate the distinct characteristics of nonidentified smokers (NIS). Students from 2 colleges in Massachusetts (N = 538; April 2016). Respondents reported by online survey whether or not they had smoked a cigarette in the past 30 days and if they self-identified as smokers. Nonsmokers (NIS) and identified smokers (IS) were then compared on their smoking attitudes and behavior. NIS made up 12.5% of the sample and 64% of all tobacco users. NIS perceived themselves as less addicted and were more confident in their ability to quit smoking. They also were less likely to smoke alone, buy their own cigarettes, or have friends who smoked. College health officials can best motivate NIS to quit smoking by focusing on peer norms and the potential of long-term addiction.

Genome-wide expression profiling of five mouse models identifies similarities and differences with human psoriasis.

PubMed

Swindell, William R; Johnston, Andrew; Carbajal, Steve; Han, Gangwen; Wohn, Christian; Lu, Jun; Xing, Xianying; Nair, Rajan P; Voorhees, John J; Elder, James T; Wang, Xiao-Jing; Sano, Shigetoshi; Prens, Errol P; DiGiovanni, John; Pittelkow, Mark R; Ward, Nicole L; Gudjonsson, Johann E

2011-04-04

Development of a suitable mouse model would facilitate the investigation of pathomechanisms underlying human psoriasis and would also assist in development of therapeutic treatments. However, while many psoriasis mouse models have been proposed, no single model recapitulates all features of the human disease, and standardized validation criteria for psoriasis mouse models have not been widely applied. In this study, whole-genome transcriptional profiling is used to compare gene expression patterns manifested by human psoriatic skin lesions with those that occur in five psoriasis mouse models (K5-Tie2, imiquimod, K14-AREG, K5-Stat3C and K5-TGFbeta1). While the cutaneous gene expression profiles associated with each mouse phenotype exhibited statistically significant similarity to the expression profile of psoriasis in humans, each model displayed distinctive sets of similarities and differences in comparison to human psoriasis. For all five models, correspondence to the human disease was strong with respect to genes involved in epidermal development and keratinization. Immune and inflammation-associated gene expression, in contrast, was more variable between models as compared to the human disease. These findings support the value of all five models as research tools, each with identifiable areas of convergence to and divergence from the human disease. Additionally, the approach used in this paper provides an objective and quantitative method for evaluation of proposed mouse models of psoriasis, which can be strategically applied in future studies to score strengths of mouse phenotypes relative to specific aspects of human psoriasis.

Gender differences in binaural speech-evoked auditory brainstem response: are they clinically significant?

PubMed

Jalaei, Bahram; Azmi, Mohd Hafiz Afifi Mohd; Zakaria, Mohd Normani

2018-05-17

Binaurally evoked auditory evoked potentials have good diagnostic values when testing subjects with central auditory deficits. The literature on speech-evoked auditory brainstem response evoked by binaural stimulation is in fact limited. Gender disparities in speech-evoked auditory brainstem response results have been consistently noted but the magnitude of gender difference has not been reported. The present study aimed to compare the magnitude of gender difference in speech-evoked auditory brainstem response results between monaural and binaural stimulations. A total of 34 healthy Asian adults aged 19-30 years participated in this comparative study. Eighteen of them were females (mean age=23.6±2.3 years) and the remaining sixteen were males (mean age=22.0±2.3 years). For each subject, speech-evoked auditory brainstem response was recorded with the synthesized syllable /da/ presented monaurally and binaurally. While latencies were not affected (p>0.05), the binaural stimulation produced statistically higher speech-evoked auditory brainstem response amplitudes than the monaural stimulation (p<0.05). As revealed by large effect sizes (d>0.80), substantive gender differences were noted in most of speech-evoked auditory brainstem response peaks for both stimulation modes. The magnitude of gender difference between the two stimulation modes revealed some distinct patterns. Based on these clinically significant results, gender-specific normative data are highly recommended when using speech-evoked auditory brainstem response for clinical and future applications. The preliminary normative data provided in the present study can serve as the reference for future studies on this test among Asian adults. Copyright © 2018 Associação Brasileira de Otorrinolaringologia e Cirurgia Cérvico-Facial. Published by Elsevier Editora Ltda. All rights reserved.

Parent socialization effects in different cultures: significance of directive parenting.

PubMed

Sorkhabi, Nadia

2012-06-01

In this article, the controversy of divergent findings in research on parental socialization effects in different cultures is addressed. Three explanations intended to address divergent findings of socialization effects in different cultures, as advanced by researchers who emphasize cultural differences, are discussed. These include cultural differences in socialization values and goals of parents, parental emotional and cognitive characteristics associated with parenting styles, and adolescents' interpretations or evaluations of their parents' parenting styles. The empirical evidence for and against each of these arguments is examined and an alternative paradigm for understanding and empirical study of developmental outcomes associated with parenting styles in different cultures is suggested. Baumrind's directive parenting style is presented as an alternative to the authoritarian parenting style in understanding the positive developmental effects associated with "strict" parenting in cultures said to have a collectivist orientation. Directions for research on the three explanations are mentioned.

Methods and Measures: Growth Mixture Modeling--A Method for Identifying Differences in Longitudinal Change among Unobserved Groups

ERIC Educational Resources Information Center

Ram, Nilam; Grimm, Kevin J.

2009-01-01

Growth mixture modeling (GMM) is a method for identifying multiple unobserved sub-populations, describing longitudinal change within each unobserved sub-population, and examining differences in change among unobserved sub-populations. We provide a practical primer that may be useful for researchers beginning to incorporate GMM analysis into their…

Medial Longitudinal Arch Angle Presents Significant Differences Between Foot Types: A Biplane Fluoroscopy Study.

PubMed

Balsdon, Megan E R; Bushey, Kristen M; Dombroski, Colin E; LeBel, Marie-Eve; Jenkyn, Thomas R

2016-10-01

The structure of the medial longitudinal arch (MLA) affects the foot's overall function and its ability to dissipate plantar pressure forces. Previous research on the MLA includes measuring the calcaneal-first metatarsal angle using a static sagittal plane radiograph, a dynamic height-to-length ratio using marker clusters with a multisegment foot model, and a contained angle using single point markers with a multisegment foot model. The objective of this study was to use biplane fluoroscopy to measure a contained MLA angle between foot types: pes planus (low arch), pes cavus (high arch), and normal arch. Fifteen participants completed the study, five from each foot type. Markerless fluoroscopic radiostereometric analysis (fRSA) was used with a three-dimensional model of the foot bones and manually matching those bones to a pair of two-dimensional radiographic images during midstance of gait. Statistically significant differences were found between barefoot arch angles of the normal and pes cavus foot types (p = 0.036), as well as between the pes cavus and pes planus foot types (p = 0.004). Dynamic walking also resulted in a statistically significant finding compared to the static standing trials (p = 0.014). These results support the classification of individuals following a physical assessment by a foot specialist for those with pes cavus and planus foot types. The differences between static and dynamic kinematic measurements were also supported using this novel method.

A view of dyslexia in context: implications for understanding differences in essay writing experience amongst higher education students identified as dyslexic.

PubMed

Carter, Christine; Sellman, Edward

2013-08-01

This article applies socio-cultural theories to explore how differences in essay writing experience are constituted for a group of students identified as dyslexic. It reports on a qualitative study with eleven student writers, seven of whom are formally identified as dyslexic, from the schools of archaeology, history and philosophy in a 'traditional' UK university. Semi-structured interviews before, during and after writing a coursework essay revealed well-documented dyslexia-related difficulties and also strong differences in how writing was experienced. The multiple and fluid dimensions that construct these differences suggest the importance of position within the context, previous and developing writing and learning experience, and metacognitive, meta-affective and metalinguistic awareness. They also suggest tensions between specialist and inclusive policies in relation to writing pedagogy for students identified as dyslexic. Copyright © 2013 John Wiley & Sons, Ltd.

Functional brain activation differences in stuttering identified with a rapid fMRI sequence

PubMed Central

Kraft, Shelly Jo; Choo, Ai Leen; Sharma, Harish; Ambrose, Nicoline G.

2011-01-01

The purpose of this study was to investigate whether brain activity related to the presence of stuttering can be identified with rapid functional MRI (fMRI) sequences that involved overt and covert speech processing tasks. The long-term goal is to develop sensitive fMRI approaches with developmentally appropriate tasks to identify deviant speech motor and auditory brain activity in children who stutter closer to the age at which recovery from stuttering is documented. Rapid sequences may be preferred for individuals or populations who do not tolerate long scanning sessions. In this report, we document the application of a picture naming and phoneme monitoring task in three minute fMRI sequences with adults who stutter (AWS). If relevant brain differences are found in AWS with these approaches that conform to previous reports, then these approaches can be extended to younger populations. Pairwise contrasts of brain BOLD activity between AWS and normally fluent adults indicated the AWS showed higher BOLD activity in the right inferior frontal gyrus (IFG), right temporal lobe and sensorimotor cortices during picture naming and and higher activity in the right IFG during phoneme monitoring. The right lateralized pattern of BOLD activity together with higher activity in sensorimotor cortices is consistent with previous reports, which indicates rapid fMRI sequences can be considered for investigating stuttering in younger participants. PMID:22133409

Significant Deregulated Pathways in Diabetes Type II Complications Identified through Expression Based Network Biology

NASA Astrophysics Data System (ADS)

Ukil, Sanchaita; Sinha, Meenakshee; Varshney, Lavneesh; Agrawal, Shipra

Type 2 Diabetes is a complex multifactorial disease, which alters several signaling cascades giving rise to serious complications. It is one of the major risk factors for cardiovascular diseases. The present research work describes an integrated functional network biology approach to identify pathways that get transcriptionally altered and lead to complex complications thereby amplifying the phenotypic effect of the impaired disease state. We have identified two sub-network modules, which could be activated under abnormal circumstances in diabetes. Present work describes key proteins such as P85A and SRC serving as important nodes to mediate alternate signaling routes during diseased condition. P85A has been shown to be an important link between stress responsive MAPK and CVD markers involved in fibrosis. MAPK8 has been shown to interact with P85A and further activate CTGF through VEGF signaling. We have traced a novel and unique route correlating inflammation and fibrosis by considering P85A as a key mediator of signals. The next sub-network module shows SRC as a junction for various signaling processes, which results in interaction between NF-kB and beta catenin to cause cell death. The powerful interaction between these important genes in response to transcriptionally altered lipid metabolism and impaired inflammatory response via SRC causes apoptosis of cells. The crosstalk between inflammation, lipid homeostasis and stress, and their serious effects downstream have been explained in the present analyses.

To identify or not to identify parathyroid glands during total thyroidectomy.

PubMed

Chang, Yuk Kwan; Lang, Brian H H

2017-12-01

Hypoparathyroidism is one of the most common complications after total thyroidectomy and may impose a significant burden to both the patient and clinician. The extent of thyroid resection, surgical techniques, concomitant central neck dissection, parathyroid gland (PG) autotransplantation and inadvertent parathyroidectomy have long been some of the risk factors for postoperative hypoparathyroidism. Although routine identification of PGs has traditionally been advocated by surgeons, recent evidence has suggested that perhaps identifying fewer number of in situ PGs during surgery (i.e., selective identification) may further lower the risk of hypoparathyroidism. One explanation is that visual identification may often lead to subtle damages to the nearby blood supply of the in situ PGs and that may increase the risk of hypoparathyroidism. However, it is worth highlighting the current literature supporting either approach (i.e., routine vs. selective) remains scarce and because of the significant differences in study design, inclusions, definitions and management protocol between studies, a pooled analysis on this important but controversial topic remains an impossible task. Furthermore, it is worth nothing that identification of PGs does not equal safe preservation, as some studies demonstrated that it is not the number of PGs identified, but the number of PG preserved in situ that matters. Therefore a non-invasive, objective and reliable way to localize PGs and assess their viability intra-operatively is warranted. In this aspect, modern technology such as the indocyanine green (ICG) as near-infrared fluorescent dye for real-time in situ PG perfusion monitoring may have a potential role in the future.

Frequencies of polymorphisms associated with BSE resistance differ significantly between Bos taurus, Bos indicus, and composite cattle

PubMed Central

Brunelle, Brian W; Greenlee, Justin J; Seabury, Christopher M; Brown, Charles E; Nicholson, Eric M

2008-01-01

Background Transmissible spongiform encephalopathies (TSEs) are neurodegenerative diseases that affect several mammalian species. At least three factors related to the host prion protein are known to modulate susceptibility or resistance to a TSE: amino acid sequence, atypical number of octapeptide repeats, and expression level. These factors have been extensively studied in breeds of Bos taurus cattle in relation to classical bovine spongiform encephalopathy (BSE). However, little is currently known about these factors in Bos indicus purebred or B. indicus × B. taurus composite cattle. The goal of our study was to establish the frequency of markers associated with enhanced susceptibility or resistance to classical BSE in B. indicus purebred and composite cattle. Results No novel or TSE-associated PRNP-encoded amino acid polymorphisms were observed for B. indicus purebred and composite cattle, and all had the typical number of octapeptide repeats. However, differences were observed in the frequencies of the 23-bp and 12-bp insertion/deletion (indel) polymorphisms associated with two bovine PRNP transcription regulatory sites. Compared to B. taurus, B. indicus purebred and composite cattle had a significantly lower frequency of 23-bp insertion alleles and homozygous genotypes. Conversely, B. indicus purebred cattle had a significantly higher frequency of 12-bp insertion alleles and homozygous genotypes in relation to both B. taurus and composite cattle. The origin of these disparities can be attributed to a significantly different haplotype structure within each species. Conclusion The frequencies of the 23-bp and 12-bp indels were significantly different between B. indicus and B. taurus cattle. No other known or potential risk factors were detected for the B. indicus purebred and composite cattle. To date, no consensus exists regarding which bovine PRNP indel region is more influential with respect to classical BSE. Should one particular indel region and

Identification of the most significant electrode positions in electromyographic evaluation of swallowing-related movements in humans.

PubMed

Zaretsky, E; Pluschinski, P; Sader, R; Birkholz, P; Neuschaefer-Rube, C; Hey, Christiane

2017-02-01

Surface electromyography (sEMG) is a well-established procedure for recording swallowing-related muscle activities. Because the use of a large number of sEMG channels is time consuming and technically sophisticated, the aim of this study was to identify the most significant electrode positions associated with oropharyngeal swallowing activities. Healthy subjects (N = 16) were tested with a total of 42 channels placed in M. masseter, M. orbicularis oris, submental and paralaryngeal regions. Each test subject swallowed 10 ml of water five times. After having identified 16 optimal electrode positions, that is, positions with the strongest signals quantified by the highest integral values, differences to 26 other ones were determined by a Mann-Whitney U test. Kruskal-Wallis H test was utilized for the analysis of differences between single subjects, subject subgroups, and single electrode positions. Factors associated with sEMG signals were examined in a linear regression. Sixteen electrode positions were chosen by a simple ranking of integral values. These positions delivered significantly higher signals than the other 26 positions. Differences between single electrode positions and between test subjects were also significant. Sixteen most significant positions were identified which represent swallowing-related muscle potentials in healthy subjects.

Computational Approach to Identify Different Injuries by Firearms.

PubMed

Costa, Sarah Teixeira; Freire, Alexandre Rodrigues; Matoso, Rodrigo Ivo; Daruge Júnior, Eduardo; Rossi, Ana Cláudia; Prado, Felippe Bevilacqua

2017-03-01

Complications arise in the analysis of gunshot wounds to the maxillofacial region, when neither the projectile nor the gun is found at the crime scene. We simulated 5- and 15-cm firing distances at a human mandible to investigate the external morphology of entrance wounds based on fire range. The ammunition models, .40-caliber S&W, .380-caliber, and 9 × 19-mm Luger, were constructed with free-form NURBS surfaces. In a dynamic simulation, projectiles were fired against mandibular body 3D model at 5 and 15 cm. All entrance wounds presented oval aspect. Maximum diameter and von Mises stress values were 16.5 mm and 50.8 MPa, both for .40-caliber S&W fired at 5 cm. The maximum energy loss was 138.4 J for .40 S&W fired at 15 cm. In conclusion, the mandible was most affected by .40-caliber S&W and morphological differences were observable in holes caused by different incoming projectile calibers fired at different distances. © 2017 American Academy of Forensic Sciences.

Comparison of Different Methods to Identify tdh-Positive Pathogenic Vibrio parahaemolyticus Isolates.

PubMed

Zhang, Hongzhi; Chen, Min

2018-01-01

We evaluated the accuracy and ease of operation of three methods to identify tdh-positive Vibrio parahaemolyticus isolates, including the Kanagawa phenomenon test (KP test), a tdh gene PCR test, and a colloidal gold immunochromatographic assay (CGIA). A total of 221 V. parahaemolyticus isolates were collected from patients, freshly harvested seafood, and fresh seawater. Using the KP test, 92% of V. parahaemolyticus isolates from patients were identified tdh-positive, including four weak KP-positive isolates. The PCR test and CGIA also identified 92% of the isolates as tdh-positive. However, PCR and CGIA only confirmed one of the four weak KP-positive isolates. Similar results were obtained using the three methods to identify V. parahaemolyticus isolates from the other sources. Among the three methods, the KP test was the simplest to perform because it lacked any requirement for sample pretreatment, and was low cost, with no equipment requirements. Therefore, the KP test has been applied widely in many first-line quarantine laboratories. However, the sensitivity and accuracy of KP test were lower than those of the other two methods. PCR can identify the tdh rapidly, specifically, and sensitively. However, PCR requires equipment and facilities that are unavailable in first-line quarantine laboratories. The CGIA can compensate for the disadvantages of the other two methods by its higher sensitivity, accuracy, and ease of operation. Therefore, the CGIA has the highest potential to be used to identify tdh-positive V. parahaemolyticus isolates to guarantee food safety.

Genome-Wide Expression Profiling of Five Mouse Models Identifies Similarities and Differences with Human Psoriasis

PubMed Central

Swindell, William R.; Johnston, Andrew; Carbajal, Steve; Han, Gangwen; Wohn, Christian; Lu, Jun; Xing, Xianying; Nair, Rajan P.; Voorhees, John J.; Elder, James T.; Wang, Xiao-Jing; Sano, Shigetoshi; Prens, Errol P.; DiGiovanni, John; Pittelkow, Mark R.; Ward, Nicole L.; Gudjonsson, Johann E.

2011-01-01

Development of a suitable mouse model would facilitate the investigation of pathomechanisms underlying human psoriasis and would also assist in development of therapeutic treatments. However, while many psoriasis mouse models have been proposed, no single model recapitulates all features of the human disease, and standardized validation criteria for psoriasis mouse models have not been widely applied. In this study, whole-genome transcriptional profiling is used to compare gene expression patterns manifested by human psoriatic skin lesions with those that occur in five psoriasis mouse models (K5-Tie2, imiquimod, K14-AREG, K5-Stat3C and K5-TGFbeta1). While the cutaneous gene expression profiles associated with each mouse phenotype exhibited statistically significant similarity to the expression profile of psoriasis in humans, each model displayed distinctive sets of similarities and differences in comparison to human psoriasis. For all five models, correspondence to the human disease was strong with respect to genes involved in epidermal development and keratinization. Immune and inflammation-associated gene expression, in contrast, was more variable between models as compared to the human disease. These findings support the value of all five models as research tools, each with identifiable areas of convergence to and divergence from the human disease. Additionally, the approach used in this paper provides an objective and quantitative method for evaluation of proposed mouse models of psoriasis, which can be strategically applied in future studies to score strengths of mouse phenotypes relative to specific aspects of human psoriasis. PMID:21483750

Allied Health Students' Learning-Styles Identified with Two Different Assessments

ERIC Educational Resources Information Center

Morton-Rias, Dawn; Dunn, Rita; Terregrossa, Ralph; Geisert, Gene; Mangione, Robert; Ortiz, Samuel; Honigsfeld, Andrea

2008-01-01

This research identified and compared the learning styles of 154 ethnically diverse, upper division undergraduate and graduate students in Allied Health utilizing the "Building Excellence" (BE) (Rundle & Dunn, 2000) and the "Productivity Environmental Preference Survey" (PEPS) (Dunn, Dunn, & Price, 1996). Relationships among age, class standing,…

The use of audit to identify maternal mortality in different settings: is it just a difference between the rich and the poor?

PubMed

van Dillen, Jeroen; Stekelenburg, Jelle; Schutte, Joke; Walraven, Gijs; van Roosmalen, Jos

2007-01-01

To illustrate how maternal mortality audit identifies different causes of and contributing factors to maternal deaths in different settings in low- and high-income countries and how this can lead to local solutions in reducing maternal deaths. Descriptive study of maternal mortality from different settings and review of data on the history of reducing maternal mortality in what are now high-income countries. Kalabo district in Zambia, Farafenni division in The Gambia, Onandjokwe district in Namibia, and the Netherlands. Population of rural areas in Zambia and The Gambia, peri-urban population in Namibia and nationwide data from the Netherlands. Data from facility-based maternal mortality audits from three African hospitals and data from the latest confidential enquiry in the Netherlands. Maternal mortality ratio (MMR), causes (direct and indirect) and characteristics. MMR ranged from 10 per 100,000 (the Netherlands) to 1,540 per 100,000 (The Gambia). Differences in causes of deaths were characterized by HIV/AIDS in Namibia, sepsis and HIV/AIDS in Zambia, (pre-)eclampsia in The Netherlands and obstructed labour in The Gambia. Differences in maternal mortality are more than just differences between the rich and poor. Acknowledging the magnitude of maternal mortality and harnessing a strong political will to tackle the issues are important factors. However, there is no single, general solution to reduce maternal mortality, and identification of problems needs to be promoted through audit, both national and local.

Transcriptional analysis of murine macrophages infected with different Toxoplasma strains identifies novel regulation of host signaling pathways.

PubMed

Melo, Mariane B; Nguyen, Quynh P; Cordeiro, Cynthia; Hassan, Musa A; Yang, Ninghan; McKell, Renée; Rosowski, Emily E; Julien, Lindsay; Butty, Vincent; Dardé, Marie-Laure; Ajzenberg, Daniel; Fitzgerald, Katherine; Young, Lucy H; Saeij, Jeroen P J

2013-01-01

Most isolates of Toxoplasma from Europe and North America fall into one of three genetically distinct clonal lineages, the type I, II and III lineages. However, in South America these strains are rarely isolated and instead a great variety of other strains are found. T. gondii strains differ widely in a number of phenotypes in mice, such as virulence, persistence, oral infectivity, migratory capacity, induction of cytokine expression and modulation of host gene expression. The outcome of toxoplasmosis in patients is also variable and we hypothesize that, besides host and environmental factors, the genotype of the parasite strain plays a major role. The molecular basis for these differences in pathogenesis, especially in strains other than the clonal lineages, remains largely unexplored. Macrophages play an essential role in the early immune response against T. gondii and are also the cell type preferentially infected in vivo. To determine if non-canonical Toxoplasma strains have unique interactions with the host cell, we infected murine macrophages with 29 different Toxoplasma strains, representing global diversity, and used RNA-sequencing to determine host and parasite transcriptomes. We identified large differences between strains in the expression level of known parasite effectors and large chromosomal structural variation in some strains. We also identified novel strain-specifically regulated host pathways, including the regulation of the type I interferon response by some atypical strains. IFNβ production by infected cells was associated with parasite killing, independent of interferon gamma activation, and dependent on endosomal Toll-like receptors in macrophages and the cytoplasmic receptor retinoic acid-inducible gene 1 (RIG-I) in fibroblasts.

Identifying Different Registers of Digital Literacy in Virtual Learning Environments

ERIC Educational Resources Information Center

Knutsson, Ola; Blasjo, Mona.; Hallsten, Stina; Karlstrom, Petter

2012-01-01

In this paper social semiotics, and systemic functional linguistics in particular, are used in order to identify registers of digital literacy in the use of virtual learning environments. The framework of social semiotics provides means to systemize and discuss digital literacy as a linguistic and semiotic issue. The following research question…

A Penalized Robust Method for Identifying Gene-Environment Interactions

PubMed Central

Shi, Xingjie; Liu, Jin; Huang, Jian; Zhou, Yong; Xie, Yang; Ma, Shuangge

2015-01-01

In high-throughput studies, an important objective is to identify gene-environment interactions associated with disease outcomes and phenotypes. Many commonly adopted methods assume specific parametric or semiparametric models, which may be subject to model mis-specification. In addition, they usually use significance level as the criterion for selecting important interactions. In this study, we adopt the rank-based estimation, which is much less sensitive to model specification than some of the existing methods and includes several commonly encountered data and models as special cases. Penalization is adopted for the identification of gene-environment interactions. It achieves simultaneous estimation and identification and does not rely on significance level. For computation feasibility, a smoothed rank estimation is further proposed. Simulation shows that under certain scenarios, for example with contaminated or heavy-tailed data, the proposed method can significantly outperform the existing alternatives with more accurate identification. We analyze a lung cancer prognosis study with gene expression measurements under the AFT (accelerated failure time) model. The proposed method identifies interactions different from those using the alternatives. Some of the identified genes have important implications. PMID:24616063

Spontaneous swallowing frequency has potential to identify dysphagia in acute stroke.

PubMed

Crary, Michael A; Carnaby, Giselle D; Sia, Isaac; Khanna, Anna; Waters, Michael F

2013-12-01

Spontaneous swallowing frequency has been described as an index of dysphagia in various health conditions. This study evaluated the potential of spontaneous swallow frequency analysis as a screening protocol for dysphagia in acute stroke. In a cohort of 63 acute stroke cases, swallow frequency rates (swallows per minute [SPM]) were compared with stroke and swallow severity indices, age, time from stroke to assessment, and consciousness level. Mean differences in SPM were compared between patients with versus without clinically significant dysphagia. Receiver operating characteristic curve analysis was used to identify the optimal threshold in SPM, which was compared with a validated clinical dysphagia examination for identification of dysphagia cases. Time series analysis was used to identify the minimally adequate time period to complete spontaneous swallow frequency analysis. SPM correlated significantly with stroke and swallow severity indices but not with age, time from stroke onset, or consciousness level. Patients with dysphagia demonstrated significantly lower SPM rates. SPM differed by dysphagia severity. Receiver operating characteristic curve analysis yielded a threshold of SPM≤0.40 that identified dysphagia (per the criterion referent) with 0.96 sensitivity, 0.68 specificity, and 0.96 negative predictive value. Time series analysis indicated that a 5- to 10-minute sampling window was sufficient to calculate spontaneous swallow frequency to identify dysphagia cases in acute stroke. Spontaneous swallowing frequency presents high potential to screen for dysphagia in acute stroke without the need for trained, available personnel.

Spontaneous Swallowing Frequency [Has Potential to] Identify Dysphagia in Acute Stroke

PubMed Central

Carnaby, Giselle D; Sia, Isaac; Khanna, Anna; Waters, Michael

2014-01-01

Background and Purpose Spontaneous swallowing frequency has been described as an index of dysphagia in various health conditions. This study evaluated the potential of spontaneous swallow frequency analysis as a screening protocol for dysphagia in acute stroke. Methods In a cohort of 63 acute stroke cases swallow frequency rates (swallows per minute: SPM) were compared to stroke and swallow severity indices, age, time from stroke to assessment, and consciousness level. Mean differences in SPM were compared between patients with vs. without clinically significant dysphagia. ROC analysis was used to identify the optimal threshold in SPM which was compared to a validated clinical dysphagia examination for identification of dysphagia cases. Time series analysis was employed to identify the minimally adequate time period to complete spontaneous swallow frequency analysis. Results SPM correlated significantly with stroke and swallow severity indices but not with age, time from stroke onset, or consciousness level. Patients with dysphagia demonstrated significantly lower SPM rates. SPM differed by dysphagia severity. ROC analysis yielded a threshold of SPM ≤ 0.40 which identified dysphagia (per the criterion referent) with 0.96 sensitivity, 0.68 specificity, and 0.96 negative predictive value. Time series analysis indicated that a 5 to 10 minute sampling window was sufficient to calculate spontaneous swallow frequency to identify dysphagia cases in acute stroke. Conclusions Spontaneous swallowing frequency presents high potential to screen for dysphagia in acute stroke without the need for trained, available personnel. PMID:24149008

Determining Semantically Related Significant Genes.

PubMed

Taha, Kamal

2014-01-01

GO relation embodies some aspects of existence dependency. If GO term xis existence-dependent on GO term y, the presence of y implies the presence of x. Therefore, the genes annotated with the function of the GO term y are usually functionally and semantically related to the genes annotated with the function of the GO term x. A large number of gene set enrichment analysis methods have been developed in recent years for analyzing gene sets enrichment. However, most of these methods overlook the structural dependencies between GO terms in GO graph by not considering the concept of existence dependency. We propose in this paper a biological search engine called RSGSearch that identifies enriched sets of genes annotated with different functions using the concept of existence dependency. We observe that GO term xcannot be existence-dependent on GO term y, if x- and y- have the same specificity (biological characteristics). After encoding into a numeric format the contributions of GO terms annotating target genes to the semantics of their lowest common ancestors (LCAs), RSGSearch uses microarray experiment to identify the most significant LCA that annotates the result genes. We evaluated RSGSearch experimentally and compared it with five gene set enrichment systems. Results showed marked improvement.

Temporospatial dynamics and public health significance of bacterial flora identified on a major leatherback turtle (Dermochelys coriacea) nesting beach in the Southern Caribbean

USGS Publications Warehouse

Phillips, Ayanna Carla N.; Couteau, Johanna; Rajh, Stacy; Stewart, Neville; Watson, Antonio; Jehu, Adam; Asmath, Hamish; Unakal, Chandrashekhar; Dziva, Francis; Holder, Ridley; Carthy, Raymond R.

2017-01-01

Grande Riviere beach, on the island of Trinidad, supports the largest nesting population of leatherback turtles in the Caribbean region. Throughout the nesting season, nests are naturally disturbed by newly nesting females, resulting in egg breakage and loss of some nest viability. This environment is ideal for the growth and proliferation of microorganisms. The range of bacterial flora present in beach sand and egg shells was examined, with emphasis on bacteria that may pose a threat to public and animal health. The extent to which the bacterial load and genera on the beach changed throughout the season was also assessed. Twenty-five genera were identified, with Pseudomonas spp. found to be the most predominant environmental bacteria. Four genera identified possess zoonotic potential, while five additional genera are known to be of public and animal health significance. Distinct shifts in the density and distribution of bacteria were observed along the beach from early to peak nesting season. Shifts were seen across heavily traversed zones, thus highlighting the potential exposure threats posed to beach visitors and animals alike. Further studies aimed at speciating this population of bacteria, as well as isolating potential fungal pathogens may mitigate this threat. Identification of bacterial agents that are specifically pathogenic to leatherback turtles, turtle eggs, hatchlings and those who may interact with these animals will serve to enhance and guide efforts to better conserve this species and protect the health of all who visit this ecologically significant site.

The Case for Use of Simple Difference Scores to Test the Significance of Differences in Mean Rates of Change in Controlled Repeated Measurements Designs

ERIC Educational Resources Information Center

Overall, John E.; Tonidandel, Scott

2010-01-01

A previous Monte Carlo study examined the relative powers of several simple and more complex procedures for testing the significance of difference in mean rates of change in a controlled, longitudinal, treatment evaluation study. Results revealed that the relative powers depended on the correlation structure of the simulated repeated measurements.…

Genetic differences in transcript responses to low-dose ionizing radiation identify tissue functions associated with breast cancer susceptibility.

PubMed

Snijders, Antoine M; Marchetti, Francesco; Bhatnagar, Sandhya; Duru, Nadire; Han, Ju; Hu, Zhi; Mao, Jian-Hua; Gray, Joe W; Wyrobek, Andrew J

2012-01-01

High dose ionizing radiation (IR) is a well-known risk factor for breast cancer but the health effects after low-dose (LD, <10 cGy) exposures remain highly uncertain. We explored a systems approach that compared LD-induced chromosome damage and transcriptional responses in strains of mice with genetic differences in their sensitivity to radiation-induced mammary cancer (BALB/c and C57BL/6) for the purpose of identifying mechanisms of mammary cancer susceptibility. Unirradiated mammary and blood tissues of these strains differed significantly in baseline expressions of DNA repair, tumor suppressor, and stress response genes. LD exposures of 7.5 cGy (weekly for 4 weeks) did not induce detectable genomic instability in either strain. However, the mammary glands of the sensitive strain but not the resistant strain showed early transcriptional responses involving: (a) diminished immune response, (b) increased cellular stress, (c) altered TGFβ-signaling, and (d) inappropriate expression of developmental genes. One month after LD exposure, the two strains showed opposing responses in transcriptional signatures linked to proliferation, senescence, and microenvironment functions. We also discovered a pre-exposure expression signature in both blood and mammary tissues that is predictive for poor survival among human cancer patients (p = 0.0001), and a post-LD-exposure signature also predictive for poor patient survival (p<0.0001). There is concordant direction of expression in the LD-exposed sensitive mouse strain, in biomarkers of human DCIS and in biomarkers of human breast tumors. Our findings support the hypothesis that genetic mechanisms that determine susceptibility to LD radiation induced mammary cancer in mice are similar to the tissue mechanisms that determine poor-survival in breast cancer patients. We observed non-linearity of the LD responses providing molecular evidence against the LNT risk model and obtained new evidence that LD responses are strongly

Expression and significance of MMP3 in synovium of knee joint at different stage in osteoarthritis patients.

PubMed

Chen, Jun-Jie; Huang, Jie-Feng; Du, Wen-Xi; Tong, Pei-Jian

2014-04-01

To investigate the expression and significance of MMP-3 in synovium of knee joint at different stage in osteoarthritis (OA) patients. Knee synovial tissue were collected in 90 OA patients (the OA group). Patients in the OA group was divided into 3 subgroups: grade I subgroup (n=30), grade II subgroup (n=30), grade III; subgroup (n=30). Thirty patients served as control group. Immunohistochemical assay was used to detect the expression of MMP-3 protein in the knee synovial tissue. MMP-3 protein was detected in all knee synovial tissue. The expression of MMP-3 protein in the OA group was significantly higher that in the normal synovium (P<0.05), and the MMP-3 protein was mainly located in the cytoplasm. There was significant difference in the expression of MMP-3 protein between the grade I subgroup and the grade II, grade III subgroups (all P<0.05). The expression of MMP-3 protein was positively related to the severity of OA (r=0.912, P<0.05). The expression of MMP-3 protein are closely related to pathogenic mechanism of OA. It may be an important indicator of early diagnosis and the activity of the disease of osteoarthritis. Copyright © 2014 Hainan Medical College. Published by Elsevier B.V. All rights reserved.

Functional significance of genetically different symbiotic algae Symbiodinium in a coral reef symbiosis.

PubMed

Loram, J E; Trapido-Rosenthal, H G; Douglas, A E

2007-11-01

The giant sea anemone Condylactis gigantea associates with members of two clades of the dinoflagellate alga Symbiodinium, either singly or in mixed infection, as revealed by clade-specific quantitative polymerase chain reaction of large subunit ribosomal DNA. To explore the functional significance of this molecular variation, the fate of photosynthetically fixed carbon was investigated by (14)C radiotracer experiments. Symbioses with algae of clades A and B released ca. 30-40% of fixed carbon to the animal tissues. Incorporation into the lipid fraction and the low molecular weight fraction dominated by amino acids was significantly higher in symbioses with algae of clade A than of clade B, suggesting that the genetically different algae in C. gigantea are not functionally equivalent. Symbioses with mixed infections yielded intermediate values, such that this functional trait of the symbiosis can be predicted from the traits of the contributing algae. Coral and sea anemone symbioses with Symbiodinium break down at elevated temperature, a process known as 'coral bleaching'. The functional response of the C. gigantea symbiosis to heat stress varied between the algae of clades A and B, with particularly depressed incorporation of photosynthetic carbon into lipid of the clade B algae, which are more susceptible to high temperature than the algae of clade A. This study provides a first exploration of how the core symbiotic function of photosynthate transfer to the host varies with the genotype of Symbiodinium, an algal symbiont which underpins corals and, hence, coral reef ecosystems.

Superfund explanation of significant difference for the Record of Decision (EPA Region 10): Umatilla Army Depot (Lagoons), Hermiston, OR, September 30, 1997

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

NONE

1998-10-01

This document presents an Explanation of Significant Difference (ESD) from the Record of Decision (ROD) for the Umatilla Depot Activity (UMDA) Explosives Washout Lagoons Soils Operable Unit issued September 25, 1992 (PB93-964610). This ESD documents the significant differences to the selected remedy outlined in the ROD. In summary, the significant difference from the selected remedy in the ROD is the utilization of the treated soil as the organic component in the re-vegetation of several designated sites on the installation rather than backfilling the former Explosive Washout Lagoons with the compost.

A Q Study of Music Teachers' Attitudes towards the Significance of Individual Differences for Teaching and Learning in Music

ERIC Educational Resources Information Center

Hewitt, Allan

2006-01-01

Classroom teachers' beliefs and attitudes regarding the role and significance of individual differences have received relatively little attention in the literature to date, notwithstanding the well-documented importance both of teachers' beliefs and factors of individual difference for the learning and teaching process. The purpose of this study…

Visualization of Differences in Data Measuring Mathematical Skills

ERIC Educational Resources Information Center

Zoubek, Lukas; Burda, Michal

2009-01-01

Identification of significant differences in sets of data is a common task of data mining. This paper describes a novel visualization technique that allows the user to interactively explore and analyze differences in mean values of analyzed attributes. Statistical tests of hypotheses are used to identify the significant differences and the results…

Identifying the perceptive users for online social systems

PubMed Central

Liu, Xiao-Lu; Guo, Qiang; Han, Jing-Ti

2017-01-01

In this paper, the perceptive user, who could identify the high-quality objects in their initial lifespan, is presented. By tracking the ratings given to the rewarded objects, we present a method to identify the user perceptibility, which is defined as the capability that a user can identify these objects at their early lifespan. Moreover, we investigate the behavior patterns of the perceptive users from three dimensions: User activity, correlation characteristics of user rating series and user reputation. The experimental results for the empirical networks indicate that high perceptibility users show significantly different behavior patterns with the others: Having larger degree, stronger correlation of rating series and higher reputation. Furthermore, in view of the hysteresis in finding the rewarded objects, we present a general framework for identifying the high perceptibility users based on user behavior patterns. The experimental results show that this work is helpful for deeply understanding the collective behavior patterns for online users. PMID:28704382

Identifying the perceptive users for online social systems.

PubMed

Liu, Jian-Guo; Liu, Xiao-Lu; Guo, Qiang; Han, Jing-Ti

2017-01-01

In this paper, the perceptive user, who could identify the high-quality objects in their initial lifespan, is presented. By tracking the ratings given to the rewarded objects, we present a method to identify the user perceptibility, which is defined as the capability that a user can identify these objects at their early lifespan. Moreover, we investigate the behavior patterns of the perceptive users from three dimensions: User activity, correlation characteristics of user rating series and user reputation. The experimental results for the empirical networks indicate that high perceptibility users show significantly different behavior patterns with the others: Having larger degree, stronger correlation of rating series and higher reputation. Furthermore, in view of the hysteresis in finding the rewarded objects, we present a general framework for identifying the high perceptibility users based on user behavior patterns. The experimental results show that this work is helpful for deeply understanding the collective behavior patterns for online users.

Hypoxia and inflammation indicate significant differences in the severity of obstructive sleep apnea within similar apnea-hypopnea index groups.

PubMed

Yilmaz Avci, Aynur; Avci, Suat; Lakadamyali, Huseyin; Can, Ufuk

2017-09-01

We determined whether hypoxia parameters are associated with C-reactive protein (CRP), mean platelet volume (MPV), white matter hyperintensity (WMH), and the severity of obstructive sleep apnea (OSA), and also evaluated whether hypoxia parameters, CRP, MPV, and WMH differ in patients with similar apnea-hypopnea index (AHI) scores. A total of 297 patients, who were evaluated using polysomnography, were assessed retrospectively. The measured hypoxia parameters included total sleep time with oxygen saturation <90% (ST 90 ), percentage of cumulative time with oxygen saturation <90% (CT 90 ), and lowest oxygen saturation (min SaO 2 ). The patients were divided into subgroups according to their CT 90 values, and patients with different AHI severities were divided into subgroups according to their ST 90 and min SaO 2 levels. Hypoxia parameters are associated with CRP, MPV, WMH, and the severity of OSA (P < 0.05). The hypoxia parameters differed in all subgroup analyses of similar AHI groups (P < 0.001), and CRP differed only in severe OSA (P < 0.008, P < 0.001). In subgroup analyses of similar AHI groups, MPV and WMH were not significantly different (P > 0.05). Above the hypoxia threshold (CT 90  ≥ 10%) of CRP, MPV increased significantly and the presence of WMH increased twofold. These data suggest that increased hypoxia severity may mediate increased inflammation and activation of platelets and contribute to the pathogenesis of WMH in patients with OSA. In addition, patients with severe OSA may show significant variability in inflammation and vascular risk. Further prospective data are needed.

Identifying significant gene‐environment interactions using a combination of screening testing and hierarchical false discovery rate control

PubMed Central

Shen, Li; Saykin, Andrew J.; Williams, Scott M.; Moore, Jason H.

2016-01-01

ABSTRACT Although gene‐environment (G× E) interactions play an important role in many biological systems, detecting these interactions within genome‐wide data can be challenging due to the loss in statistical power incurred by multiple hypothesis correction. To address the challenge of poor power and the limitations of existing multistage methods, we recently developed a screening‐testing approach for G× E interaction detection that combines elastic net penalized regression with joint estimation to support a single omnibus test for the presence of G× E interactions. In our original work on this technique, however, we did not assess type I error control or power and evaluated the method using just a single, small bladder cancer data set. In this paper, we extend the original method in two important directions and provide a more rigorous performance evaluation. First, we introduce a hierarchical false discovery rate approach to formally assess the significance of individual G× E interactions. Second, to support the analysis of truly genome‐wide data sets, we incorporate a score statistic‐based prescreening step to reduce the number of single nucleotide polymorphisms prior to fitting the first stage penalized regression model. To assess the statistical properties of our method, we compare the type I error rate and statistical power of our approach with competing techniques using both simple simulation designs as well as designs based on real disease architectures. Finally, we demonstrate the ability of our approach to identify biologically plausible SNP‐education interactions relative to Alzheimer's disease status using genome‐wide association study data from the Alzheimer's Disease Neuroimaging Initiative (ADNI). PMID:27578615

Can Australians identify snakes?

PubMed

Morrison, J J; Pearn, J H; Covacevich, J; Nixon, J

1983-07-23

A study of the ability of Australians to identify snakes was undertaken, in which 558 volunteers (primary and secondary schoolchildren, doctors and university science and medical students) took part. Over all, subjects correctly identified an average of 19% of snakes; 28% of subjects could identify a taipan, 59% could identify a death adder, 18% a tiger snake, 23% an eastern (or common) brown snake, and 0.5% a rough-scaled snake. Eighty-six per cent of subjects who grew up in rural areas could identify a death adder; only 4% of those who grew up in an Australian capital city could identify a nonvenomous python. Male subjects identified snakes more accurately than did female subjects. Doctors and medical students correctly identified an average of 25% of snakes. The ability to identify medically significant Australian snakes was classified according to the observer's background, education, sex, and according to the individual snake species. Australians need to be better educated about snakes indigenous to this country.

Why significant variables aren't automatically good predictors.

PubMed

Lo, Adeline; Chernoff, Herman; Zheng, Tian; Lo, Shaw-Hwa

2015-11-10

Thus far, genome-wide association studies (GWAS) have been disappointing in the inability of investigators to use the results of identified, statistically significant variants in complex diseases to make predictions useful for personalized medicine. Why are significant variables not leading to good prediction of outcomes? We point out that this problem is prevalent in simple as well as complex data, in the sciences as well as the social sciences. We offer a brief explanation and some statistical insights on why higher significance cannot automatically imply stronger predictivity and illustrate through simulations and a real breast cancer example. We also demonstrate that highly predictive variables do not necessarily appear as highly significant, thus evading the researcher using significance-based methods. We point out that what makes variables good for prediction versus significance depends on different properties of the underlying distributions. If prediction is the goal, we must lay aside significance as the only selection standard. We suggest that progress in prediction requires efforts toward a new research agenda of searching for a novel criterion to retrieve highly predictive variables rather than highly significant variables. We offer an alternative approach that was not designed for significance, the partition retention method, which was very effective predicting on a long-studied breast cancer data set, by reducing the classification error rate from 30% to 8%.

Significant Centers of Tectonic Activity as Identified by Wrinkle Ridges for the Western Hemisphere of Mars

NASA Technical Reports Server (NTRS)

Anderson, R.C.; Haldemann, A. F. C.; Golombek, M. P.; Franklin, B. J.; Dohm, J. M.; Lias, J.

2000-01-01

The western hemisphere region of Mars has been the site of numerous scientific investigations regarding its tectonic evolution. For this region of Mars, the dominant tectonic region is the Tharsis province. Tharsis is characterized by an enormous system of radiating grabens and a circumferential system of wrinkle ridges. Past investigations of grabens associated with Tharsis have identified specific centers of tectonic activity. A recent structural analysis of the western hemisphere region of Mars which includes the Tharsis region, utilized 25,000 structures to determine the history of local and regional centers of tectonic activity based primarily on the spatial and temporal relationships of extensional features. This investigation revealed that Tharsis is more structurally complex (heterogeneous) than has been previously identified: it consists of numerous regional and local centers of tectonic activity (some are more dominant and/or more long lived than others). Here we use the same approach as Anderson et al. to determine whether the centers of tectonic activity that formed the extensional features also contributed to wrinkle ridge (compressional) formation.

Stakeholders identify similar barriers but different strategies to facilitate return-to-work: A vignette of a worker with an upper extremity condition.

PubMed

Peters, Susan E; Truong, Anthony P; Johnston, Venerina

2018-01-01

Stakeholders involved in the return-to-work (RTW) process have different roles and qualificationsOBJECTIVE:To explore the perspectives of Australian stakeholders of the RTW barriers and strategies for a worker with an upper extremity condition and a complex workers' compensation case. Using a case vignette, stakeholders were asked to identify barriers and recommend strategies to facilitate RTW. Content analysis was performed on the open-ended responses. The responses were categorised into RTW barriers and strategies using the biopsychosocial model. Pearson's Chi Square and ANOVA were performed to establish group differences. 621 participants (488 healthcare providers (HCPs), 62 employers, 55 insurers and 16 lawyers) identified 36 barriers (31 modifiable): 4 demographic; 8 biological; 15 psychological and 9 social barriers. 484 participants reported 16 RTW strategies: 4 biological; 6 psychological and 6 social strategies. 'Work relationship stressors' (83.4%) and 'Personal relationship stressors' (64.7%) were the most frequently nominated barriers. HCPs most frequently nominated 'Pain management' (49.6%), while employers, insurers and lawyers nominated 'RTW planning/Suitable duties programs' (40.5%; 42.9%; 80%). Stakeholders perceived similar barriers for RTW but recommended different strategies. Stakeholders appeared to be more proficient in identifying barriers than recommending strategies. Future research should focus on tools to both identify RTW barriers and direct intervention.

No Clinically Significant Difference Between Adult and Pediatric IKDC Subjective Knee Evaluation Scores in Adults.

PubMed

Stegmeier, Nicole; Oak, Sameer R; O'Rourke, Colin; Strnad, Greg; Spindler, Kurt P; Jones, Morgan; Farrow, Lutul D; Andrish, Jack; Saluan, Paul

Two versions of the International Knee Documentation Committee (IKDC) Subjective Knee Evaluation form currently exist: the original version (1999) and a recently modified pediatric-specific version (2011). Comparison of the pediatric IKDC with the adult version in the adult population may reveal that either version could be used longitudinally. We hypothesize that the scores for the adult IKDC and pediatric IKDC will not be clinically different among adult patients aged 18 to 50 years. Randomized crossover study design. Level 2. The study consisted of 100 participants, aged 18 to 50 years, who presented to orthopaedic outpatient clinics with knee problems. All participants completed both adult and pediatric versions of the IKDC in random order with a 10-minute break in between. We used a paired t test to test for a difference between the scores and a Welch's 2-sample t test to test for equivalence. A least-squares regression model was used to model adult scores as a function of pediatric scores, and vice versa. A paired t test revealed a statistically significant 1.6-point difference between the mean adult and pediatric scores. However, the 95% confidence interval (0.54-2.66) for this difference did not exceed our a priori threshold of 5 points, indicating that this difference was not clinically important. Equivalence testing with an equivalence region of 5 points further supported this finding. The adult and pediatric scores had a linear relationship and were highly correlated with an R 2 of 92.6%. There is no clinically relevant difference between the scores of the adult and pediatric IKDC forms in adults, aged 18 to 50 years, with knee conditions. Either form, adult or pediatric, of the IKDC can be used in this population for longitudinal studies. If the pediatric version is administered in adolescence, it can be used for follow-up into adulthood.

Accuracy of different cutoff points of body mass index to identify overweight according to body fat values estimated by DEXA.

PubMed

Anzolin, Caroline Cristina; Silva, Diego Augusto Santos; Zanuto, Edner Fernando; Cayres, Suziane Ungari; Codogno, Jamile Sanches; Costa Junior, Paulo; Machado, Dalmo Roberto Lopes; Christofaro, Diego Giulliano Destro

To evaluate the sensitivity and specificity of different cutoff points of body mass index for predicting overweight/obesity according to body fat values estimated by DEXA among Brazilian adolescents. Cross-sectional study including 229 male adolescents aged 10-15 years, in which body adiposity and anthropometric measures were assessed. Nutritional status was classified by BMI according to cutoff points described in scientific literature. Moderate agreements were observed between body fat estimated by DEXA and cutoffs proposed by Cole et al. (K=0.61), Conde and Monteiro (K=0.65), Must et al. (K=0.61) and WHO (K=0.63). The BMI in continuous form showed good agreement with the Dexa (ICC=0.72). The highest sensitivity was observed for cutoff by Conde and Monteiro (0.74 [0.62, 0.84]) and the highest specificity by Cole et al. (0.98 [0.94, 0.99]). For the areas under the ROC curve of cutoff points analyzed, significant difference comparing the cutoff points by Cole et al. and Conde and Monteiro (0.0449 [0.00294, 0.0927]) was observed. The cutoff proposed by Conde and Monteiro was more sensitive in identifying overweight and obesity when compared to the reference method, and the cutoff proposed by Cole et al. presented the highest specificity for such outcomes. Copyright © 2016 Sociedade Brasileira de Pediatria. Published by Elsevier Editora Ltda. All rights reserved.

Using genome wide association studies to identify common QTL regions in three different genetic backgrounds based on Iberian pig breed.

PubMed

Martínez-Montes, Ángel M; Fernández, Almudena; Muñoz, María; Noguera, Jose Luis; Folch, Josep M; Fernández, Ana I

2018-01-01

One of the major limitation for the application of QTL results in pig breeding and QTN identification has been the limited number of QTL effects validated in different animal material. The aim of the current work was to validate QTL regions through joint and specific genome wide association and haplotype analyses for growth, fatness and premier cut weights in three different genetic backgrounds, backcrosses based on Iberian pigs, which has a major role in the analysis due to its high productive relevance. The results revealed nine common QTL regions, three segregating in all three backcrosses on SSC1, 0-3 Mb, for body weight, on SSC2, 3-9 Mb, for loin bone-in weight, and on SSC7, 3 Mb, for shoulder weight, and six segregating in two of the three backcrosses, on SSC2, SSC4, SSC6 and SSC10 for backfat thickness, shoulder and ham weights. Besides, 18 QTL regions were specifically identified in one of the three backcrosses, five identified only in BC_LD, seven in BC_DU and six in BC_PI. Beyond identifying and validating QTL, candidate genes and gene variants within the most interesting regions have been explored using functional annotation, gene expression data and SNP identification from RNA-Seq data. The results allowed us to propose a promising list of candidate mutations, those identified in PDE10A, DHCR7, MFN2 and CCNY genes located within the common QTL regions and those identified near ssc-mir-103-1 considered PANK3 regulators to be further analysed.

Using genome wide association studies to identify common QTL regions in three different genetic backgrounds based on Iberian pig breed

PubMed Central

Martínez-Montes, Ángel M.; Fernández, Almudena; Muñoz, María; Noguera, Jose Luis; Folch, Josep M.

2018-01-01

One of the major limitation for the application of QTL results in pig breeding and QTN identification has been the limited number of QTL effects validated in different animal material. The aim of the current work was to validate QTL regions through joint and specific genome wide association and haplotype analyses for growth, fatness and premier cut weights in three different genetic backgrounds, backcrosses based on Iberian pigs, which has a major role in the analysis due to its high productive relevance. The results revealed nine common QTL regions, three segregating in all three backcrosses on SSC1, 0–3 Mb, for body weight, on SSC2, 3–9 Mb, for loin bone-in weight, and on SSC7, 3 Mb, for shoulder weight, and six segregating in two of the three backcrosses, on SSC2, SSC4, SSC6 and SSC10 for backfat thickness, shoulder and ham weights. Besides, 18 QTL regions were specifically identified in one of the three backcrosses, five identified only in BC_LD, seven in BC_DU and six in BC_PI. Beyond identifying and validating QTL, candidate genes and gene variants within the most interesting regions have been explored using functional annotation, gene expression data and SNP identification from RNA-Seq data. The results allowed us to propose a promising list of candidate mutations, those identified in PDE10A, DHCR7, MFN2 and CCNY genes located within the common QTL regions and those identified near ssc-mir-103-1 considered PANK3 regulators to be further analysed. PMID:29522525

A philosophical taxonomy of ethically significant moral distress.

PubMed

Thomas, Tessy A; McCullough, Laurence B

2015-02-01

Moral distress is one of the core topics of clinical ethics. Although there is a large and growing empirical literature on the psychological aspects of moral distress, scholars, and empirical investigators of moral distress have recently called for greater conceptual clarity. To meet this recognized need, we provide a philosophical taxonomy of the categories of what we call ethically significant moral distress: the judgment that one is not able, to differing degrees, to act on one's moral knowledge about what one ought to do. We begin by unpacking the philosophical components of Andrew Jameton's original formulation from his landmark 1984 work and identify two key respects in which that formulation remains unclear: the origins of moral knowledge and impediments to acting on that moral knowledge. We then selectively review subsequent literature that shows that there is more than one concept of moral distress and that explores the origin of the values implicated in moral distress and impediments to acting on those values. This review sets the stage for identifying the elements of a philosophical taxonomy of ethically significant moral distress. The taxonomy uses these elements to create six categories of ethically significant moral distress: challenges to, threats to, and violations of professional integrity; and challenges to, threats to, and violations of individual integrity. We close with suggestions about how the proposed philosophical taxonomy of ethically significant moral distress sheds light on the concepts of moral residue and crescendo effect of moral distress and how the proposed taxonomy might usefully guide prevention of and future qualitative and quantitative empirical research on ethically significant moral distress. © The Author 2014. Published by Oxford University Press, on behalf of the Journal of Medicine and Philosophy Inc. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Mining the Immune Cell Proteome to Identify Ovarian Cancer-Specific Biomarkers

DTIC Science & Technology

2012-03-01

data and are in the process of identifying gene signatures that can be used as biomarkers for the identification of ovarian cancer-specific biomarkers...groups. The groups showed significant difference in age as well as gestational age, which is expected when considering the disease process . Isolation of...MUC4 in intracellular signaling.32 Oligosaccharides attached to the extracellular domains of mucins have also been shown to interact with different

Method and system employing graphical electric load categorization to identify one of a plurality of different electric load types

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

Yang, Yi; Du, Liang

A system for different electric loads includes sensors structured to sense voltage and current signals for each of the different electric loads; a hierarchical load feature database having a plurality of layers, with one of the layers including a plurality of different load categories; and a processor. The processor acquires voltage and current waveforms from the sensors for a corresponding one of the different electric loads; maps a voltage-current trajectory to a grid including a plurality of cells, each of which is assigned a binary value of zero or one; extracts a plurality of different features from the mapped gridmore » of cells as a graphical signature of the corresponding one of the different electric loads; derives a category of the corresponding one of the different electric loads from the database; and identifies one of a plurality of different electric load types for the corresponding one of the different electric loads.« less

Significant factors for work attractiveness and how these differ from the current work situation among operating department nurses.

PubMed

Björn, Catrine; Lindberg, Magnus; Rissén, Dag

2016-01-01

The aim was to examine significant factors for work attractiveness and how these differ from the current work situation among operating department nurses. A second objective was to examine the associations between age, gender, length of employment, work engagement, work ability, self-rated health indicators and attractiveness of the current work situation. The attractiveness of work is rarely taken into account in research on nurse retention. To expand this knowledge, it is relevant to examine factors that make work attractive and their associations with related concepts. Correlational, cross-sectional survey using a convenience sample. Questionnaires were answered by 147 nurses in four operating departments in Sweden. Correlation and regression analyses were conducted. The nurses rated the significance of all factors of work attractiveness higher than they rated those factors in their current work situation; salary, organisation and physical work environment had the largest differences. The most significant attractive factors were relationships, leadership and status. A statistically significant positive correlation between work engagement and attractive work was found. In the multiple regression model, the independent variables work engagement and older age significantly predicted work attractiveness. Several factors should be considered in the effort to increase work attractiveness in operating departments and thereby to encourage nurse retention. Positive aspects of work seem to unite work engagement and attractive work, while work ability and self-rated health indicators are other important dimensions in nurse retention. The great discrepancies between the significance of attractive factors and the current work situation in salary, organisation and physical work environment suggest ways in which work attractiveness may be increased. To discover exactly what needs to be improved may require a deeper look into the construct of the examined factors. © 2015 John

Identifying Differences among Novice Database Users: Implications for Training Material Effectiveness.

ERIC Educational Resources Information Center

Antonucci, Yvonne Lederer; Wozny, Lucy Anne

1996-01-01

Identifies and describes sublevels of novices using a database management package, clustering those whose interaction is effective, partially effective, and totally ineffective. Among assistance documentation, functional tree diagrams (FTDs) were more beneficial to partially effective users than traditional reference material. The results have…

Comparison of Far-Field Noise for Three Significantly Different Model Turbofans

NASA Technical Reports Server (NTRS)

Woodward, Richard P.

2008-01-01

Far-field noise sound power level (PWL) spectra and overall sound pressure level (OASPL) directivities were compared for three significantly different model fan stages which were tested in the NASA Glenn 9x15 Low Speed Wind Tunnel. The test fans included the Advanced Ducted Propulsor (ADP) Fan1, the baseline Source Diagnostic Test (SDT) fan, and the Quiet High Speed Fan2 (QHSF2) These fans had design rotor tangential tip speeds from 840 to 1474 ft/s and stage pressure ratios from 1.29 to 1.82. Additional parameters included rotor-stator spacing, stator sweep, and downstream support struts. Acoustic comparison points were selected on the basis of stage thrust. Acoustic results for the low tip speed/low pressure ratio fan (ADP Fan1) were thrust-adjusted to show how a geometrically-scaled version of this fan might compare at the higher design thrust levels of the other two fans. Lowest noise levels were typically observed for ADP Fan1 (which had a radial stator) and for the intermediate tip speed fan (Source Diagnostics Test, SDT, R4 rotor) with a swept stator. Projected noise levels for the ADP fan to the SDT swept stator configuration at design point conditions showed the fans to have similar noise levels. However, it is possible that the ADP fan could be 2 to 3 dB quieter with incorporation of a swept stator. Benefits of a scaled ADP fan include avoidance of multiple pure tones associated with transonic and higher blade tip speeds. Penalties of a larger size ADP fan would include increased nacelle size and drag.

Comparison of Far-field Noise for Three Significantly Different Model Turbofans

NASA Technical Reports Server (NTRS)

Woodward, Richard P.

2008-01-01

Far-field noise sound power level (PWL) spectra and overall sound pressure level (OASPL) directivities were compared for three significantly different model fan stages which were tested in the NASA Glenn 9 15 Low Speed Wind Tunnel. The test fans included the Advanced Ducted Propulsor (ADP) Fan1, the baseline Source Diagnostic Test (SDT) fan, and the Quiet High Speed Fan2 (QHSF2). These fans had design rotor tangential tip speeds from 840 to 1474 ft/s and stage pressure ratios from 1.29 to 1.82. Additional parameters included rotor-stator spacing, stator sweep, and downstream support struts. Acoustic comparison points were selected on the basis of stage thrust. Acoustic results for the low tip speed/low pressure ratio fan (ADP Fan1) were thrust-adjusted to show how a geometrically-scaled version of this fan might compare at the higher design thrust levels of the other two fans. Lowest noise levels were typically observed for ADP Fan1 (which had a radial stator) and for the intermediate tip speed fan (Source Diagnostics Test, SDT, R4 rotor) with a swept stator. Projected noise levels for the ADP fan to the SDT swept stator configuration at design point conditions showed the fans to have similar noise levels. However, it is possible that the ADP fan could be 2 to 3 dB quieter with incorporation of a swept stator. Benefits of a scaled ADP fan include avoidance of multiple pure tones associated with transonic and higher blade tip speeds. Penalties of a larger size ADP fan would include increased nacelle size and drag.

Metabolomics and transcriptomics identify pathway differences between visceral and subcutaneous adipose tissue in colorectal cancer patients: the ColoCare study.

PubMed

Liesenfeld, David B; Grapov, Dmitry; Fahrmann, Johannes F; Salou, Mariam; Scherer, Dominique; Toth, Reka; Habermann, Nina; Böhm, Jürgen; Schrotz-King, Petra; Gigic, Biljana; Schneider, Martin; Ulrich, Alexis; Herpel, Esther; Schirmacher, Peter; Fiehn, Oliver; Lampe, Johanna W; Ulrich, Cornelia M

2015-08-01

Metabolic and transcriptomic differences between visceral adipose tissue (VAT) and subcutaneous adipose tissue (SAT) compartments, particularly in the context of obesity, may play a role in colorectal carcinogenesis. We investigated the differential functions of their metabolic compositions. Biochemical differences between adipose tissues (VAT compared with SAT) in patients with colorectal carcinoma (CRC) were investigated by using mass spectrometry metabolomics and gene expression profiling. Metabolite compositions were compared between VAT, SAT, and serum metabolites. The relation between patients' tumor stage and metabolic profiles was assessed. Presurgery blood and paired VAT and SAT samples during tumor surgery were obtained from 59 CRC patients (tumor stages I-IV) of the ColoCare cohort. Gas chromatography time-of-flight mass spectrometry and liquid chromatography quadrupole time-of-flight mass spectrometry were used to measure 1065 metabolites in adipose tissue (333 identified compounds) and 1810 metabolites in serum (467 identified compounds). Adipose tissue gene expression was measured by using Illumina's HumanHT-12 Expression BeadChips. Compared with SAT, VAT displayed elevated markers of inflammatory lipid metabolism, free arachidonic acid, phospholipases (PLA2G10), and prostaglandin synthesis-related enzymes (PTGD/PTGS2S). Plasmalogen concentrations were lower in VAT than in SAT, which was supported by lower gene expression of FAR1, the rate-limiting enzyme for ether-lipid synthesis in VAT. Serum sphingomyelin concentrations were inversely correlated (P = 0.0001) with SAT adipose triglycerides. Logistic regression identified lipids in patients' adipose tissues, which were associated with CRC tumor stage. As one of the first studies, we comprehensively assessed differences in metabolic, lipidomic, and transcriptomic profiles between paired human VAT and SAT and their association with CRC tumor stage. We identified markers of inflammation in VAT, which

Cross-national differences in clinically significant cannabis problems: epidemiologic evidence from 'cannabis-only' smokers in the United States, Mexico, and Colombia.

PubMed

Fiestas, Fabian; Radovanovic, Mirjana; Martins, Silvia S; Medina-Mora, Maria E; Posada-Villa, Jose; Anthony, James C

2010-03-23

Epidemiological studies show wide variability in the occurrence of cannabis smoking and related disorders across countries. This study aims to estimate cross-national variation in cannabis users' experience of clinically significant cannabis-related problems in three countries of the Americas, with a focus on cannabis users who may have tried alcohol or tobacco, but who have not used cocaine, heroin, LSD, or other internationally regulated drugs. Data are from the World Mental Health Surveys Initiative and the National Latino and Asian American Study, with probability samples in Mexico (n = 4426), Colombia (n = 5,782) and the United States (USA; n = 8,228). The samples included 212 'cannabis only' users in Mexico, 260 in Colombia and 1,724 in the USA. Conditional GLM with GEE and 'exact' methods were used to estimate variation in the occurrence of clinically significant problems in cannabis only (CO) users across these surveyed populations. The experience of cannabis-related problems was quite infrequent among CO users in these countries, with weighted frequencies ranging from 1% to 5% across survey populations, and with no appreciable cross-national variation in general. CO users in Colombia proved to be an exception. As compared to CO users in the USA, the Colombia smokers were more likely to have experienced cannabis-associated 'social problems' (odds ratio, OR = 3.0; 95% CI = 1.4, 6.3; p = 0.004) and 'legal problems' (OR = 9.7; 95% CI = 2.7, 35.2; p = 0.001). This study's most remarkable finding may be the similarity in occurrence of cannabis-related problems in this cross-national comparison within the Americas. Wide cross-national variations in estimated population-level cumulative incidence of cannabis use disorders may be traced to large differences in cannabis smoking prevalence, rather than qualitative differences in cannabis experiences. More research is needed to identify conditions that might make cannabis-related social and legal problems more

Detection of Significant Pneumococcal Meningitis Biomarkers by Ego Network.

PubMed

Wang, Qian; Lou, Zhifeng; Zhai, Liansuo; Zhao, Haibin

2017-06-01

To identify significant biomarkers for detection of pneumococcal meningitis based on ego network. Based on the gene expression data of pneumococcal meningitis and global protein-protein interactions (PPIs) data recruited from open access databases, the authors constructed a differential co-expression network (DCN) to identify pneumococcal meningitis biomarkers in a network view. Here EgoNet algorithm was employed to screen the significant ego networks that could accurately distinguish pneumococcal meningitis from healthy controls, by sequentially seeking ego genes, searching candidate ego networks, refinement of candidate ego networks and significance analysis to identify ego networks. Finally, the functional inference of the ego networks was performed to identify significant pathways for pneumococcal meningitis. By differential co-expression analysis, the authors constructed the DCN that covered 1809 genes and 3689 interactions. From the DCN, a total of 90 ego genes were identified. Starting from these ego genes, three significant ego networks (Module 19, Module 70 and Module 71) that could predict clinical outcomes for pneumococcal meningitis were identified by EgoNet algorithm, and the corresponding ego genes were GMNN, MAD2L1 and TPX2, respectively. Pathway analysis showed that these three ego networks were related to CDT1 association with the CDC6:ORC:origin complex, inactivation of APC/C via direct inhibition of the APC/C complex pathway, and DNA strand elongation, respectively. The authors successfully screened three significant ego modules which could accurately predict the clinical outcomes for pneumococcal meningitis and might play important roles in host response to pathogen infection in pneumococcal meningitis.

Multiple Comparisons of Observation Means--Are the Means Significantly Different?

ERIC Educational Resources Information Center

Fahidy, T. Z.

2009-01-01

Several currently popular methods of ascertaining which treatment (population) means are different, via random samples obtained under each treatment, are briefly described and illustrated by evaluating catalyst performance in a chemical reactor.

Borreliacidal OspC Antibody Response of Canines with Lyme Disease Differs Significantly from That of Humans with Lyme Disease▿

PubMed Central

Lovrich, Steven D.; La Fleur, Rhonda L.; Jobe, Dean A.; Johnson, Jennifer C.; Asp, Krista E.; Schell, Ronald F.; Callister, Steven M.

2007-01-01

Humans reliably produce high concentrations of borreliacidal OspC antibodies specific for the seven C-terminal amino acids shortly after infection with Borrelia burgdorferi. We show that dogs also produce OspC borreliacidal antibodies but that their frequencies, intensities, and antigenicities differ significantly. The findings therefore confirm a major difference between the borreliacidal antibody responses of humans and canines with Lyme disease. PMID:17344346

Hot spot analysis applied to identify ecosystem services potential in Lithuania

NASA Astrophysics Data System (ADS)

Pereira, Paulo; Depellegrin, Daniel; Misiune, Ieva

2016-04-01

Hot spot analysis are very useful to identify areas with similar characteristics. This is important for a sustainable use of the territory, since we can identify areas that need to be protected, or restored. This is a great advantage in terms of land use planning and management, since we can allocate resources, reduce the economical costs and do a better intervention in the landscape. Ecosystem services (ES) are different according land use. Since landscape is very heterogeneous, it is of major importance understand their spatial pattern and where are located the areas that provide better ES and the others that provide less services. The objective of this work is to use hot-spot analysis to identify areas with the most valuable ES in Lithuania. CORINE land-cover (CLC) of 2006 was used as the main spatial information. This classification uses a grid of 100 m resolution and extracted a total of 31 land use types. ES ranking was carried out based on expert knowledge. They were asked to evaluate the ES potential of each different CLC from 0 (no potential) to 5 (very high potential). Hot spot analysis were evaluated using the Getis-ord test, which identifies cluster analysis available in ArcGIS toolbox. This tool identifies areas with significantly high low values and significant high values at a p level of 0.05. In this work we used hot spot analysis to assess the distribution of providing, regulating cultural and total (sum of the previous 3) ES. The Z value calculated from Getis-ord was used to statistical analysis to access the clusters of providing, regulating cultural and total ES. ES with high Z value show that they have a high number of cluster areas with high potential of ES. The results showed that the Z-score was significantly different among services (Kruskal Wallis ANOVA =834. 607, p<0.001). The Z score of providing services (0.096±2.239) were significantly higher than the total (0.093±2.045), cultural (0.080±1.979) and regulating (0.076±1.961). These

Case study: Possible differences in phthalates exposure among the Czech, Hungarian, and Slovak populations identified based on the DEMOCOPHES pilot study results.

PubMed

Černá, Milena; Malý, Marek; Rudnai, Peter; Középesy, Szilvia; Náray, Miklós; Halzlová, Katarina; Jajcaj, Michal; Grafnetterová, Anna; Krsková, Andrea; Antošová, Danuše; Forysová, Kateřina; Den Hond, Elly; Schoeters, Greet; Joas, Reinhard; Casteleyn, Ludwine; Joas, Anke; Biot, Pierre; Aerts, Dominique; Angerer, Jürgen; Bloemen, Louis; Castaño, Argelia; Esteban, Marta; Koch, Holger M; Kolossa-Gehring, Marike; Gutleb, Arno C; Pavloušková, Jana; Vrbík, Karel

2015-08-01

Phthalates and their metabolites are classified as endocrine modulators. They affect the hormonal balance in both children and adults. The aim of this publication was to compare the urinary levels of phthalate metabolites in selected populations of the Czech Republic (CZ), Slovakia (SK), and Hungary (HU) in relation to the sources of phthalate exposure identified by means of questionnaire (personal care products, floor and wall coverings, plastic toys, and some kinds of foods). Data were obtained through the twin projects COPHES (COnsortium to Perform Human biomonitoring on a European Scale) and DEMOCOPHES (DEMOnstration of a study to COordinate and Perform Human biomonitoring on a European Scale) from 2009 to 2012. The target groups were children aged 6-11 years old and their mothers up to 45 years of age. The metabolites of phthalates (monomethyl phthalate (MMP), monoethyl phthalate (MEP), monobenzyl phthalate (MBzP), mono-cyclohexyl phthalate (MCHP), mono-(2-ethylhexyl) phthalate (MEHP), mono-(2-ethyl-5-hydroxyhexyl) phthalate (5OH-MEHP), and mono-(2-ethyl-5-oxohexyl) phthalate (5OXO-MEHP)) were analysed in first morning urine samples. After enzymatic glucuronide cleavage, the urine sample analyses were performed using ultra-high-performance liquid chromatography-electrospray ionization tandem mass spectrometry (UHPLC-ESI-MS/MS) in one laboratory that qualified in the External Quality Assessment exercises organised by COPHES. Significant differences in phthalate exposure between countries were revealed for children only but not for mothers. The concentrations of 5-OH-MEHP (P<0.001), 5OXO-MEHP (P<0.001), and their sum (P<0.001) were the highest in SK compared to CZ and HU. The health based guidance values for the sum of DEHP metabolites 5-OH MEHP and 5OXO-MEHP established by the German Commission for biomonitoring of 300 µg/L and 500 µg/L for women adults and children, respectively, were only exceeded in one mother and three boys. A significant difference was

[The expression and significance of VIP and its receptor in the cochlea of different degrees of chronic alcoholism rats].

PubMed

Feng, Jing; Liu, Haibing

2015-07-01

To determine whether chronic alcoholism alters the expression levels of Vasoactive intestinal polypeptide (VIP) and its receptor (VIPR1) in the cochlea of chronic alcoholism rats. We measured their expression levels in 30 SD rats, in which we created models of different degrees of chronic alcoholism. We investigated the presence of the mRNA of VIP in the cochlea of chronic alcoholism rats and controls by reverse transcription-polymerase chain reaction (RT-PCR) method. We investigated the presence of proteins of VIPR1 in poisoned rats and controls by western blot. We also evaluated the local distribution of VIP cells by immunohistochemistry. We found that the levels of VIP and VIPR1 were downregulated in the chronic alcoholism groups compared to the controls group. The differences in some expression levels were significant different between chronic alcoholism rats and control rats. Moreover, at different degrees of alcohol poisoning in rats, the contents of VIP and VIPR1 differed. Decreased levels of VIP and VIPR1 were detected in the deep chronic alcoholism group compared to the group with low-degree poisoning (P < 0.05). In spiral ganglion cell plasm the expression of VIP and VIPR1 had no significant difference in three groups (P > 0.05). These results suggest that VIP and VIPR1 play an important role in the auditory function in rats with chronic alcoholism. Chronic alcoholism may cause a peptide hormone secretion imbalance in the auditory system, eventually leading to hearing loss.

Subgroups of Paediatric Acute Lymphoblastic Leukaemia Might Differ Significantly in Genetic Predisposition to Asparaginase Hypersensitivity

PubMed Central

Kutszegi, Nóra; Semsei, Ágnes F.; Gézsi, András; Sági, Judit C.; Nagy, Viktória; Csordás, Katalin; Jakab, Zsuzsanna; Lautner-Csorba, Orsolya; Gábor, Krisztina Míta; Kovács, Gábor T.; Erdélyi, Dániel J.; Szalai, Csaba

2015-01-01

L-asparaginase (ASP) is a key element in the treatment of paediatric acute lymphoblastic leukaemia (ALL). However, hypersensitivity reactions (HSRs) to ASP are major challenges in paediatric patients. Our aim was to investigate genetic variants that may influence the risk to Escherichia coli-derived ASP hypersensitivity. Sample and clinical data collection was carried out from 576 paediatric ALL patients who were treated according to protocols from the Berlin—Frankfurt—Münster Study Group. A total of 20 single nucleotide polymorphisms (SNPs) in GRIA1 and GALNT10 genes were genotyped. Patients with GRIA1 rs4958351 AA/AG genotype showed significantly reduced risk to ASP hypersensitivity compared to patients with GG genotype in the T-cell ALL subgroup (OR = 0.05 (0.01–0.26); p = 4.70E-04), while no such association was found in pre-B-cell ALL. In the medium risk group two SNPs of GRIA1 (rs2055083 and rs707176) were associated significantly with the occurrence of ASP hypersensitivity (OR = 0.21 (0.09–0.53); p = 8.48E-04 and OR = 3.02 (1.36–6.73); p = 6.76E-03, respectively). Evaluating the genders separately, however, the association of rs707176 with ASP HSRs was confined only to females. Our results suggest that genetic variants of GRIA1 might influence the risk to ASP hypersensitivity, but subgroups of patients can differ significantly in this respect. PMID:26457809

Identifying influential nodes in complex networks: A node information dimension approach

NASA Astrophysics Data System (ADS)

Bian, Tian; Deng, Yong

2018-04-01

In the field of complex networks, how to identify influential nodes is a significant issue in analyzing the structure of a network. In the existing method proposed to identify influential nodes based on the local dimension, the global structure information in complex networks is not taken into consideration. In this paper, a node information dimension is proposed by synthesizing the local dimensions at different topological distance scales. A case study of the Netscience network is used to illustrate the efficiency and practicability of the proposed method.

Functional Brain Activation Differences in Stuttering Identified with a Rapid fMRI Sequence

ERIC Educational Resources Information Center

Loucks, Torrey; Kraft, Shelly Jo; Choo, Ai Leen; Sharma, Harish; Ambrose, Nicoline G.

2011-01-01

The purpose of this study was to investigate whether brain activity related to the presence of stuttering can be identified with rapid functional MRI (fMRI) sequences that involved overt and covert speech processing tasks. The long-term goal is to develop sensitive fMRI approaches with developmentally appropriate tasks to identify deviant speech…

No Clinically Significant Difference Between Adult and Pediatric IKDC Subjective Knee Evaluation Scores in Adults

PubMed Central

Stegmeier, Nicole; Oak, Sameer R.; O’Rourke, Colin; Strnad, Greg; Spindler, Kurt P.; Jones, Morgan; Farrow, Lutul D.; Andrish, Jack; Saluan, Paul

2017-01-01

Background: Two versions of the International Knee Documentation Committee (IKDC) Subjective Knee Evaluation form currently exist: the original version (1999) and a recently modified pediatric-specific version (2011). Comparison of the pediatric IKDC with the adult version in the adult population may reveal that either version could be used longitudinally. Hypothesis: We hypothesize that the scores for the adult IKDC and pediatric IKDC will not be clinically different among adult patients aged 18 to 50 years. Study Design: Randomized crossover study design. Level of Evidence: Level 2. Methods: The study consisted of 100 participants, aged 18 to 50 years, who presented to orthopaedic outpatient clinics with knee problems. All participants completed both adult and pediatric versions of the IKDC in random order with a 10-minute break in between. We used a paired t test to test for a difference between the scores and a Welch’s 2-sample t test to test for equivalence. A least-squares regression model was used to model adult scores as a function of pediatric scores, and vice versa. Results: A paired t test revealed a statistically significant 1.6-point difference between the mean adult and pediatric scores. However, the 95% confidence interval (0.54-2.66) for this difference did not exceed our a priori threshold of 5 points, indicating that this difference was not clinically important. Equivalence testing with an equivalence region of 5 points further supported this finding. The adult and pediatric scores had a linear relationship and were highly correlated with an R2 of 92.6%. Conclusion: There is no clinically relevant difference between the scores of the adult and pediatric IKDC forms in adults, aged 18 to 50 years, with knee conditions. Clinical Relevance: Either form, adult or pediatric, of the IKDC can be used in this population for longitudinal studies. If the pediatric version is administered in adolescence, it can be used for follow-up into adulthood. PMID

Gait and Balance Measures Can Identify Change From a Cerebrospinal Fluid Tap Test in Idiopathic Normal Pressure Hydrocephalus.

PubMed

Gallagher, Ryan; Marquez, Jodie; Osmotherly, Peter

2018-04-25

To identify in patients with idiopathic normal pressure hydrocephalus (iNPH) undergoing a cerebrospinal fluid (CSF) tap test (TT) for consideration of a ventricular peritoneal (VP) shunt: (1) gait and balance measures, which identify symptom change; (2) differences present between pre- and post-CSF TT scores between patients classified as responders and nonresponder; (3) ability of patients with iNPH to accurately quantify change in their gait and balance symptoms from a CSF TT. Prospective observational study. Post-CSF TT assessment was completed 2-4 hours post. Tertiary referral neurological and neurosurgical hospital. Patients (N=74) with iNPH receiving a 30 mL CSF TT for consideration of a VP shunt. Patients underwent a battery of gait and balance measures pre- and post-CSF TT and indicated their perceived change on a global rating of change (GRC). Patients deemed to improve and offered VP shunt insertion by a neurologist or neurosurgeon were labeled responders. Performance oriented mobility assessment (Tinetti), Berg Balance Scale (BBS), timed Up and Go (TUG), 10-meter walk test (10MWT), GRC. Forty patients were classified responders, 34 nonresponders. Significant differences were identified for responders: Tinetti (3.88 points), TUG (3.98 seconds), 10MWT (0.08 m/sec), and BBS (5.29 points). Significant differences were found for nonresponders for the Tinetti (0.91 points) and BBS (2.06 points). Change scores for responders and nonresponders were significantly different for all tests between responders and nonresponders. GRC scores for gait (+2 for responders, 0 for nonresponders) and balance (+2.5 for responders, 0 for nonresponders) were both significantly different. The Tinetti, BBS, and TUG can identify change in patients undergoing a CSF TT for iNPH. Patients appear to be able to accurately identify if change has occurred. Copyright © 2018 American Congress of Rehabilitation Medicine. Published by Elsevier Inc. All rights reserved.

Collecting and learning to identify edible fungi in southeastern Poland: age and gender differences.

PubMed

Luczaj, Lukasz; Nieroda, Zofia

2011-01-01

The gathering of 17 folk taxa of edible fungi (most commonly Boletus edulis, Leccinum spp., Xerocomus spp., Suillus spp., Cantharellus cibarius, Armillaria spp., Russula spp., Lactarius salmonicolor, Macrolepiota procera, Boletus erythropus) was recorded in three villages in southeast Poland, but only 13 of them are gathered by children. Gender and age differences were small (apart from the fact that more adults than children collect non-Boletaceae species), and relatives of both sexes took part in teaching children about mushrooms, although fathers were most frequently mentioned as first teachers. Collecting mushrooms, mainly for own use, sometimes for sale, is still a culturally significant activity.

A Matter of Timing: Identifying Significant Multi-Dose Radiotherapy Improvements by Numerical Simulation and Genetic Algorithm Search

PubMed Central

Angus, Simon D.; Piotrowska, Monika Joanna

2014-01-01

Multi-dose radiotherapy protocols (fraction dose and timing) currently used in the clinic are the product of human selection based on habit, received wisdom, physician experience and intra-day patient timetabling. However, due to combinatorial considerations, the potential treatment protocol space for a given total dose or treatment length is enormous, even for relatively coarse search; well beyond the capacity of traditional in-vitro methods. In constrast, high fidelity numerical simulation of tumor development is well suited to the challenge. Building on our previous single-dose numerical simulation model of EMT6/Ro spheroids, a multi-dose irradiation response module is added and calibrated to the effective dose arising from 18 independent multi-dose treatment programs available in the experimental literature. With the developed model a constrained, non-linear, search for better performing cadidate protocols is conducted within the vicinity of two benchmarks by genetic algorithm (GA) techniques. After evaluating less than 0.01% of the potential benchmark protocol space, candidate protocols were identified by the GA which conferred an average of 9.4% (max benefit 16.5%) and 7.1% (13.3%) improvement (reduction) on tumour cell count compared to the two benchmarks, respectively. Noticing that a convergent phenomenon of the top performing protocols was their temporal synchronicity, a further series of numerical experiments was conducted with periodic time-gap protocols (10 h to 23 h), leading to the discovery that the performance of the GA search candidates could be replicated by 17–18 h periodic candidates. Further dynamic irradiation-response cell-phase analysis revealed that such periodicity cohered with latent EMT6/Ro cell-phase temporal patterning. Taken together, this study provides powerful evidence towards the hypothesis that even simple inter-fraction timing variations for a given fractional dose program may present a facile, and highly cost

A matter of timing: identifying significant multi-dose radiotherapy improvements by numerical simulation and genetic algorithm search.

PubMed

Angus, Simon D; Piotrowska, Monika Joanna

2014-01-01

Multi-dose radiotherapy protocols (fraction dose and timing) currently used in the clinic are the product of human selection based on habit, received wisdom, physician experience and intra-day patient timetabling. However, due to combinatorial considerations, the potential treatment protocol space for a given total dose or treatment length is enormous, even for relatively coarse search; well beyond the capacity of traditional in-vitro methods. In constrast, high fidelity numerical simulation of tumor development is well suited to the challenge. Building on our previous single-dose numerical simulation model of EMT6/Ro spheroids, a multi-dose irradiation response module is added and calibrated to the effective dose arising from 18 independent multi-dose treatment programs available in the experimental literature. With the developed model a constrained, non-linear, search for better performing cadidate protocols is conducted within the vicinity of two benchmarks by genetic algorithm (GA) techniques. After evaluating less than 0.01% of the potential benchmark protocol space, candidate protocols were identified by the GA which conferred an average of 9.4% (max benefit 16.5%) and 7.1% (13.3%) improvement (reduction) on tumour cell count compared to the two benchmarks, respectively. Noticing that a convergent phenomenon of the top performing protocols was their temporal synchronicity, a further series of numerical experiments was conducted with periodic time-gap protocols (10 h to 23 h), leading to the discovery that the performance of the GA search candidates could be replicated by 17-18 h periodic candidates. Further dynamic irradiation-response cell-phase analysis revealed that such periodicity cohered with latent EMT6/Ro cell-phase temporal patterning. Taken together, this study provides powerful evidence towards the hypothesis that even simple inter-fraction timing variations for a given fractional dose program may present a facile, and highly cost-effecitive means

[Expression and significance of p75NTR in dorsal root ganglia in different injury models].

PubMed

Li, Fang; Cai, Yan; Zhang, Jian-Yi

2008-12-01

To determine the expression and significance of p75NTR in the neuron and glia of dorsal root ganglia (DRG) in different injury models. The models of sciatic nerve injury, spinal cord injury, and combined injury (sciatic nerve injury one week prior to spinal cord injury) were established. The rats were randomly divided into a normal group,a sciatic nerve injury group,a spinal cord injury group, and a combined injury group. The sensory neurons in the DRG were labeled by fast blue (FB) injected in the dorsal column of spinal cord 0.5mm rostral to the transection site. The expression of p75NTR in the neurons and glia of the DRG was examined with immunofluorescence histochemistry after different kinds of injury and its expression in the FB positive neurons was further observed with immunofluorescence histochemistry combined with FB retrograde labeling. The expression of p75NTR was increased in the glia, but was downregulated in sensory neurons in the sciatic nerve injury group compared with the normal group. p75NTR immunoreactive products were downregulated in the glia in the spinal cord injury group compared with the sciatic nerve injury group or the combined injury group. In the combined lesion animals, the expression of p75NTR was similar to that of the sciatic nerve injury group. Its expression in the sensory neurons of DRG was downregulated,but was upregulated in the glia. The majority of sensory neurons labeled by FB in the combined injury group were p75NTR-negative, but surrounded by p75NTR-positive glia. p75NTR immunoreactive products in the glia and neurons of DRG have significant discrepancy after injury. The glial p75NTR in the DRG may play a role in the enhanced regeneration of acsending tract in the injured spinal cord after combined injury.

Identified motor terminals in Drosophila larvae show distinct differences in morphology and physiology

NASA Technical Reports Server (NTRS)

Lnenicka, G. A.; Keshishian, H.

2000-01-01

In Drosophila, the type I motor terminals innervating the larval ventral longitudinal muscle fibers 6 and 7 have been the most popular preparation for combining synaptic studies with genetics. We have further characterized the normal morphological and physiological properties of these motor terminals and the influence of muscle size on terminal morphology. Using dye-injection and physiological techniques, we show that the two axons supplying these terminals have different innervation patterns: axon 1 innervates only muscle fibers 6 and 7, whereas axon 2 innervates all of the ventral longitudinal muscle fibers. This difference in innervation pattern allows the two axons to be reliably identified. The terminals formed by axons 1 and 2 on muscle fibers 6 and 7 have the same number of branches; however, axon 2 terminals are approximately 30% longer than axon 1 terminals, resulting in a corresponding greater number of boutons for axon 2. The axon 1 boutons are approximately 30% wider than the axon 2 boutons. The excitatory postsynaptic potential (EPSP) produced by axon 1 is generally smaller than that produced by axon 2, although the size distributions show considerable overlap. Consistent with vertebrate studies, there is a correlation between muscle fiber size and terminal size. For a single axon, terminal area and length, the number of terminal branches, and the number of boutons are all correlated with muscle fiber size, but bouton size is not. During prolonged repetitive stimulation, axon 2 motor terminals show synaptic depression, whereas axon 1 EPSPs facilitate. The response to repetitive stimulation appears to be similar at all motor terminals of an axon. Copyright 2000 John Wiley & Sons, Inc.

Is magnetic resonance imaging in addition to a computed tomographic scan necessary to identify clinically significant cervical spine injuries in obtunded blunt trauma patients?

PubMed

Fisher, Brian M; Cowles, Steven; Matulich, Jennifer R; Evanson, Bradley G; Vega, Diana; Dissanaike, Sharmila

2013-12-01

Guidelines are in place directing the clearance of the cervical spine in patients who are awake, alert, and oriented, but a gold standard has not been recognized for patients who are obtunded. Our study is designed to determine if magnetic resonance imaging (MRI) detects clinically significant injuries not seen on computed tomographic (CT) scans. The trauma registry was used to identify and retrospectively review medical records of blunt trauma patients from January 1, 2005, to March 30, 2012. Only obtunded patients with a CT scan and MRI of the cervical spine were included. The study cohort consisted of 277 patients. In 13 (5%) patients, MRI detected clinically significant cervical spine injuries that were missed by CT scans, and in 7 (3%) these injuries required intervention. The number needed to screen with MRI to prevent 1 missed injury was 21. The findings suggest that the routine use of MRI in clearing the cervical spine in the obtunded blunt trauma patient. Copyright © 2013 Elsevier Inc. All rights reserved.

Numerical simulations of significant orographic precipitation in Madeira island

NASA Astrophysics Data System (ADS)

Couto, Flavio Tiago; Ducrocq, Véronique; Salgado, Rui; Costa, Maria João

2016-03-01

High-resolution simulations of high precipitation events with the MESO-NH model are presented, and also used to verify that increasing horizontal resolution in zones of complex orography, such as in Madeira island, improve the simulation of the spatial distribution and total precipitation. The simulations succeeded in reproducing the general structure of the cloudy systems over the ocean in the four periods considered of significant accumulated precipitation. The accumulated precipitation over the Madeira was better represented with the 0.5 km horizontal resolution and occurred under four distinct synoptic situations. Different spatial patterns of the rainfall distribution over the Madeira have been identified.

Genetic polymorphisms in the formaldehyde dehydrogenase gene and their biological significance.

PubMed

Just, Walter; Zeller, Jasmin; Riegert, Clarissa; Speit, Günter

2011-11-30

The GSH-dependent formaldehyde dehydrogenase (FDH) is the most important enzyme for the metabolic inactivation of formaldehyde. We studied three polymorphisms of this gene with the intention to elucidate their relevance for inter-individual differences in the protection against the (geno-)toxicity of FA. The first polymorphism (rs11568816) was investigated using real-time PCR and restriction fragment analysis in 150 subjects. However, we did not find the polymorphic sequence in any of the subjects. We studied a second polymorphism (rs17028487), representing a base exchange (c.*114A>G) in exon 9 of the FDH gene. We analyzed 70 subjects with the SNaPshot Primer Extension method and subsequent analysis in a ABI PRISM 3100, but no variant allele was identified. A third polymorphism, rs13832 in exon 9 (c.*493G>T), was studied in a group of 105 subjects by the SNaPshot Primer Extension method. 43 of the subjects were heterozygous for the polymorphism (G/T), 46 homozygous for the T allele, and 16 were homozygous for the G-allele. Real-time RT-PCR measurements of FDH mRNA did not indicate a significant difference in transcript levels between the heterozygous and the homozygous groups. The in vitro comet assay after FA exposure of blood samples obtained from 5 homozygous GG and 3 homozygous TT subjects did not lead to a significant difference between these two groups. Altogether, our study did not identify biologically relevant polymorphisms in transcribed regions of the FDH gene, which may lead to inter-individual differences in the metabolic inactivation of FA. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

Historical Significance from Turkish Students' Perspective

ERIC Educational Resources Information Center

Avarogullari, Muhammet; Kolcu, Nurten

2016-01-01

The purpose of this study is to determine how students in a south-western province of Turkey employ historical significance which is one of the second order concepts of historical thinking. 44 11th and 12th grade students participated in the study. They were asked to identify the most significant 10 persons in the history and provide their reasons…

Eye-hand preference in schizophrenia: sex differences and significance for hand function.

PubMed

Liu, Yi-Chia; Yang, Yen Kuang; Lee, I Hui; Lin, Keh-Chung; Jeffries, Keith J; Lee, Li-Ching

2004-06-01

Hand preference and eye dominance were investigated in 73 (30 women, 43 men) schizophrenic patients and 71 (30 women, 41 men) healthy controls. There were significantly more schizophrenic patients and normal controls who were significantly right-hand dominant. However, schizophrenic patients showed a significant excess of left-eye dominance relative to controls (65.8% vs 29.6%; Odds Ratio= 4.75, p< .001). In addition, female schizophrenic patients showed a higher rate of nonright (either left or inconsistent) eye dominance (80%) than male schizophrenic patients (55.8%) and controls (33.3%). Analysis of hand performance on the Purdue Pegboard Test indicated that schizophrenic patients who showed crossed eye-hand dominance scored higher than did patients without crossed eye-hand dominance.

Arabidopsis plants grown in the field and climate chambers significantly differ in leaf morphology and photosystem components

PubMed Central

2012-01-01

Background Plants exhibit phenotypic plasticity and respond to differences in environmental conditions by acclimation. We have systematically compared leaves of Arabidopsis thaliana plants grown in the field and under controlled low, normal and high light conditions in the laboratory to determine their most prominent phenotypic differences. Results Compared to plants grown under field conditions, the "indoor plants" had larger leaves, modified leaf shapes and longer petioles. Their pigment composition also significantly differed; indoor plants had reduced levels of xanthophyll pigments. In addition, Lhcb1 and Lhcb2 levels were up to three times higher in the indoor plants, but differences in the PSI antenna were much smaller, with only the low-abundance Lhca5 protein showing altered levels. Both isoforms of early-light-induced protein (ELIP) were absent in the indoor plants, and they had less non-photochemical quenching (NPQ). The field-grown plants had a high capacity to perform state transitions. Plants lacking ELIPs did not have reduced growth or seed set rates, but their mortality rates were sometimes higher. NPQ levels between natural accessions grown under different conditions were not correlated. Conclusion Our results indicate that comparative analysis of field-grown plants with those grown under artificial conditions is important for a full understanding of plant plasticity and adaptation. PMID:22236032

Is valve choice a significant determinant of paravalular leak post-transcatheter aortic valve implantation? A systematic review and meta-analysis.

PubMed

O'Sullivan, Katie E; Gough, Aideen; Segurado, Ricardo; Barry, Mitchel; Sugrue, Declan; Hurley, John

2014-05-01

Paravalvular regurgitation (PVR) following transcatheter aortic valve implantation (TAVI) is associated with poor survival. The two main valve delivery systems used to date differ significantly in both structure and deployment technique. The primary objective of this study was to perform a systematic review and meta-analysis of studies identifying PVR in patients post-TAVI using Medtronic CoreValve (MCV) and Edward Sapien (ES) valves in order to identify whether a significant difference exists between valve types. The secondary objective was to identify additional factors predisposing to PVR to provide an overview of the other associated considerations. A systematic review and meta-analysis of the current literature to identify PVR rate in patients with MCV and ES valves was performed. We also sought to examine other factors predisposing to PVR. A total of 5910 patients were identified from 9 studies. PVR rates for MCV and ES were analysed. MCV was associated with a higher PVR rate of 15.75% [95% confidence interval (CI) 12.48-19.32] compared with ES 3.93% [95% CI 1.05-8.38]. We separately reviewed predisposing factors associated with PVR. A formal comparison of the MCV and ES valve leakage rates by mixed-effects meta-regression with a fixed-effect moderator variable for valve type (MCV or ES) suggested a statistically significant difference in leakage rate between the two valve types (P = 0.0002). Unfavourable anatomical and pathological factors as well as valve choice have an impact on rates of PVR. Additionally, certain anatomical features dictate valve choice. A direct comparison of all the predisposing factors at this time is not possible and will require prospective multivariate analysis. There is, however, a significant difference in the PVR rates between valves based on the published observational data available to date. The ES valve associated with a lower incidence of PVR overall; therefore, we conclude that valve choice is indeed a significant

Using Voronoi Tessellations to identify groups in N-body Simulation

NASA Astrophysics Data System (ADS)

Gonzalez, R. E.; Theuns, T.

Dark matter N-body simulations often use a friends-of-friends (FOF) group finder to link together particles above a specified density threshold. An over density of 200 picks-out objects that can be identified with virialised dark matter haloes, based on the spherical collapse model for the formation of structure. When the halo contains significant substructure, as is the case in very high resolution simulations, then FOF will simply link all substructure to the parent halo. Many cosmological simulations now also include gas and stars, and these are often distributed differently from the dark matter. It is then not clear whether the structures identified by FOF are very physical. Here we use Voronoi tesselations to identify structures in hydrodynamical cosmological simulations, that contain dark matter, gas and stars. This adaptive technique allows accurate estimates of densities, and density gradients, for a non-structured distribution of points. We discuss how these estimates allow us to identify structures in the dark matter that can be identified with haloes, and in the stars, to identify galaxies.

An Allometric Modelling Approach to Identify the Optimal Body Shape Associated with, and Differences between Brazilian and Peruvian Youth Motor Performance

PubMed Central

Silva, Simonete; Bustamante, Alcibíades; Nevill, Alan; Katzmarzyk, Peter T.; Freitas, Duarte; Prista, António; Maia, José

2016-01-01

Children from developed and developing countries differ in their body size and shape due to marked differences across their life history caused by social, economic and cultural differences which are also linked to their motor performance (MP). We used allometric models to identify size/shape characteristics associated with MP tests between Brazilian and Peruvian schoolchildren. A total of 4,560 subjects, 2,385 girls and 2,175 boys aged 9–15 years were studied. Height and weight were measured; biological maturation was estimated with the maturity offset technique; MP measures included the 12 minute run (12MR), handgrip strength (HG), standing long jump (SLJ) and the shuttle run speed (SR) tests; physical activity (PA) was assessed using the Baecke questionnaire. A multiplicative allometric model was adopted to adjust for body size differences across countries. Reciprocal ponderal index (RPI) was found to be the most suitable body shape indicator associated with the 12MR, SLJ, HG and SR performance. A positive maturation offset parameter was also associated with a better performance in SLJ, HG and SR tests. Sex differences were found in all motor tests. Brazilian youth showed better scores in MP than their Peruvian peers, even when controlling for their body size differences The current study identified the key body size associated with four body mass-dependent MP tests. Biological maturation and PA were associated with strength and motor performance. Sex differences were found in all motor tests, as well as across countries favoring Brazilian children even when accounting for their body size/shape differences. PMID:26939118

An Allometric Modelling Approach to Identify the Optimal Body Shape Associated with, and Differences between Brazilian and Peruvian Youth Motor Performance.

PubMed

Silva, Simonete; Bustamante, Alcibíades; Nevill, Alan; Katzmarzyk, Peter T; Freitas, Duarte; Prista, António; Maia, José

2016-01-01

Children from developed and developing countries differ in their body size and shape due to marked differences across their life history caused by social, economic and cultural differences which are also linked to their motor performance (MP). We used allometric models to identify size/shape characteristics associated with MP tests between Brazilian and Peruvian schoolchildren. A total of 4,560 subjects, 2,385 girls and 2,175 boys aged 9-15 years were studied. Height and weight were measured; biological maturation was estimated with the maturity offset technique; MP measures included the 12 minute run (12MR), handgrip strength (HG), standing long jump (SLJ) and the shuttle run speed (SR) tests; physical activity (PA) was assessed using the Baecke questionnaire. A multiplicative allometric model was adopted to adjust for body size differences across countries. Reciprocal ponderal index (RPI) was found to be the most suitable body shape indicator associated with the 12MR, SLJ, HG and SR performance. A positive maturation offset parameter was also associated with a better performance in SLJ, HG and SR tests. Sex differences were found in all motor tests. Brazilian youth showed better scores in MP than their Peruvian peers, even when controlling for their body size differences The current study identified the key body size associated with four body mass-dependent MP tests. Biological maturation and PA were associated with strength and motor performance. Sex differences were found in all motor tests, as well as across countries favoring Brazilian children even when accounting for their body size/shape differences.

Influence of affective significance on different levels of processing using pupil dilation in an analogical reasoning task.

PubMed

Prehn, Kristin; Heekeren, Hauke R; van der Meer, Elke

2011-02-01

The present study investigates the interaction of cognition and emotion in decision making, using an analogical reasoning task. In this task, two word pairs were presented simultaneously. Each word pair could be characterized by an associative conceptual relation (object, actor, or location relation) as well as an emotional relation (negative, neutral, or positive valence). Both types of relations were equally task-relevant: Participants had to identify both types of relations, to compare them, and to decide whether or not the word pairs were analogous, i.e., corresponding in both conceptual and emotional relations. Behavioral data showed that emotional relations were identified preferentially and faster than conceptual relations. Pupil dilations reflected the descending difficulty of the conditions and were greatest in amplitude when both conceptual and emotional correspondence was shown, intermediate when only one type of relation (either the emotional or the conceptual) corresponded, and least when neither correspondence existed. Additionally, a negative valence of the word material slowed down response times and increased pupil dilation relative to positive and neutral items. In summary, pupil and response time data together support recent (neurobiological) models concerning the interaction of emotion and cognition by showing that affective significance leads to a processing advantage at a cognitively lower level of information processing (here, identification or retrieval of relations from long-term memory) but can also distract people from higher level cognitive processes (here, from the controlled comparison of retrieved relations). Copyright © 2010 Elsevier B.V. All rights reserved.

Principal component analysis of normalized full spectrum mass spectrometry data in multiMS-toolbox: An effective tool to identify important factors for classification of different metabolic patterns and bacterial strains.

PubMed

Cejnar, Pavel; Kuckova, Stepanka; Prochazka, Ales; Karamonova, Ludmila; Svobodova, Barbora

2018-06-15

Explorative statistical analysis of mass spectrometry data is still a time-consuming step. We analyzed critical factors for application of principal component analysis (PCA) in mass spectrometry and focused on two whole spectrum based normalization techniques and their application in the analysis of registered peak data and, in comparison, in full spectrum data analysis. We used this technique to identify different metabolic patterns in the bacterial culture of Cronobacter sakazakii, an important foodborne pathogen. Two software utilities, the ms-alone, a python-based utility for mass spectrometry data preprocessing and peak extraction, and the multiMS-toolbox, an R software tool for advanced peak registration and detailed explorative statistical analysis, were implemented. The bacterial culture of Cronobacter sakazakii was cultivated on Enterobacter sakazakii Isolation Agar, Blood Agar Base and Tryptone Soya Agar for 24 h and 48 h and applied by the smear method on an Autoflex speed MALDI-TOF mass spectrometer. For three tested cultivation media only two different metabolic patterns of Cronobacter sakazakii were identified using PCA applied on data normalized by two different normalization techniques. Results from matched peak data and subsequent detailed full spectrum analysis identified only two different metabolic patterns - a cultivation on Enterobacter sakazakii Isolation Agar showed significant differences to the cultivation on the other two tested media. The metabolic patterns for all tested cultivation media also proved the dependence on cultivation time. Both whole spectrum based normalization techniques together with the full spectrum PCA allow identification of important discriminative factors in experiments with several variable condition factors avoiding any problems with improper identification of peaks or emphasis on bellow threshold peak data. The amounts of processed data remain still manageable. Both implemented software utilities are available

Identifying gender differences in reported occupational information from three US population-based case-control studies.

PubMed

Locke, Sarah J; Colt, Joanne S; Stewart, Patricia A; Armenti, Karla R; Baris, Dalsu; Blair, Aaron; Cerhan, James R; Chow, Wong-Ho; Cozen, Wendy; Davis, Faith; De Roos, Anneclaire J; Hartge, Patricia; Karagas, Margaret R; Johnson, Alison; Purdue, Mark P; Rothman, Nathaniel; Schwartz, Kendra; Schwenn, Molly; Severson, Richard; Silverman, Debra T; Friesen, Melissa C

2014-12-01

Growing evidence suggests that gender-blind assessment of exposure may introduce exposure misclassification, but few studies have characterised gender differences across occupations and industries. We pooled control responses to job-specific, industry-specific and exposure-specific questionnaires (modules) that asked detailed questions about work activities from three US population-based case-control studies to examine gender differences in work tasks and their frequencies. We calculated the ratio of female-to-male controls that completed each module. For four job modules (assembly worker, machinist, health professional, janitor/cleaner) and for subgroups of jobs that completed those modules, we evaluated gender differences in task prevalence and frequency using χ(2) and Mann-Whitney U tests, respectively. The 1360 female and 2245 male controls reported 6033 and 12 083 jobs, respectively. Gender differences in female:male module completion ratios were observed for 39 of 45 modules completed by ≥20 controls. Gender differences in task prevalence varied in direction and magnitude. For example, female janitors were significantly more likely to polish furniture (79% vs 44%), while male janitors were more likely to strip floors (73% vs 50%). Women usually reported more time spent on tasks than men. For example, the median hours per week spent degreasing for production workers in product manufacturing industries was 6.3 for women and 3.0 for men. Observed gender differences may reflect actual differences in tasks performed or differences in recall, reporting or perception, all of which contribute to exposure misclassification and impact relative risk estimates. Our findings reinforce the need to capture subject-specific information on work tasks. 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.

Illness perceptions in the context of differing work participation outcomes: exploring the influence of significant others in persistent back pain

PubMed Central

2013-01-01

Background Previous research has demonstrated that the significant others of individuals with persistent back pain may have important influences on work participation outcomes. The aim of this study was to extend previous research by including individuals who have remained in work despite persistent back pain in addition to those who had become incapacitated for work, along with their significant others. The purpose of this research was to explore whether the illness beliefs of significant others differed depending on their relative’s working status, and to make some preliminary identification of how significant others may facilitate or hinder work participation for those with persistent back pain. Methods Interviews structured around the Illness Perception Questionnaire (chronic pain version) were conducted with back pain patients recruited from a hospital pain management clinic along with their significant others. Some patients had remained in work despite their back pain; others had ceased employment. Data were analysed using template analysis. Results There were clear differences between beliefs about, and reported responses to, back pain symptoms amongst the significant others of individuals who had remained in employment compared with the significant others of those who had ceased work. Three overarching themes emerged: perceived consequences of back pain, specific nature of employment and the impact of back pain on patient identity. Conclusions Significant others of employed individuals with back pain focused on the extent to which activity could still be undertaken despite back pain symptoms. Individuals out of work due to persistent back pain apparently self-limited their activity and were supported in their beliefs and behaviours by their significant others. To justify incapacity due to back pain, this group had seemingly become entrenched in a position whereby it was crucial that the individual with back pain was perceived as completely disabled. We

Conducting tests for statistically significant differences using forest inventory data

Treesearch

James A. Westfall; Scott A. Pugh; John W. Coulston

2013-01-01

Many forest inventory and monitoring programs are based on a sample of ground plots from which estimates of forest resources are derived. In addition to evaluating metrics such as number of trees or amount of cubic wood volume, it is often desirable to make comparisons between resource attributes. To properly conduct statistical tests for differences, it is imperative...

Trustworthy persistent identifier systems of the future

NASA Astrophysics Data System (ADS)

Golodoniuc, Pavel; Klump, Jens; Car, Nicholas

2016-04-01

Over the last two decades, persistent identifier (PID) systems have seen some significant changes in their governance policies, system capabilities, and technology. The development of most systems was driven by two main application areas, namely archives and libraries. Guidelines and criteria for trustworthy PID systems have been clearly devised (Bütikofer, 2009) and many PID system implementations for the identification of static digital objects have been built (e.g., PURL). However systems delivering persistent identifiers for dynamic datasets are not yet mature. There has been a rapid proliferation of different PID systems caused by the specific technical or organisational requirements of various communities that could not be met by existing systems such as DOI, ISBN, and EAN. Many of these different systems were limited by their inability to provide native means of persistent identifier resolution. This has prompted a decoupling of PID-associated data from the resolution service and this is where the Handle system has played a significant role. The Handle allowed to build a distributed system of independently managed resolver services. A trustworthy PID system must be designed to outlive the objects it provides persistent identifiers for, which may cease to exist or otherwise be deprecated, and the technology used to implement it, which will certainly need to change with time. We propose that such a system should rest on four pillars of agreements - (i) definitions, (ii) policies, (iii) services, and (iv) data services, to ensure longevity. While we believe all four pillars are equally important, we intentionally leave regulating aspects of issuing of identifiers and their registration out of the scope of this paper and focus on the agreements that have to be established between PID resolver services and the data sources indicated by the persistent identifiers. We propose an approach to development of PID systems that combines the use of (a) the Handle system

Significance of the Hygiene Charter towards different sectors in Hong Kong.

PubMed

Lee, A; Cheng, F F K; Yuen, H S K; Ho, M; Ngan, W P; Suen, Y P; Au, S M Y; Li, S N; Tso, C Y; Ng, P P Y; Wong, Y P; Keung, M W; Lo, A S C; Wong, W S; Siu, D C H; Yuen, W K; Mok, K K; Fung, W Y; Wong, K K

2004-01-01

The occurrence of SARS in March 2003 has resulted in an increased interest, worldwide in emerging infectious diseases. The SARS experience provided us a lesson on the importance of promoting hygienic practices among individuals and different working sectors. In Hong Kong, a voluntary organization called the UNITE proposed a Hygiene Charter which aimed at taking hygiene to new levels. This action has been supported by individuals and different sectors including the Personal and Family, Management, Buildings, Catering, Education, Finance and Commercial, Industrial, Medical and Health, Public Transportation, Social Welfare, Sports and Culture and Tourism. As promotion and maintenance of environmental health requires input from different sectors, the signing of the Hygiene Charter provides an opportunity for individuals and the public to show their pledge and commitment to good hygiene practices. As a result, with environment improvement and good infectious disease control measures, prevention of epidemics of infectious diseases is deemed to be possible.

Determining local and contextual features describing appearance of difficult to identify mitotic figures

NASA Astrophysics Data System (ADS)

Gandomkar, Ziba; Brennan, Patrick C.; Mello-Thoms, Claudia

2017-03-01

Mitotic count is helpful in determining the aggressiveness of breast cancer. In previous studies, it was shown that the agreement among pathologists for grading mitotic index is fairly modest, as mitoses have a large variety of appearances and they could be mistaken for other similar objects. In this study, we determined local and contextual features that differ significantly between easily identifiable mitoses and challenging ones. The images were obtained from the Mitosis-Atypia 2014 challenge. In total, the dataset contained 453 mitotic figures. Two pathologists annotated each mitotic figure. In case of disagreement, an opinion from a third pathologist was requested. The mitoses were grouped into three categories, those recognized as "a true mitosis" by both pathologists ,those labelled as "a true mitosis" by only one of the first two readers and also the third pathologist, and those annotated as "probably a mitosis" by all readers or the majority of them. After color unmixing, the mitoses were segmented from H channel. Shape-based features along with intensity-based and textural features were extracted from H-channel, blue ratio channel and five different color spaces. Holistic features describing each image were also considered. The Kruskal-Wallis H test was used to identify significantly different features. Multiple comparisons were done using the rank-based version of Tukey-Kramer test. The results indicated that there are local and global features which differ significantly among different groups. In addition, variations between mitoses in different groups were captured in the features from HSL and LCH color space more than other ones.

Probability of identifying different salmonella serotypes in poultry samples

USDA-ARS?s Scientific Manuscript database

Recent work has called attention to the unequal competitive abilities of different Salmonella serotypes in standard broth culture and plating media. Such serotypes include Enteritidis and Typhimurium that are specifically targeted in some regulatory and certification programs because they cause a l...

Pregnant Women's Preferences for Men's Faces Differ Significantly from Nonpregnant Women.

PubMed

Limoncin, Erika; Ciocca, Giacomo; Gravina, Giovanni Luca; Carosa, Eleonora; Mollaioli, Daniele; Cellerino, Alessandro; Mennucci, Andrea; Di Sante, Stefania; Lenzi, Andrea; Jannini, Emmanuele A

2015-05-01

There is evidence that women's preferences for facial characteristics in men's faces change according to menstrual phase and sexual hormones. Literature indicates that the pregnancy is characterized by a specific sexual hormonal pattern with respect to all other physiological conditions concerning the sexual hormone status during the reproductive age, configuring this physiological condition as an excellent surrogate to study how the sexual hormones may affect many of the aspects concerning the sexual behavior. The aim of this study was to investigate pregnancy as a model of hormonal influence on women's facial preferences in short-term and long-term relationships and compare the choices of pregnant women with those of nonpregnant women. Measurement of women's preferences for synthetic men's faces, morphed from hyper-masculine to hypomasculine shape. Forty-six women in the third trimester of pregnancy, and 70 nonpregnant women took part in the study. All women were shown a composite male face. The sexual dimorphism of the images was enhanced or reduced in a continuous fashion using an open-source morphing program that produced a sequence of 21 pictures of the same face warped from a feminized to a masculinized shape. Pregnant women's choices differed significantly from those of nonpregnant women. In fact, in the context of both a hypothetical short- (M = -0.4 ± 0.11) and long-term relationship (M = -0.4 ± 0.07) pregnant women showed a clear preference for a less masculine man's face than the other group (short-term: M = 0.15 ± 0.13; long-term: M = -0.06 ± 0.15; P < 0.0001). Women in the third trimester of pregnancy clearly prefer more feminine men's faces, distancing themselves from the choices of women in other physiological conditions concerning the sexual hormonal status during the reproductive age. However, other psychosocial variables may explain this interesting finding. © 2015 International Society for Sexual Medicine.

A DNA Barcoding Based Study to Identify Main Mosquito Species in Taiwan and its Difference from Those in Mainland China.

PubMed

Gao, Bo; Fang, Yiliang; Zhang, Jianqing; Wu, Rongquan; Xu, Baohai; Xie, Lianhui

2017-01-01

Mosquitoes can transmit many types of viruses such as West Nile virus and Zika virus and are responsible for a number of virus-causing diseases including malaria, dengue fever, yellow fever, lymphatic filariasis, and Japanese B encephalitis. On January 19, 2016, the first case of Zika virus infection was identified in Taiwan, which presents the need for studying the mosquito species in the Taiwan Strait and evaluating the risk of the outbreak of this infection. In this study, we have collected 144 mosquito specimens from 42 species belonging to nine genera from both sides of the Taiwan Strait during 2013 and 2014. We then applied the COI DNA Barcoding technique to classify the specimens and performed a phylogenetic analysis to infer the evolutionary history of these mosquitoes. Based on the analyses, we found that though the mosquitoes from different sides of the Taiwan Strait share a lot of commonality, they have a few regional specificities. Our results also suggested a very small divergences (1%~9%) between specimens from the same mosquito species and relatively large divergences (8%~25%) between specimens from different mosquito species. Within the same species, the divergence of specimens from the same region is significantly smaller than that between two regions. A few highly divergent species between Fujian and Taiwan (e.g., An.maculatus and Ae.elsiae) might be formed due to the so-called "cryptic evolutionary events", in which the species has differentiation into cryptic species due to geographical differences without changing morphological characteristics. In conclusion, the phylogenetic analyses showed a very similar taxonomy to the historical one based on morphological characteristics, validating again the application of COI DNA Barcoding technique in classifying mosquito species. However, there are also some inconsistencies between COI DNA Barcoding and historical taxonomy, which points out the differences between mosquito DNA and morphological

Validating Difference and Counting the Cost of Exclusion in the Lives of People Who Identify as on the Autistic Spectrum

ERIC Educational Resources Information Center

Young, Lauren L.

2012-01-01

This current issues piece will explore how autobiographies written by people with autism can help identify sensory processing differences that might be viewed as possible attributes in an enabling society, but for which ableist perceptions are often negative. In concrete terms, these constructions may be preventing people from entering employment…

Detection of significant differences between absorption spectra of neutral helium and low temperature photoionized helium plasmas

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

Bartnik, A.; Wachulak, P.; Fiedorowicz, H.

2013-11-15

In this work, spectral investigations of photoionized He plasmas were performed. The photoionized plasmas were created by irradiation of helium stream, with intense pulses from laser-plasma extreme ultraviolet (EUV) source. The EUV source was based on a double-stream Xe/Ne gas-puff target irradiated with 10 ns/10 J Nd:YAG laser pulses. The most intense emission from the source spanned a relatively narrow spectral region below 20 nm, however, spectrally integrated intensity at longer wavelengths was also significant. The EUV radiation was focused onto a gas stream, injected into a vacuum chamber synchronously with the EUV pulse. The long-wavelength part of the EUVmore » radiation was used for backlighting of the photoionized plasmas to obtain absorption spectra. Both emission and absorption spectra in the EUV range were investigated. Significant differences between absorption spectra acquired for neutral helium and low temperature photoionized plasmas were demonstrated for the first time. Strong increase of intensities and spectral widths of absorption lines, together with a red shift of the K-edge, was shown.« less

Unanticipated ankle inversions are significantly different from anticipated ankle inversions during drop landings: overcoming anticipation bias.

PubMed

Dicus, Jeremy R; Seegmiller, Jeff G

2012-05-01

Few ankle inversion studies have taken anticipation bias into account or collected data with an experimental design that mimics actual injury mechanisms. Twenty-three participants performed randomized single-leg vertical drop landings from 20 cm. Subjects were blinded to the landing surface (a flat force plate or 30° inversion wedge on the force plate). After each trial, participants reported whether they anticipated the landing surface. Participant responses were validated with EMG data. The protocol was repeated until four anticipated and four unanticipated landings onto the inversion wedge were recorded. Results revealed a significant main effect for landing condition. Normalized vertical ground reaction force (% body weights), maximum ankle inversion (degrees), inversion velocity (degrees/second), and time from contact to peak muscle activation (seconds) were significantly greater in unanticipated landings, and the time from peak muscle activation to maximum VGRF (second) was shorter. Unanticipated landings presented different muscle activation patterns than landings onto anticipated surfaces, which calls into question the usefulness of clinical studies that have not controlled for anticipation bias.

Mobile NBM - Android medical mobile application designed to help in learning how to identify the different regions of interest in the brain's white matter.

PubMed

Sánchez-Rola, Iskander; Zapirain, Begoña García

2014-07-18

One of the most critical tasks when conducting neurological studies is identifying the different regions of interest in the brain's white matter. Currently few programs or applications are available that serve as an interactive guide in this process. This is why a mobile application has been designed and developed in order to teach users how to identify the referred regions of the brain. It also enables users to share the results obtained and take an examination on the knowledge thus learnt. In order to provide direct user-user or user-developer contact, the project includes a website and a Twitter account. An application has been designed with a basic, minimalist look, which anyone can access easily in order to learn to identify a specific region in the brain's white matter. A survey has also been conducted on people who have used it, which has shown that the application is attractive both in the student (final mean satisfaction of 4.2/5) and in the professional (final mean satisfaction of 4.3/5) environment. The response obtained in the online part of the project reflects the high practical value and quality of the application, as shown by the fact that the website has seen a large number of visitors (over 1000 visitors) and the Twitter account has a high number of followers (over 280 followers). Mobile NBM is the first mobile application to be used as a guide in the process of identifying a region of interest in the brain's white matter. Although initially not many areas are available in the application, new ones can be added as required by users in their respective studies. Apart from the application itself, the online resources provided (website and Twitter account) significantly enhance users' experience.

Statistical Significance vs. Practical Significance: An Exploration through Health Education

ERIC Educational Resources Information Center

Rosen, Brittany L.; DeMaria, Andrea L.

2012-01-01

The purpose of this paper is to examine the differences between statistical and practical significance, including strengths and criticisms of both methods, as well as provide information surrounding the application of various effect sizes and confidence intervals within health education research. Provided are recommendations, explanations and…

Significant differences in B-cell subpopulations characterize patients with chronic graft-versus-host disease-associated dysgammaglobulinemia.

PubMed

Kuzmina, Zoya; Greinix, Hildegard T; Weigl, Roman; Körmöczi, Ulrike; Rottal, Arno; Frantal, Sophie; Eder, Sandra; Pickl, Winfried F

2011-02-17

Manifestations of chronic graft-versus-host disease (cGVHD) can resemble those seen in immunodeficiency states and autoimmune disorders. Reports by us and others suggest an involvement of B cells in the pathogenesis of cGVHD. We investigated B-lymphocyte subpopulations in cGVHD cohorts defined by serum immunoglobulin G (IgG) levels to characterize novel biomarkers for impairment of humoral immunity after allogeneic hematopoietic stem cell transplantation. Seventy-six patients were enrolled a median of 46 months after hematopoietic stem cell transplantation. The hypogammaglobulinemia group had significantly diminished CD19(+) B cells (165 vs 454 vs 417 × 10⁶L) with elevated CD19(+)CD21(low) immature (16.5%, 7.7%, and 9.1%) and CD19(+)CD21(int-high)CD38(high)IgM(high) transitional (10.5% vs 4.2% vs 6.3%) B-cell proportions compared with the normogammaglobulinemia and hypergammaglobulinemia groups. CD19(+)CD10(-)CD27(-)CD21(high) naive B cells were highly elevated in all patients with cGVHD. CD19(+)CD27(+)IgD(+) non-class-switched (4 vs 12 vs 11 × 10⁶/L) and class-switched (7 vs 35 vs 42 × 10⁶/L) memory B cells were significantly lower in the hypogammaglobulinemia group compared with the others. Besides significantly higher B-cell activation factor/B-cell ratios, significantly more cGVHD patients with hypergammaglobulinemia had autoantibodies compared with the hypogammaglobulinemia subgroup (68% vs 24%, P = .024). In conclusion, B-cell subpopulations can serve as novel cellular biomarkers for immunodeficiency and autoimmunity indicating different pathogenetic mechanisms of cGVHD and encouraging future prospective longitudinal studies.

Significant Differences in Pediatric Psychotropic Side Effects: Implications for School Performance

ERIC Educational Resources Information Center

Kubiszyn, Thomas; Mire, Sarah; Dutt, Sonia; Papathopoulos, Katina; Burridge, Andrea Backsheider

2012-01-01

Some side effects (SEs) of increasingly prescribed psychotropic medications can impact student performance in school. SE risk varies, even among drugs from the same class (e.g., antidepressants). Knowing which SEs occur significantly more often than others may enable school psychologists to enhance collaborative risk-benefit analysis, medication…

Sex and gender differences in autism spectrum disorder: summarizing evidence gaps and identifying emerging areas of priority.

PubMed

Halladay, Alycia K; Bishop, Somer; Constantino, John N; Daniels, Amy M; Koenig, Katheen; Palmer, Kate; Messinger, Daniel; Pelphrey, Kevin; Sanders, Stephan J; Singer, Alison Tepper; Taylor, Julie Lounds; Szatmari, Peter

2015-01-01

One of the most consistent findings in autism spectrum disorder (ASD) research is a higher rate of ASD diagnosis in males than females. Despite this, remarkably little research has focused on the reasons for this disparity. Better understanding of this sex difference could lead to major advancements in the prevention or treatment of ASD in both males and females. In October of 2014, Autism Speaks and the Autism Science Foundation co-organized a meeting that brought together almost 60 clinicians, researchers, parents, and self-identified autistic individuals. Discussion at the meeting is summarized here with recommendations on directions of future research endeavors.

Genome wide profiling in oral squamous cell carcinoma identifies a four genetic marker signature of prognostic significance

PubMed Central

Vincent-Chong, Vui King; Salahshourifar, Iman; Woo, Kar Mun; Anwar, Arif; Razali, Rozaimi; Gudimella, Ranganath; Rahman, Zainal Ariff Abdul; Ismail, Siti Mazlipah; Kallarakkal, Thomas George; Ramanathan, Anand; Wan Mustafa, Wan Mahadzir; Abraham, Mannil Thomas; Tay, Keng Kiong; Zain, Rosnah Binti

2017-01-01

Background Cancers of the oral cavity are primarily oral squamous cell carcinomas (OSCCs). Many of the OSCCs present at late stages with an exceptionally poor prognosis. A probable limitation in management of patients with OSCC lies in the insufficient knowledge pertaining to the linkage between copy number alterations in OSCC and oral tumourigenesis thereby resulting in an inability to deliver targeted therapy. Objectives The current study aimed to identify copy number alterations (CNAs) in OSCC using array comparative genomic hybridization (array CGH) and to correlate the CNAs with clinico-pathologic parameters and clinical outcomes. Materials and methods Using array CGH, genome-wide profiling was performed on 75 OSCCs. Selected genes that were harboured in the frequently amplified and deleted regions were validated using quantitative polymerase chain reaction (qPCR). Thereafter, pathway and network functional analysis were carried out using Ingenuity Pathway Analysis (IPA) software. Results Multiple chromosomal regions including 3q, 5p, 7p, 8q, 9p, 10p, 11q were frequently amplified, while 3p and 8p chromosomal regions were frequently deleted. These findings were in confirmation with our previous study using ultra-dense array CGH. In addition, amplification of 8q, 11q, 7p and 9p and deletion of 8p chromosomal regions showed a significant correlation with clinico-pathologic parameters such as the size of the tumour, metastatic lymph nodes and pathological staging. Co-amplification of 7p, 8q, 9p and 11q regions that harbored amplified genes namely CCND1, EGFR, TPM2 and LRP12 respectively, when combined, continues to be an independent prognostic factor in OSCC. Conclusion Amplification of 3q, 5p, 7p, 8q, 9p, 10p, 11q and deletion of 3p and 8p chromosomal regions were recurrent among OSCC patients. Co-alteration of 7p, 8q, 9p and 11q was found to be associated with clinico-pathologic parameters and poor survival. These regions contain genes that play critical roles

Using Wavelet Analysis To Assist in Identification of Significant Events in Molecular Dynamics Simulations.

PubMed

Heidari, Zahra; Roe, Daniel R; Galindo-Murillo, Rodrigo; Ghasemi, Jahan B; Cheatham, Thomas E

2016-07-25

Long time scale molecular dynamics (MD) simulations of biological systems are becoming increasingly commonplace due to the availability of both large-scale computational resources and significant advances in the underlying simulation methodologies. Therefore, it is useful to investigate and develop data mining and analysis techniques to quickly and efficiently extract the biologically relevant information from the incredible amount of generated data. Wavelet analysis (WA) is a technique that can quickly reveal significant motions during an MD simulation. Here, the application of WA on well-converged long time scale (tens of μs) simulations of a DNA helix is described. We show how WA combined with a simple clustering method can be used to identify both the physical and temporal locations of events with significant motion in MD trajectories. We also show that WA can not only distinguish and quantify the locations and time scales of significant motions, but by changing the maximum time scale of WA a more complete characterization of these motions can be obtained. This allows motions of different time scales to be identified or ignored as desired.

Clinical significance of coryneform Gram-positive rods from blood identified by MALDI-TOF mass spectrometry and their susceptibility profiles - a retrospective chart review.

PubMed

Mushtaq, Ammara; Chen, Derrick J; Strand, Gregory J; Dylla, Brenda L; Cole, Nicolynn C; Mandrekar, Jayawant; Patel, Robin

2016-07-01

With the advent of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS), most Gram-positive rods (GPRs) are readily identified; however, their clinical relevance in blood cultures remains unclear. Herein, we assessed the clinical significance of GPRs isolated from blood and identified in the era of MALDI-TOF MS. A retrospective chart review of patients presenting to the Mayo Clinic, Rochester, MN, from January 1, 2013, to October 13, 2015, was performed. Any episode of a positive blood culture for a GPR was included. We assessed the number of bottles positive for a given isolate, time to positivity of blood cultures, patient age, medical history, interpretation of culture results by the healthcare team and whether infectious diseases consultation was obtained. We also evaluated the susceptibility profiles of a larger collection of GPRs tested in the clinical microbiology laboratory of the Mayo Clinic, Rochester, MN from January 1, 2013, to October 31, 2015. There were a total of 246 GPRs isolated from the blood of 181 patients during the study period. 56% (n = 101) were deemed contaminants by the healthcare team and were not treated; 33% (n = 59) were clinically determined to represent true bacteremia and were treated; and 8% (n = 14) were considered of uncertain significance, with patients prescribed treatment regardless. Patient characteristics associated with an isolate being treated on univariate analysis included younger age (P = 0.02), identification to the species level (P = 0.02), higher number of positive blood culture sets (P < 0.0001), lower time to positivity (P < 0.0001), immunosuppression (P = 0.03), and recommendation made by an infectious disease consultant (P = 0.0005). On multivariable analysis, infectious diseases consultation (P = 0.03), higher number of positive blood culture sets (P = 0.0005) and lower time to positivity (P = 0.03) were associated with an isolate being treated. 100, 83, 48 and 34% of GPRs

Stress Encountered by Significant Others of Cancer Patients Receiving Chemotherapy.

ERIC Educational Resources Information Center

Hart, Kay

1987-01-01

Attempts to identify and describe perceived stress and coping responses of family and nonfamily significant others of cancer patients receiving chemotherapy. Significant others were asked to identify stressful events related to treatment factors, relationship factors, and perception of the patient's condition. Coping responses were categorized in…

Identifying Cancer Driver Genes Using Replication-Incompetent Retroviral Vectors

PubMed Central

Bii, Victor M.; Trobridge, Grant D.

2016-01-01

Identifying novel genes that drive tumor metastasis and drug resistance has significant potential to improve patient outcomes. High-throughput sequencing approaches have identified cancer genes, but distinguishing driver genes from passengers remains challenging. Insertional mutagenesis screens using replication-incompetent retroviral vectors have emerged as a powerful tool to identify cancer genes. Unlike replicating retroviruses and transposons, replication-incompetent retroviral vectors lack additional mutagenesis events that can complicate the identification of driver mutations from passenger mutations. They can also be used for almost any human cancer due to the broad tropism of the vectors. Replication-incompetent retroviral vectors have the ability to dysregulate nearby cancer genes via several mechanisms including enhancer-mediated activation of gene promoters. The integrated provirus acts as a unique molecular tag for nearby candidate driver genes which can be rapidly identified using well established methods that utilize next generation sequencing and bioinformatics programs. Recently, retroviral vector screens have been used to efficiently identify candidate driver genes in prostate, breast, liver and pancreatic cancers. Validated driver genes can be potential therapeutic targets and biomarkers. In this review, we describe the emergence of retroviral insertional mutagenesis screens using replication-incompetent retroviral vectors as a novel tool to identify cancer driver genes in different cancer types. PMID:27792127

Geometric differences of the mitral apparatus between ischemic and dilated cardiomyopathy with significant mitral regurgitation: real-time three-dimensional echocardiography study

NASA Technical Reports Server (NTRS)

Kwan, Jun; Shiota, Takahiro; Agler, Deborah A.; Popovic, Zoran B.; Qin, Jian Xin; Gillinov, Marc A.; Stewart, William J.; Cosgrove, Delos M.; McCarthy, Patrick M.; Thomas, James D.

2003-01-01

BACKGROUND: This study was conducted to elucidate the geometric differences of the mitral apparatus in patients with significant mitral regurgitation caused by ischemic cardiomyopathy (ICM-MR) and by idiopathic dilated cardiomyopathy (DCM-MR) by use of real-time 3D echocardiography (RT3DE). METHODS AND RESULTS: Twenty-six patients with ICM-MR caused by posterior infarction, 18 patients with DCM-MR, and 8 control subjects were studied. With the 3D software, commissure-commissure plane and 3 perpendicular anteroposterior (AP) planes were generated for imaging the medial, central, and lateral sides of the mitral valve (MV) during mid systole. In 3 AP planes, the angles between the annular plane and each leaflet (anterior, Aalpha; posterior, Palpha) were measured. In ICM-MR, Aalpha measured in the medial and central planes was significantly larger than that in the lateral plane (39+/-5 degrees, 34+/-6 degrees, and 27+/-5 degrees, respectively; P<0.01), whereas Palpha showed no significant difference in any of the 3 AP planes (61+/-7 degrees, 57+/-7 degrees, and 56+/-7 degrees, P>0.05). In DCM-MR, both Aalpha (38+/-8 degrees, 37+/-9 degrees, and 36+/-7 degrees, P>0.05) and Palpha (59+/-6 degrees, 58+/-5 degrees, and 57+/-6 degrees, P>0.05) revealed no significant differences in the 3 planes. CONCLUSIONS: The pattern of MV deformation from the medial to the lateral side was asymmetrical in ICM-MR, whereas it was symmetrical in DCM-MR. RT3DE is a helpful tool for differentiating the geometry of the mitral apparatus between these 2 different types of functional mitral regurgitation.

Lack of significant differences in immunity against diphtheria between populations of Eastern and Western regions of Poland.

PubMed

Chudnicka, Alina; Walory, Jarosław

2003-01-01

Incidents of diphtheria in countries which were formerly part of the Soviet Union (Ukraine, Russia and Belorus) resulted in the need to evaluate thoroughly the effectiveness of preventive vaccination in Poland, especially in the border regions of the country where the biggest migration of population can be observed. The aim of this work was a comparison of the immunity to diphtheria in two geographically different regions of Poland--eastern (Lublin) and western (Zielona Gora) ones. It showed immunoprophylaxis to diphtheria that was implemented on these areas. Diphtheria antitoxin level (IgG) was determined with application of the ELISA method in 1236 (529/707) people. No significant differences were found in the level of antibodies in the groups < 2 years of age and > 19 years of age in people below the protective titre (0.1 IU/ml). The difference occurring in the interval between 2nd and 18th year of life (in western Poland 7.6% and in eastern Poland 16%) may result from different implementation of the vaccination program in these regions (booster doses). Recommendations for vaccination to diphtheria in people over 25 years of age should be implemented especially in the frontier regions of Poland adjoining countries threatened with diphtheria occurrence.

Rapid identifying high-influence nodes in complex networks

NASA Astrophysics Data System (ADS)

Song, Bo; Jiang, Guo-Ping; Song, Yu-Rong; Xia, Ling-Ling

2015-10-01

A tiny fraction of influential individuals play a critical role in the dynamics on complex systems. Identifying the influential nodes in complex networks has theoretical and practical significance. Considering the uncertainties of network scale and topology, and the timeliness of dynamic behaviors in real networks, we propose a rapid identifying method (RIM) to find the fraction of high-influential nodes. Instead of ranking all nodes, our method only aims at ranking a small number of nodes in network. We set the high-influential nodes as initial spreaders, and evaluate the performance of RIM by the susceptible-infected-recovered (SIR) model. The simulations show that in different networks, RIM performs well on rapid identifying high-influential nodes, which is verified by typical ranking methods, such as degree, closeness, betweenness, and eigenvector centrality methods. Project supported by the National Natural Science Foundation of China (Grant Nos. 61374180 and 61373136), the Ministry of Education Research in the Humanities and Social Sciences Planning Fund Project, China (Grant No. 12YJAZH120), and the Six Projects Sponsoring Talent Summits of Jiangsu Province, China (Grant No. RLD201212).

Population differences in platinum toxicity as a means to identify novel genetic susceptibility variants

PubMed Central

O'Donnell, Peter H.; Gamazon, Eric; Zhang, Wei; Stark, Amy L.; Kistner-Griffin, Emily O.; Huang, R. Stephanie; Dolan, M. Eileen

2010-01-01

Objectives Clinical studies show that Asians (ASN) are more susceptible to toxicities associated with platinum-containing regimens. We hypothesized that studying ASN as an `enriched phenotype' population could enable the discovery of novel genetic determinants of platinum susceptibility. Methods Using well-genotyped lymphoblastoid cell lines from the HapMap, we determined cisplatin and carboplatin cytotoxicity phenotypes (IC50s) for ASN, Caucasians (CEU), and Africans (YRI). IC50s were used in genome-wide association studies. Results ASN were most sensitive to platinums, corroborating clinical findings. ASN genome-wide association studies produced 479 single-nucleotide polymorphisms (SNPs) associating with cisplatin susceptibility and 199 with carboplatin susceptibility (P<10−4). Considering only the most significant variants (P< 9.99 × 10−6), backwards elimination was then used to identify reduced-model SNPs, which robustly described the drug phenotypes within ASN. These SNPs comprised highly descriptive genetic signatures of susceptibility, with 12 SNPs explaining more than 95% of the susceptibility phenotype variation for cisplatin, and eight SNPs approximately 75% for carboplatin. To determine the possible function of these variants in ASN, the SNPs were tested for association with differential expression of target genes. SNPs were highly associated with the expression of multiple target genes, and notably, the histone H3 family was implicated for both drugs, suggesting a platinum-class mechanism. Histone H3 has repeatedly been described as regulating the formation of platinum-DNA adducts, but this is the first evidence that specific genetic variants might mediate these interactions in a pharmacogenetic manner. Finally, to determine whether any ASN-identified SNPs might also be important in other human populations, we interrogated all 479/199 SNPs for association with platinum susceptibility in an independent combined CEU/YRI population. Three unique SNPs

Oral challenges with four apple cultivars result in significant differences in oral allergy symptoms.

PubMed

Nybom, Hilde; Cervin-Hoberg, Charlotte; Andersson, Morgan

2013-01-01

We analyzed the hypoallergenic potential of a recently bred apple selection with unusually low content of Mal d 1, using an oral challenge model with three additional apple cultivars for comparison. Sixty-six birch pollen-allergic individuals with a history of oral allergy syndrome after apple intake were subjected to a double-blind oral provocation with two apple cultivars (B:0654 and 'Discovery'). Thirteen also tested two other apple cultivars ('Ingrid Marie' and 'Gloster'). Three doses were given consecutively, 30 min apart: 10 g without peel, and 10 and 50 g with peel. A final assessment was conducted 30 min after the last intake. Oral symptoms were graded from 0 to 5. Total oral symptom score (TOS) included all scores for each cultivar at all time points. B:0654 induced significantly higher TOS than 'Discovery' when tested by 66 individuals, in spite of its lower Mal d 1 content. TOS values were higher in females and increased with increasing age of the individuals when challenged with 'Discovery'. Among the 13 individuals who tested all four cultivars, B:0654 produced a higher score after the second dose compared to 'Ingrid Marie'. This was also the case after the third dose compared to 'Ingrid Marie' and 'Gloster', and again 30 min after the last intake compared to each of the other three cultivars, as well as a higher TOS compared to each of the other three cultivars (all p < 0.01). Our test was safe and well tolerated, and produced significant differences among the apple cultivars. Contrary to expectations, B:0654 was less well tolerated than the other three cultivars. Copyright © 2013 S. Karger AG, Basel.

Identifying the Factors Affecting Science and Mathematics Achievement Using Data Mining Methods

ERIC Educational Resources Information Center

Kiray, S. Ahmet; Gok, Bilge; Bozkir, A. Selman

2015-01-01

The purpose of this article is to identify the order of significance of the variables that affect science and mathematics achievement in middle school students. For this aim, the study deals with the relationship between science and math in terms of different angles using the perspectives of multiple causes-single effect and of multiple…

Integrated genetic and epigenetic analysis identifies three different subclasses of colon cancer

PubMed Central

Shen, Lanlan; Toyota, Minoru; Kondo, Yutaka; Lin, E; Zhang, Li; Guo, Yi; Hernandez, Natalie Supunpong; Chen, Xinli; Ahmed, Saira; Konishi, Kazuo; Hamilton, Stanley R.; Issa, Jean-Pierre J.

2007-01-01

Colon cancer has been viewed as the result of progressive accumulation of genetic and epigenetic abnormalities. However, this view does not fully reflect the molecular heterogeneity of the disease. We have analyzed both genetic (mutations of BRAF, KRAS, and p53 and microsatellite instability) and epigenetic alterations (DNA methylation of 27 CpG island promoter regions) in 97 primary colorectal cancer patients. Two clustering analyses on the basis of either epigenetic profiling or a combination of genetic and epigenetic profiling were performed to identify subclasses with distinct molecular signatures. Unsupervised hierarchical clustering of the DNA methylation data identified three distinct groups of colon cancers named CpG island methylator phenotype (CIMP) 1, CIMP2, and CIMP negative. Genetically, these three groups correspond to very distinct profiles. CIMP1 are characterized by MSI (80%) and BRAF mutations (53%) and rare KRAS and p53 mutations (16% and 11%, respectively). CIMP2 is associated with 92% KRAS mutations and rare MSI, BRAF, or p53 mutations (0, 4, and 31% respectively). CIMP-negative cases have a high rate of p53 mutations (71%) and lower rates of MSI (12%) or mutations of BRAF (2%) or KRAS (33%). Clustering based on both genetic and epigenetic parameters also identifies three distinct (and homogeneous) groups that largely overlap with the previous classification. The three groups are independent of age, gender, or stage, but CIMP1 and 2 are more common in proximal tumors. Together, our integrated genetic and epigenetic analysis reveals that colon cancers correspond to three molecularly distinct subclasses of disease. PMID:18003927

Identifying and characterizing the most significant β-glucosidase of the novel species Aspergillus saccharolyticus

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

Sorensen, Anette; Ahring, Birgitte K.; Lubeck, Mette

2012-08-20

A newly discovered fungal species, Aspergillus saccharolyticus, was found to produce a culture broth rich in beta-glucosidase activity. In this present work, the main beta-glucosidase of A. saccharolyticus responsible for the efficient hydrolytic activity was identified, isolated, and characterized. Ion exchange chromatography was used to fractionate the culture broth, yielding fractions with high beta-glucosidase activity and only one visible band on an SDS-PAGE gel. Mass spectrometry analysis of this band gave peptide matches to beta-glucosidases from aspergilli. Through a PCR approach using degenerate primers and genome walking, a 2919 base pair sequence encoding the 860 amino acid BGL1 polypeptide wasmore » determined. BGL1 of A. saccharolyticus has 91% and 82% identity with BGL1 from Aspergillus aculeatus and BGL1 from Aspergillus niger, respectively, both belonging to Glycoside hydrolase family 3. Homology modeling studies suggested beta-glucosidase activity with preserved retaining mechanism and a wider catalytic pocket compared to other beta-glucosidases. The bgl1 gene was heterologously expressed in Trichoderma reesei QM6a, purified, and characterized by enzyme kinetics studies. The enzyme can hydrolyze cellobiose, pNPG, and cellodextrins. The enzyme showed good thermostability, was stable at 50°C, and at 60°C it had a half-life of approximately 6 hours.« less

Significant lexical relationships

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

Pedersen, T.; Kayaalp, M.; Bruce, R.

Statistical NLP inevitably deals with a large number of rare events. As a consequence, NLP data often violates the assumptions implicit in traditional statistical procedures such as significance testing. We describe a significance test, an exact conditional test, that is appropriate for NLP data and can be performed using freely available software. We apply this test to the study of lexical relationships and demonstrate that the results obtained using this test are both theoretically more reliable and different from the results obtained using previously applied tests.

Metadata, Identifiers, and Physical Samples

NASA Astrophysics Data System (ADS)

Arctur, D. K.; Lenhardt, W. C.; Hills, D. J.; Jenkyns, R.; Stroker, K. J.; Todd, N. S.; Dassie, E. P.; Bowring, J. F.

2016-12-01

Physical samples are integral to much of the research conducted by geoscientists. The samples used in this research are often obtained at significant cost and represent an important investment for future research. However, making information about samples - whether considered data or metadata - available for researchers to enable discovery is difficult: a number of key elements related to samples are difficult to characterize in common ways, such as classification, location, sample type, sampling method, repository information, subsample distribution, and instrumentation, because these differ from one domain to the next. Unifying these elements or developing metadata crosswalks is needed. The iSamples (Internet of Samples) NSF-funded Research Coordination Network (RCN) is investigating ways to develop these types of interoperability and crosswalks. Within the iSamples RCN, one of its working groups, WG1, has focused on the metadata related to physical samples. This includes identifying existing metadata standards and systems, and how they might interoperate with the International Geo Sample Number (IGSN) schema (schema.igsn.org) in order to help inform leading practices for metadata. For example, we are examining lifecycle metadata beyond the IGSN `birth certificate.' As a first step, this working group is developing a list of relevant standards and comparing their various attributes. In addition, the working group is looking toward technical solutions to facilitate developing a linked set of registries to build the web of samples. Finally, the group is also developing a comparison of sample identifiers and locators. This paper will provide an overview and comparison of the standards identified thus far, as well as an update on the technical solutions examined for integration. We will discuss how various sample identifiers might work in complementary fashion with the IGSN to more completely describe samples, facilitate retrieval of contextual information, and

Potential Reporting Bias in Neuroimaging Studies of Sex Differences.

PubMed

David, Sean P; Naudet, Florian; Laude, Jennifer; Radua, Joaquim; Fusar-Poli, Paolo; Chu, Isabella; Stefanick, Marcia L; Ioannidis, John P A

2018-04-17

Numerous functional magnetic resonance imaging (fMRI) studies have reported sex differences. To empirically evaluate for evidence of excessive significance bias in this literature, we searched for published fMRI studies of human brain to evaluate sex differences, regardless of the topic investigated, in Medline and Scopus over 10 years. We analyzed the prevalence of conclusions in favor of sex differences and the correlation between study sample sizes and number of significant foci identified. In the absence of bias, larger studies (better powered) should identify a larger number of significant foci. Across 179 papers, median sample size was n = 32 (interquartile range 23-47.5). A median of 5 foci related to sex differences were reported (interquartile range, 2-9.5). Few articles (n = 2) had titles focused on no differences or on similarities (n = 3) between sexes. Overall, 158 papers (88%) reached "positive" conclusions in their abstract and presented some foci related to sex differences. There was no statistically significant relationship between sample size and the number of foci (-0.048% increase for every 10 participants, p = 0.63). The extremely high prevalence of "positive" results and the lack of the expected relationship between sample size and the number of discovered foci reflect probable reporting bias and excess significance bias in this literature.

Males Perform Better in Identifying Voices During Menstruation Than Females: A Pilot Study.

PubMed

Wang, Xue; Xu, Xin; Liu, Yangyang

2016-10-01

The objective of the present study is to investigate gender differences in the ability to identify females' voice during menstruation. In Study 1, 55 male participants (M age = 19.6 years, SD = 1.0) were asked to listen to vocal samples from women during both ovulation and menstruation and to identify which recordings featured menstruating women. The results showed that the accuracy of men's responses (M = 56.73%, SD = 0.21) was significantly higher than 50%. In Study 2, 118 female students (M age = 19.4 years, SD = 1.6) completed the same task. The results indicated that the accuracy of women's performance was nearly 50%. These preliminary findings suggest that men are better able to identify women's voices during menstruation than women. Future work could consider several significant variables for the purpose of validating the results. © The Author(s) 2016.

Metabolomics and transcriptomics identify pathway differences between visceral and subcutaneous adipose tissue in colorectal cancer patients: the ColoCare study12

PubMed Central

Liesenfeld, David B; Grapov, Dmitry; Fahrmann, Johannes F; Salou, Mariam; Scherer, Dominique; Toth, Reka; Habermann, Nina; Böhm, Jürgen; Schrotz-King, Petra; Gigic, Biljana; Schneider, Martin; Ulrich, Alexis; Herpel, Esther; Schirmacher, Peter; Fiehn, Oliver; Lampe, Johanna W; Ulrich, Cornelia M

2015-01-01

Background: Metabolic and transcriptomic differences between visceral adipose tissue (VAT) and subcutaneous adipose tissue (SAT) compartments, particularly in the context of obesity, may play a role in colorectal carcinogenesis. We investigated the differential functions of their metabolic compositions. Objectives: Biochemical differences between adipose tissues (VAT compared with SAT) in patients with colorectal carcinoma (CRC) were investigated by using mass spectrometry metabolomics and gene expression profiling. Metabolite compositions were compared between VAT, SAT, and serum metabolites. The relation between patients’ tumor stage and metabolic profiles was assessed. Design: Presurgery blood and paired VAT and SAT samples during tumor surgery were obtained from 59 CRC patients (tumor stages I–IV) of the ColoCare cohort. Gas chromatography time-of-flight mass spectrometry and liquid chromatography quadrupole time-of-flight mass spectrometry were used to measure 1065 metabolites in adipose tissue (333 identified compounds) and 1810 metabolites in serum (467 identified compounds). Adipose tissue gene expression was measured by using Illumina’s HumanHT-12 Expression BeadChips. Results: Compared with SAT, VAT displayed elevated markers of inflammatory lipid metabolism, free arachidonic acid, phospholipases (PLA2G10), and prostaglandin synthesis–related enzymes (PTGD/PTGS2S). Plasmalogen concentrations were lower in VAT than in SAT, which was supported by lower gene expression of FAR1, the rate-limiting enzyme for ether-lipid synthesis in VAT. Serum sphingomyelin concentrations were inversely correlated (P = 0.0001) with SAT adipose triglycerides. Logistic regression identified lipids in patients’ adipose tissues, which were associated with CRC tumor stage. Conclusions: As one of the first studies, we comprehensively assessed differences in metabolic, lipidomic, and transcriptomic profiles between paired human VAT and SAT and their association with CRC

The role of baryons in creating statistically significant planes of satellites around Milky Way-mass galaxies

NASA Astrophysics Data System (ADS)

Ahmed, Sheehan H.; Brooks, Alyson M.; Christensen, Charlotte R.

2017-04-01

We investigate whether the inclusion of baryonic physics influences the formation of thin, coherently rotating planes of satellites such as those seen around the Milky Way and Andromeda. For four Milky Way-mass simulations, each run both as dark matter-only and with baryons included, we are able to identify a planar configuration that significantly maximizes the number of plane satellite members. The maximum plane member satellites are consistently different between the dark matter-only and baryonic versions of the same run due to the fact that satellites are both more likely to be destroyed and to infall later in the baryonic runs. Hence, studying satellite planes in dark matter-only simulations is misleading, because they will be composed of different satellite members than those that would exist if baryons were included. Additionally, the destruction of satellites in the baryonic runs leads to less radially concentrated satellite distributions, a result that is critical to making planes that are statistically significant compared to a random distribution. Since all planes pass through the centre of the galaxy, it is much harder to create a plane of a given height from a random distribution if the satellites have a low radial concentration. We identify Andromeda's low radial satellite concentration as a key reason why the plane in Andromeda is highly significant. Despite this, when corotation is considered, none of the satellite planes identified for the simulated galaxies are as statistically significant as the observed planes around the Milky Way and Andromeda, even in the baryonic runs.

The environment associated with significant tornadoes in Bangladesh

NASA Astrophysics Data System (ADS)

Bikos, Dan; Finch, Jonathan; Case, Jonathan L.

2016-01-01

This paper investigates the environmental parameters favoring significant tornadoes in Bangladesh through a simulation of ten high-impact events. A climatological perspective is first presented on classifying significant tornadoes in Bangladesh, noting the challenges since reports of tornadoes are not documented in a formal manner. The statistical relationship between United States and Bangladesh tornado-related deaths suggests that significant tornadoes do occur in Bangladesh so this paper identifies the most significant tornadic events and analyzes the environmental conditions associated with these events. Given the scarcity of observational data to assess the near-storm environment in this region, high-resolution (3-km horizontal grid spacing) numerical weather prediction simulations are performed for events identified to be associated with a significant tornado. In comparison to similar events over the United States, significant tornado environments in Bangladesh are characterized by relatively high convective available potential energy, sufficient deep-layer vertical shear, and a propensity for deviant (i.e., well to the right of the mean flow) storm motion along a low-level convergence boundary.

ANTHROPOMETRY TO IDENTIFY HIGH VISCERAL FAT AREA IN POSTMENOPAUSAL WOMEN.

PubMed

Gondim Pitanga, Francisco José; Seara Pitanga, Cristiano Penas; Calçada Dias Gabriel, Ronaldo Eugénio; Cristina Beck, Carmem; Rodrigues Moreira, Maria Helena

2015-12-01

the evaluation of the body fat distribution by anthropometry can serve to identify excess visceral fat. This diagnosis will enable implementation of specific measures to both prevent and treat excess visceral fat in postmenopausal women. the aim of this study was to analyze different anthropometric indicators and identify the best cutoff points to discriminate subjects with high visceral fat area (HVFA) in postmenopausal women. cross-sectional study with a sample of 255 postmenopausal women. Different Receiver Operating Characteristic (ROC) curves were constructed and the areas under them compared in terms of the conicity index (C-index), body mass index (BMI), waist-to-hip ratio (WHR), waist circumference (WC), weight-to-height ratio (WHtR) and HVFA. Sensitivity and specificity identified the best cutoff points between the different anthropometric indicators in order to discriminate subjects with HVFA. The confidence interval was set at 95%. statistically significant areas under the ROC curve were found for all anthropometric indicators analyzed. The following cutoff points, with their respective sensitivities and specificities to discriminate subjects with HVFA, were suggested: C-index (1.19; 75.00%- 74.77%); BMI (27.3 kg/m2; 81.08%-80.37%); WHR (0.98; 90.54%-83.18%); WC (85 cm; 85.14%-81.31%); and WHtR (0.55; 80.41%-80.37%). these results demonstrate that anthropometric indicators identify HVFA well in postmenopausal women and can be used instead of more sophisticated exams to detect high levels of visceral fat. Copyright AULA MEDICA EDICIONES 2014. Published by AULA MEDICA. All rights reserved.

No significant differences in short-term renal prognosis between living kidney donors with and without diabetes.

PubMed

Shinzato, Takahiro; Kurosawa, Akira; Kubo, Taro; Shimizu, Toshihiro; Kimura, Takaaki; Nanmoku, Koji; Yagisawa, Takashi

2018-06-01

Renal prognosis in living kidney donors with diabetes is currently not known. In this study, we sought to investigate renal prognosis in living kidney donors with diabetes. We retrospectively investigated 241 living kidney donors who underwent nephrectomy at Jichi Medical University Hospital between January 2000 and December 2015. Donors with a follow-up period of less than 1 year were excluded. The remaining donors were divided into a diabetic group and a non-diabetic group. Their clinical parameters before donation and renal prognosis after donation were compared. Of the 241 donors, 16 were excluded due to their follow-up period being less than 1 year. Of the remaining 225 donors, 14 were diabetic and 211 were non-diabetic. There were no significant differences in variables at pre-donation. The median follow-up period was 4.3 (1.5-10.7) and 4.6 (1.0-13.0) years in kidney donors with and without diabetes, respectively. At the end of follow-up, the estimated glomerular filtration rate was 51.7 ± 7.1 ml/min/1.73 m 2 in the diabetic group and 52.1 ± 12.2 ml/min/1.73 m 2 (p = 0.906) in the non-diabetic group; urine albumin excretion was 9.5 (2-251) mg/day (or mg/g creatinine) in the diabetic group and 6 (0-626) mg/day (or mg/g creatinine) in the non-diabetic group (p = 0.130); and urine protein excretion was 0.079 (0-0.41) g/day in the diabetic group and 0.051 (0-3.7) g/day in the non-diabetic group (p = 0.455). There were no significant differences in short-term renal prognosis between kidney donors with and without diabetes.

Gene expression differences between Noccaea caerulescens ecotypes help to identify candidate genes for metal phytoremediation.

PubMed

Halimaa, Pauliina; Lin, Ya-Fen; Ahonen, Viivi H; Blande, Daniel; Clemens, Stephan; Gyenesei, Attila; Häikiö, Elina; Kärenlampi, Sirpa O; Laiho, Asta; Aarts, Mark G M; Pursiheimo, Juha-Pekka; Schat, Henk; Schmidt, Holger; Tuomainen, Marjo H; Tervahauta, Arja I

2014-03-18

Populations of Noccaea caerulescens show tremendous differences in their capacity to hyperaccumulate and hypertolerate metals. To explore the differences that could contribute to these traits, we undertook SOLiD high-throughput sequencing of the root transcriptomes of three phenotypically well-characterized N. caerulescens accessions, i.e., Ganges, La Calamine, and Monte Prinzera. Genes with possible contribution to zinc, cadmium, and nickel hyperaccumulation and hypertolerance were predicted. The most significant differences between the accessions were related to metal ion (di-, trivalent inorganic cation) transmembrane transporter activity, iron and calcium ion binding, (inorganic) anion transmembrane transporter activity, and antioxidant activity. Analysis of correlation between the expression profile of each gene and the metal-related characteristics of the accessions disclosed both previously characterized (HMA4, HMA3) and new candidate genes (e.g., for nickel IRT1, ZIP10, and PDF2.3) as possible contributors to the hyperaccumulation/tolerance phenotype. A number of unknown Noccaea-specific transcripts also showed correlation with Zn(2+), Cd(2+), or Ni(2+) hyperaccumulation/tolerance. This study shows that N. caerulescens populations have evolved great diversity in the expression of metal-related genes, facilitating adaptation to various metalliferous soils. The information will be helpful in the development of improved plants for metal phytoremediation.

Identifying gender differences in reported occupational information from three U.S. population-based case-control studies

PubMed Central

Locke, Sarah J.; Colt, Joanne S.; Stewart, Patricia A.; Armenti, Karla R.; Baris, Dalsu; Blair, Aaron; Cerhan, James R.; Chow, Wong-Ho; Cozen, Wendy; Davis, Faith; De Roos, Anneclaire J.; Hartge, Patricia; Karagas, Margaret R.; Johnson, Alison; Purdue, Mark P.; Rothman, Nathaniel; Schwartz, Kendra; Schwenn, Molly; Severson, Richard; Silverman, Debra T.; Friesen, Melissa C.

2014-01-01

Objectives Growing evidence suggests that gender-blind assessment of exposure may introduce exposure misclassification, but few studies have characterized gender differences across occupations and industries. We pooled control responses to job-, industry-, and exposure-specific questionnaires (modules) that asked detailed questions about work activities from three US population-based case-control studies to examine gender differences in work tasks and their frequencies. Methods We calculated the ratio of female to male controls that completed each module. For four job modules (assembly worker, machinist, health professional, janitor/cleaner) and for subgroups of jobs that completed those modules, we evaluated gender differences in task prevalence and frequency using Chi-square and Mann-Whitney U-tests, respectively. Results The 1,360 female and 2,245 male controls reported 6,033 and 12,083 jobs, respectively. Gender differences in female:male module completion ratios were observed for 39 of 45 modules completed by ≥20 controls. Gender differences in task prevalence varied in direction and magnitude. For example, female janitors were significantly more likely to polish furniture (79% vs. 44%), while male janitors were more likely to strip floors (73% vs. 50%). Women usually reported more time spent on tasks than men. For example, the median hours per week spent degreasing for production workers in product manufacturing industries was 6.3 for women and 3.0 for men. Conclusions Observed gender differences may reflect actual differences in tasks performed or differences in recall, reporting, or perception, all of which contribute to exposure misclassification and impact relative risk estimates. Our findings reinforce the need to capture subject-specific information on work tasks. PMID:24683012

A Cochrane Systematic Review finds no significant difference in outcome or risk of postoperative complications between day care and in-patient cataract surgery.

PubMed

Fedorowicz, Zbigniew; Lawrence, David J; Gutierrez, Peter

2006-09-01

This review was conducted to determine reliable evidence regarding the safety, feasibility, effectiveness, and cost-effectiveness of cataract extraction performed as a day care versus in-patient procedure. The search to identify randomized controlled trials comparing day care and in-patient surgery for age-related cataract included the Cochrane Eyes and Vision Group Trials Register, the Cochrane Central Register of Controlled Trials, MEDLINE, EMBASE and LILACS Latin American and Caribbean Literature on Health Sciences. Assessment of methodological quality was based on criteria defined by the Cochrane Collaboration. The primary outcome was the achievement of a satisfactory visual acuity 6 weeks after operation. Two trials, involving a total of 1284 people, are included. One trial reported statistically significant differences in early postoperative complication rates in the day care group, which had no clinical relevance to visual outcomes 4 months postoperatively. Mean change in visual acuity Snellen lines of the operated eye 4 months postoperatively was 4.1 standard deviation SD 2.3 for the day care group and 4.1 SD 2.2 for the in-patient group. Costs were 20% more for the in-patient group attributable to higher costs for overnight stay.

Changes in Healthcare Spending After Diagnosis of Comorbidities Among Endometriosis Patients: A Difference-in-Differences Analysis.

PubMed

Epstein, Andrew J; Soliman, Ahmed M; Davis, Matthew; Johnson, Scott J; Snabes, Michael C; Surrey, Eric S

2017-11-01

We sought to characterize changes in healthcare spending associated with the onset of 22 endometriosis-related comorbidities. Women aged 18-49 years with endometriosis (N = 180,278) were extracted from 2006-2015 de-identified Clinformatics ® DataMart claims data. For 22 comorbidities, comorbidity patients were identified on the basis of having a first comorbidity diagnosis after their initial endometriosis diagnosis. Controls were identified on the basis of having no comorbidity diagnosis and were matched 1:1 to comorbidity patients on demographics and baseline spending. Total medical and pharmacy spending was measured during 12 months before and after each patient's index date (first comorbidity diagnosis for comorbidity patients, and equal number of days after earliest endometriosis claim for controls). Pre-post spending differences were compared using difference-in-differences linear regression. Total and comorbidity-related cumulative spending per patient for all endometriosis patients were calculated annually for the 5 years following endometriosis diagnosis. The number of endometriosis patients with each comorbidity varied between 121 for endometrial cancer and 16,177 for fatigue. Healthcare spending increased significantly with the onset of eight comorbidities: breast cancer, ovarian cancer, pregnancy complications, systemic lupus erythematosus/rheumatoid arthritis/Sjogren's/multiple sclerosis, infertility, uterine fibroids, ovarian cyst, and headache [p < 0.001 except for headache (p = 0.045)]. Spending decreased significantly for fatigue, cystitis/UTI, and eczema [p < 0.001 except for fatigue (p = 0.048)] and was not statistically different for the other 11 comorbidities. Difference-in-differences estimates were significantly higher for comorbidity patients for all comorbidities except eczema (p ≤ 0.003). Mean 5-year total cumulative spending was $58,191 per endometriosis patient, of which between 11% and 23% was attributable to

Worsening renal function in patients hospitalized with acute heart failure: risk factors and prognostic significances.

PubMed

Verdiani, Valerio; Lastrucci, Vieri; Nozzoli, Carlo

2010-10-11

Objectives. To determine the prevalence, the clinical predictors, and the prognostic significances of Worsening Renal Function (WRF) in hospitalized patients with Acute Heart Failure (AHF). Methods. 394 consecutively hospitalized patients with AHF were evaluated. WRF was defined as an increase in serum creatinine of ≥0.3 mg/dL from baseline to discharge. Results. Nearly 11% of patients developed WRF. The independent predictors of WRF analyzed with a multivariable logistic regression were history of chronic kidney disease (P = .047), age >75 years (P = .049), and admission heart rates ≥100 bpm (P = .004). Mortality or rehospitalization rates at 1 month, 6 months, and 1year were not significantly different between patients with WRF and those without WRF. Conclusion. Different clinical predictors at hospital admission can be used to identify patients at increased risk for developing WRF. Patients with WRF compared with those without WRF experienced no significant differences in hospital length of stay, mortality, or rehospitalization rates.

Worsening Renal Function in Patients Hospitalized with Acute Heart Failure: Risk Factors and Prognostic Significances

PubMed Central

Verdiani, Valerio; Lastrucci, Vieri; Nozzoli, Carlo

2011-01-01

Objectives. To determine the prevalence, the clinical predictors, and the prognostic significances of Worsening Renal Function (WRF) in hospitalized patients with Acute Heart Failure (AHF). Methods. 394 consecutively hospitalized patients with AHF were evaluated. WRF was defined as an increase in serum creatinine of ≥0.3 mg/dL from baseline to discharge. Results. Nearly 11% of patients developed WRF. The independent predictors of WRF analyzed with a multivariable logistic regression were history of chronic kidney disease (P = .047), age >75 years (P = .049), and admission heart rates ≥100 bpm (P = .004). Mortality or rehospitalization rates at 1 month, 6 months, and 1year were not significantly different between patients with WRF and those without WRF. Conclusion. Different clinical predictors at hospital admission can be used to identify patients at increased risk for developing WRF. Patients with WRF compared with those without WRF experienced no significant differences in hospital length of stay, mortality, or rehospitalization rates. PMID:21188211

Significant wilderness qualities: can they be identified and monitored?

Treesearch

David N. Cole; Robert C. Lucas

1989-01-01

The third Research Colloquium, sponsored by the National Outdoor Leadership School (NOLS), convened the week of August 10-15 in the Popo Agie Wilderness, Shoshone National Forest, Wyoming. The purpose of these colloquia is to facilitate interaction and discussion between wilderness managers, researchers, and NOLS personnel in a wilderness setting. At each colloquium,...

Significance of atypical squamous cells of undetermined significance on ThinPrep papanicolaou smears.

PubMed

Eltabbakh, G H; Lipman, J N; Mount, S L; Morgan, A

2000-10-01

The aim of this study was to assess the prevalence and risk factors predictive of dysplasia among women seen in a gynecologic oncology service with the cytologic diagnosis of atypical squamous cells of undetermined significance (ASCUS) on Papanicolaou smears obtained by the ThinPrep method. Patients with ASCUS ThinPrep Papanicolaou smears seen at the Division of Gynecologic Oncology, University of Vermont, between 1997 and 1999 were identified. The cytologic smears were reviewed and subtyped into reactive or suggestive of squamous intraepithelial lesion (SIL). The charts of these patients were reviewed and the following information was abstracted: age, gravidity, parity, menopausal status, use of hormonal replacement therapy, smoking, history of pelvic cancer, history of radiation therapy, history of abnormal Papanicolaou smear and its treatment, history of human papillomavirus (HPV) infection, and follow-up information including results of repeat Papanicolaou smears, colposcopy, and biopsies. The prevalence of dysplasia was calculated. The demographic features of women with ASCUS, reactive, were compared with those with ASCUS, SIL, using a two-sample t test, chi(2), and Fisher's exact test. Risk factors predictive of dysplasia were calculated using the odds ratio and the 95% confidence interval. P < 0.05 was considered significant. One hundred twenty-six patients with ASCUS on ThinPrep Papanicolaou smear were identified; 63 patients had ASCUS, reactive, and 63 patients had ASCUS, SIL. The demographic features of both groups were similar. The overall prevalence of dysplasia was 15.9% and was significantly higher among women with ASCUS, SIL, than among women with ASCUS, reactive (25.4% versus 6.4%, P = 0.003). The type of ASCUS cytology (reactive versus SIL), smoking, and history of HPV were significant risk factors for dysplasia (P = 0.003, 0.037, and 0. 042, respectively). The prevalence of dysplasia among women seen in a gynecologic oncology service with ASCUS

Evaluation of the BD Vacutainer(®) RST blood collection tube for routine chemistry analytes: clinical significance of differences and stability study.

PubMed

Kocijancic, Marija; Cargonja, Jelena; Delic-Knezevic, Alma

2014-01-01

Preanalytical variables account for most of laboratory errors. There is a wide range of factors that affect the reliability of laboratory report. Most convenient sample type for routine laboratory analysis is serum. BD Vacutainer(®) Rapid Serum Tube (RST) (Becton, Dickinson and Company, Franklin Lakes, NJ, USA) blood collection tube provides rapid clotting time allowing fast serum separation. Our aim was to evaluate the comparability of routine chemistry parameters in BD Vacutainer(®) RST blood collection tube in reference with the BD Vacutainer(®) Serum Separating Tubes II Advance Tube (SST) (Becton, Dickinson and Company, Franklin Lakes, NJ, USA). Blood specimens were collected from 90 participants for evaluation on its results, clotting time and stability study of six routine biochemistry parameters: glucose (Glu), aspartate aminotransferase (AST), alanine aminotransferase (ALT), calcium (Ca), lactate dehidrogenase (LD) and potassium (K) measured with Olympus AU2700 analyzer (Beckman Coulter, Tokyo, Japan). The significance of the differences between samples was assessed by paired t-test or Wilcoxon Matched-Pairs Rank test after checking for normality. Clotting process was significantly shorter in the RSTs compared to SSTs (2.49 min vs. 19.47 min, respectively; P < 0.001). There was a statistically significant difference between the RST and SST II tubes for glucose, calcium and LD (P < 0.001). Differences for glucose and LD were also clinically significant. Analyte stability studies showed that all analytes were stable for 24 h at 4 °C. Most results (except LD and glucose) from RST are comparable with those from SST. In addition, RST tube provides shorter clotting time.

Mobile NBM - android medical mobile application designed to help in learning how to identify the different regions of interest in the brain’s white matter

PubMed Central

2014-01-01

Background One of the most critical tasks when conducting neurological studies is identifying the different regions of interest in the brain’s white matter. Currently few programs or applications are available that serve as an interactive guide in this process. This is why a mobile application has been designed and developed in order to teach users how to identify the referred regions of the brain. It also enables users to share the results obtained and take an examination on the knowledge thus learnt. In order to provide direct user-user or user-developer contact, the project includes a website and a Twitter account. Results An application has been designed with a basic, minimalist look, which anyone can access easily in order to learn to identify a specific region in the brain’s white matter. A survey has also been conducted on people who have used it, which has shown that the application is attractive both in the student (final mean satisfaction of 4.2/5) and in the professional (final mean satisfaction of 4.3/5) environment. The response obtained in the online part of the project reflects the high practical value and quality of the application, as shown by the fact that the website has seen a large number of visitors (over 1000 visitors) and the Twitter account has a high number of followers (over 280 followers). Conclusions Mobile NBM is the first mobile application to be used as a guide in the process of identifying a region of interest in the brain’s white matter. Although initially not many areas are available in the application, new ones can be added as required by users in their respective studies. Apart from the application itself, the online resources provided (website and Twitter account) significantly enhance users’ experience. PMID:25037858

Novel quality indicators for metastatic colorectal cancer management identify significant variations in these measures across treatment centers in Australia.

PubMed

Turner, Natalie Heather; Wong, Hui-Li; Field, Kathryn; Wong, Rachel; Shapiro, Jeremy; Yip, Desmond; Nott, Louise; Tie, Jeanne; Kosmider, Suzanne; Tran, Ben; Desai, Jayesh; McKendrick, Joseph; Zimet, Allan; Richardson, Gary; Iddawela, Mahesh; Gibbs, Peter

2015-09-01

Defining multidisciplinary quality of care indicators (QCIs) for metastatic colorectal cancer (mCRC) could improve understanding of variations in routine practice care. This may identify areas of below-average performance, which could then be addressed by clinicians to improve the quality of care delivered. This study aimed to define a panel of QCIs in mCRC and, based on these QCIs, to evaluate quality of care across multiple Australian sites. A panel of clinicians with expertise in colorectal cancer defined evidence-based or best practice-based QCIs relevant to the routine multidisciplinary management of mCRC patients through structured consensus discussion. Related data were extracted from the Treatment of Recurrent and Advanced Colorectal Cancer (TRACC) registry, a prospectively maintained database recording comprehensive details on consecutive mCRC patients across multiple Australian hospitals. Variations in QCIs across sites were explored. Of 13 QCIs defined, data related to 10 were reliably extracted from TRACC. Analysis of data on 1276 patients across 10 sites demonstrated low rates of screening for hereditary nonpolyposis colorectal cancer in young patients and significant variation in surveillance-detected recurrences, lung resection rates and palliative chemotherapy use. Exploratory analyses suggested correlation between liver resection rates and survival. We have defined a novel set of mCRC QCIs and have demonstrated wide variation in the quality of care of mCRC across multiple Australian sites. With further validation to confirm a direct correlation between QCI and patient outcomes, these QCIs could be applied to improve the quality of care received by all mCRC patients. © 2015 Wiley Publishing Asia Pty Ltd.

A Novel Method to Identify Differential Pathways in Hippocampus Alzheimer's Disease.

PubMed

Liu, Chun-Han; Liu, Lian

2017-05-08

BACKGROUND Alzheimer's disease (AD) is the most common type of dementia. The objective of this paper is to propose a novel method to identify differential pathways in hippocampus AD. MATERIAL AND METHODS We proposed a combined method by merging existed methods. Firstly, pathways were identified by four known methods (DAVID, the neaGUI package, the pathway-based co-expressed method, and the pathway network approach), and differential pathways were evaluated through setting weight thresholds. Subsequently, we combined all pathways by a rank-based algorithm and called the method the combined method. Finally, common differential pathways across two or more of five methods were selected. RESULTS Pathways obtained from different methods were also different. The combined method obtained 1639 pathways and 596 differential pathways, which included all pathways gained from the four existing methods; hence, the novel method solved the problem of inconsistent results. Besides, a total of 13 common pathways were identified, such as metabolism, immune system, and cell cycle. CONCLUSIONS We have proposed a novel method by combining four existing methods based on a rank product algorithm, and identified 13 significant differential pathways based on it. These differential pathways might provide insight into treatment and diagnosis of hippocampus AD.

Significant drug-nutrient interactions.

PubMed

Kirk, J K

1995-04-01

Many nutrients substantially interfere with pharmacotherapeutic goals. The presence of certain nutrients in the gastrointestinal tract affects the bioavailability and disposition of many oral medications. Drug-nutrient interactions can also have positive effects that result in increased drug absorption or reduced gastrointestinal irritation. Knowing the significant drug-nutrient interactions can help the clinician identify the nutrients to avoid with certain medications, as well as the therapeutic agents that should be administered with food. This information can be used to educate patients and optimize pharmacotherapy.

The Italian external quality assessment for RAS testing in colorectal carcinoma identifies methods-related inter-laboratory differences.

PubMed

Normanno, Nicola; Pinto, Carmine; Castiglione, Francesca; Fenizia, Francesca; Barberis, Massimo; Marchetti, Antonio; Fontanini, Gabriella; De Rosa, Gaetano; Taddei, Gian Luigi

2015-09-03

In 2014 the European Medicines Agency included exon 2, 3 and 4 KRAS and NRAS testing for the selection of metastatic colorectal cancer (mCRC) patients eligible for the therapy with anti-EGFR monoclonal antibodies. The Italian Association of Medical Oncology (AIOM) and the Italian Society of Pathology and Cytology (SIAPEC) organized an external quality assessment (EQA) scheme for CRC to evaluate inter-laboratory consistency and to ensure standardization of the results in the transition from KRAS to all-RAS testing. Ten formalin fixed paraffin embedded specimens including KRAS/NRAS (exons 2, 3, 4) and BRAF (codon 600) mutations were validated by three referral laboratories and sent to 88 participant centers. Molecular pathology sample reports were also requested to each laboratory. A board of assessors from AIOM and SIAPEC evaluated the results according to a predefined scoring system. The scheme was composed of two rounds. In the first round 36% of the 88 participants failed, with 23 centers having at least one false positive or false negative while 9 centers did not meet the deadline. The genotyping error rate was higher when Sanger sequencing was employed for testing as compared with pyrosequencing (3 vs 1.3%; p = 0.01; Pearson Chi Square test). In the second round, the laboratories improved their performance, with 23/32 laboratories passing the round. Overall, 79/88 participants passed the RAS EQA scheme. Standardized Human Genome Variation Society nomenclature was incorrectly used to describe the mutations identified and relevant variations were noticed in the genotype specification. The results of the Italian RAS EQA scheme indicate that the mutational analyses are performed with good quality in many Italian centers, although significant differences in the methods used were highlighted. The relatively high number of centers failing the first round underlines the fundamental role in continued education covered by EQA schemes.

10 CFR 51.32 - Finding of no significant impact.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 2 2010-01-01 2010-01-01 false Finding of no significant impact. 51.32 Section 51.32... Section 102(2) Finding of No Significant Impact § 51.32 Finding of no significant impact. (a) A finding of no significant impact will: (1) Identify the proposed action; (2) State that the Commission has...

TNF-α in CRPS and 'normal' trauma--significant differences between tissue and serum.

PubMed

Krämer, Heidrun H; Eberle, Tatiana; Uçeyler, Nurcan; Wagner, Ina; Klonschinsky, Thomas; Müller, Lars P; Sommer, Claudia; Birklein, Frank

2011-02-01

Posttraumatic TNF-alpha signaling may be one of the factors responsible for pain and hyperalgesia in complex regional pain syndromes (CRPS). In order to further specify the role of TNF-alpha we investigated tissue (skin) and serum concentrations in three different patient groups: patients with osteoarthritis and planned surgery, with acute traumatic upper limb bone fracture waiting for surgery, and with CRPS I. Thirty patients (10 in each group) were recruited. Mean CRPS duration was 36.1 ± 8.1 weeks (range 8- 90 weeks). Skin punch biopsies were taken at the beginning of the surgery in osteoarthritis and fracture patients and from the affected side in CRPS patients. Blood samples were taken before the respective procedures. Skin and serum TNF-alpha levels were quantified by ELISA. Compared to patients with osteoarthritis, skin TNF-alpha was significantly elevated in CRPS (p<0.001) and fracture patients (p<0.04). Skin TNF-alpha in CRPS patients was higher than in patients with acute bone fracture (p<0.02). In contrast, serum TNF-alpha values were the same in osteoarthritis and CRPS, and lower in fracture patients (p<0.03). Our results indicate a local but not systemic increase of TNF-alpha in CRPS patients. This increase persists for months after limb trauma and may offer the opportunity for targeted treatment. Copyright © 2010 International Association for the Study of Pain. Published by Elsevier B.V. All rights reserved.

Different extraction pretreatments significantly change the flavonoid contents of Scutellaria baicalensis

PubMed Central

Yu, Chunhao; Qu, Fengyun; Mao, Yanyong; Li, Dong; Zhen, Zhong; Nass, Rachael; Calway, Tyler; Wang, Yunwei; Yuan, Chun-Su; Wang, Chong-Zhi

2014-01-01

Context Scutellaria baicalensis is one of the most commonly used medicinal herbs, especially in traditional Chinese medicine. However, compared to many pharmacological studies of this botanical, much less attention has been paid to the quality control of the herb’s pretreatment prior to extract preparation, an issue that may affect therapeutic outcomes. Objective The current study was designed to evaluate whether different pretreatment conditions change the contents of its four major flavonoids in the herb, i.e., two glycosides (baicalin and wogonoside) and two aglycons (baicalein and wogonin). Materials and methods An HPLC assay was used to quantify the contents of these four flavonoids. The composition changes of four flavonoids by different pretreatment conditions including solvent, treatment time, temperature, pH value, and herb/solvent ratio were evaluated. Results After selection of the first order time-curve kinetics, our data showed that at 50°C, 1:5 herb/water (in w/v) ratio and pH 6.67 yielded an optimal conversion rate from flavonoid glycosides to their aglycons. In this optimized condition, the contents of baicalin and wogonoside were decreased to 1/70 and 1/13, while baicalein and wogonin were increased 3.5 and 3.1 folds, respectively, compared to untreated herb. Discussion and conclusion The markedly variable conversion rates by different pretreatment conditions complicated the quality control of this herb, mainly due to the high amount of endogenous enzymes of S. baicalensis. Optimal pretreatment conditions obtained from this study could be used obtain the highest level of desired constituents to achieve better pharmacological effects. PMID:23738852

Different extraction pretreatments significantly change the flavonoid contents of Scutellaria baicalensis.

PubMed

Yu, Chunhao; Qu, Fengyun; Mao, Yanyong; Li, Dong; Zhen, Zhong; Nass, Rachael; Calway, Tyler; Wang, Yunwei; Yuan, Chun-Su; Wang, Chong-Zhi

2013-10-01

Scutellaria baicalensis Georgi (Labiatae) is one of the most commonly used medicinal herbs, especially in traditional Chinese medicine. However, compared to many pharmacological studies of this botanical, much less attention has been paid to the quality control of the herb's pretreatment prior to extract preparation, an issue that may affect therapeutic outcomes. The current study was designed to evaluate whether different pretreatment conditions change the contents of the four major flavonoids in the herb, i.e., two glycosides (baicalin and wogonoside) and two aglycones (baicalein and wogonin). A high-performance liquid chromatography assay was used to quantify the contents of these four flavonoids. The composition changes of four flavonoids by different pretreatment conditions, including solvent, treatment time, temperature, pH value and herb/solvent ratio were evaluated. After selection of the first order time-curve kinetics, our data showed that at 50 °C, 1:5 herb/water (in w/v) ratio and pH 6.67 yielded an optimal conversion rate from flavonoid glycosides to their aglycones. In this optimized condition, the contents of baicalin and wogonoside were decreased to 1/70 and 1/13, while baicalein and wogonin were increased 3.5- and 3.1-fold, respectively, compared to untreated herb. The markedly variable conversion rates by different pretreatment conditions complicated the quality control of this herb, mainly due to the high amount of endogenous enzymes of S. baicalensis. Optimal pretreatment conditions observed in this study could be used obtain the highest level of desired constituents to achieve better pharmacological effects.

Human exposure to brominated flame retardants through dust in different indoor environments: Identifying the sources of concentration differences in hair from men and women.

PubMed

Li, Junqi; Dong, Zheng; Wang, Ying; Bao, Junsong; Yan, Yijun; Liu, Anming; Jin, Jun

2018-08-01

Brominated flame retardants (BFRs) can accumulate in humans and are associated with adverse health effects. The study was conducted to determine the differences in Polybrominated diphenyl ethers (PBDEs) and alternative brominated flame retardant (Alt-BFR) concentrations between men and women. We analyzed hair samples from 14 male and 20 female university students, paired dust samples from their dormitories (10 for males and 8 for females), and six dust samples from university teaching buildings. The total PBDE concentrations in hair from females were significantly (three times) higher (p = 0.012) than that from males (means 372 and 109 ng/g, respectively). The mean total PBDE concentrations in classroom and dormitory dust were 36100 and 2012 ng/g, respectively. The PBDE patterns were different in the male and female hair samples, as were the patterns in the classroom and dormitory dust. There are no reports concerning human exposure to BFRs through dust that was assessed considering academic and residential environments simultaneously. The differences between BFR exposure for males and females and the differences between BFR concentrations in hair samples from males and females were consistent for 71.4% of the compounds. However, using only dormitory dust in the calculations gave consistent differences only for 28.6% of the compounds, suggesting that the BFR concentration differences in hair were mainly because females spent much more time than males in classrooms. Copyright © 2018 Elsevier Ltd. All rights reserved.

Gender-differences in risk factors for suicidal behaviour identified by perceived burdensomeness, thwarted belongingness and acquired capability: cross-sectional analysis from a longitudinal cohort study.

PubMed

Donker, Tara; Batterham, Philip J; Van Orden, Kimberly A; Christensen, Helen

2014-01-01

The Interpersonal-Psychological Theory of Suicidal Behavior (IPT) is supported by recent epidemiological data. Unique risk factors for the IPT constructs have been identified in community epidemiological studies. Gender differences in these risk factors may contribute substantially to our understanding of suicidal risk, and require further investigation. The present study explores gender differences in the predictors and correlates of perceived burdensomeness, thwarted belongingness and acquired capability for suicide. Participants (547 males, 739 females) aged 32-38 from the PATH through Life study, an Australian population-based longitudinal cohort study (n=1,177) were assessed on perceived burdensomeness, thwarted belongingness and acquired capability for suicide using the Interpersonal Needs Questionnaire and Acquired Capability for Suicide Survey, and on a range of demographic, social support, psychological, mental health and physical health measures. Gender differences in the predictors of the IPT constructs were assessed using linear regression analyses. Higher perceived burdensomeness increased suicide ideation in both genders, while higher thwarted belongingness increased suicide ideation only in females. In females, thwarted belongingness was uniquely related to perceived burdensomeness, while greater physical health was significantly associated with greater thwarted belongingness in males but not in females. There were trends suggesting greater effects of being single and greater perceived burdensomeness for men, and stronger effects of less positive friendship support for women associated with greater thwarted belongingness. Men and women differ in the pattern of psychological characteristics that predict suicide ideation, and in the factors predicting vulnerability. Suicide prevention strategies need to take account of gender differences.

Method and system employing finite state machine modeling to identify one of a plurality of different electric load types

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

Du, Liang; Yang, Yi; Harley, Ronald Gordon

A system is for a plurality of different electric load types. The system includes a plurality of sensors structured to sense a voltage signal and a current signal for each of the different electric loads; and a processor. The processor acquires a voltage and current waveform from the sensors for a corresponding one of the different electric load types; calculates a power or current RMS profile of the waveform; quantizes the power or current RMS profile into a set of quantized state-values; evaluates a state-duration for each of the quantized state-values; evaluates a plurality of state-types based on the powermore » or current RMS profile and the quantized state-values; generates a state-sequence that describes a corresponding finite state machine model of a generalized load start-up or transient profile for the corresponding electric load type; and identifies the corresponding electric load type.« less

Identifying Technical Vocabulary

ERIC Educational Resources Information Center

Chung, Teresa Mihwa; Nation, Paul

2004-01-01

This study compared four different approaches to identifying technical words in an anatomy text. The first approach used a four step rating scale, and was used as the comparison for evaluating the other three approaches. It had a high degree of reliability. The least successful approach was that using clues provided by the writer such as labels in…

Metabolic Differences between Dogs of Different Body Sizes

PubMed Central

Lacroix, Sebastien; Kennedy, Adam D.; Beloshapka, Alison; Kaput, Jim

2017-01-01

Introduction The domesticated dog, Canis lupus familiaris, has been selectively bred to produce extreme diversity in phenotype and genotype. Dogs have an immense diversity in weight and height. Specific differences in metabolism have not been characterized in small dogs as compared to larger dogs. Objectives This study aims to identify metabolic, clinical, and microbiota differences between small and larger dogs. Methods Gas chromatography/mass spectrometry, liquid chromatography/tandem mass spectrometry, clinical chemistry analysis, dual-energy X-ray absorptiometry, and 16S pyrosequencing were used to characterize blood metabolic, clinical, and fecal microbiome systems, respectively. Eighty-three canines from seven different breeds, fed the same kibble diet for 5 weeks, were used in the study. Results 449 metabolites, 16 clinical parameters, and 6 bacteria (at the genus level) were significantly different between small and larger dogs. Hierarchical clustering of the metabolites yielded 8 modules associated with small dog size. Conclusion Small dogs had a lower antioxidant status and differences in circulating amino acids. Some of the amino acid differences could be attributed to differences in microflora. Additionally, analysis of small dog metabolites and clinical parameters reflected a network which strongly associates with kidney function. PMID:29225968

Advanced Electrocardiography Can Identify Occult Cardiomyopathy in Doberman Pinschers

NASA Technical Reports Server (NTRS)

Spiljak, M.; Petric, A. Domanjko; Wilberg, M.; Olsen, L. H.; Stepancic, A.; Schlegel, T. T.; Starc, V.

2011-01-01

Recently, multiple advanced resting electrocardiographic (A-ECG) techniques have improved the diagnostic value of short-duration ECG in detection of dilated cardiomyopathy (DCM) in humans. This study investigated whether 12-lead A-ECG recordings could accurately identify the occult phase of DCM in dogs. Short-duration (3-5 min) high-fidelity 12-lead ECG recordings were obtained from 31 privately-owned, clinically healthy Doberman Pinschers (5.4 +/- 1.7 years, 11/20 males/females). Dogs were divided into 2 groups: 1) 19 healthy dogs with normal echocardiographic M-mode measurements: left ventricular internal diameter in diastole (LVIDd . 47mm) and in systole (LVIDs . 38mm) and normal 24-hour ECG recordings (<50 ventricular premature complexes, VPCs); and 2) 12 dogs with occult DCM: 11/12 dogs had increased M-mode measurements (LVIDd . 49mm and/or LVIDs . 40mm) and 5/11 dogs had also >100 VPCs/24h; 1/12 dogs had only abnormal 24-hour ECG recordings (>100 VPCs/24h). ECG recordings were evaluated via custom software programs to calculate multiple parameters of high-frequency (HF) QRS ECG, heart rate variability, QT variability, waveform complexity and 3-D ECG. Student's t-tests determined 19 ECG parameters that were significantly different (P < 0.05) between groups. Principal component factor analysis identified a 5-factor model with 81.4% explained variance. QRS dipolar and non-dipolar voltages, Cornell voltage criteria and QRS waveform residuum were increased significantly (P < 0.05), whereas mean HF QRS amplitude was decreased significantly (P < 0.05) in dogs with occult DCM. For the 5 selected parameters the prediction of occult DCM was performed using a binary logistic regression model with Chi-square tested significance (P < 0.01). ROC analyses showed that the five selected ECG parameters could identify occult ECG with sensitivity 89% and specificity 83%. Results suggest that 12-lead A-ECG might improve diagnostic value of short-duration ECG in earlier detection

Responsiveness of the EQ-5D to HADS-identified anxiety and depression.

PubMed

Whynes, David K

2009-10-01

The use of generic measures of health-related quality of life enables cost effectiveness comparisons of different health care interventions to be made. Nevertheless, there exists a concern that generic instruments may be insufficiently sensitive to detect the differences or changes in outcome identified by condition-specific instruments. This paper compares the psychometric properties of the EQ-5D generic instrument with a widely used specific measure of distress, the Hospital Anxiety and Depression Scale (HADS). The analysis was based on data obtained from a large sample of women (n = 3119) with low-grade cervical cytological abnormalities detected at routine screening. These women completed EQ-5D and HADS questionnaires at recruitment and at 12 months thereafter. We examined the strength of association between HADS-determined severity of distress and EQ-5D scores at recruitment and between changes in severity and in scores over time. A higher likelihood of HADS-identified anxiety and/or depression was associated with significantly lower EQ-5D index and visual analogue scores. Over time, the EQ-5D score rose significantly when the likelihood of an individual representing a HADS-defined anxiety and/or depression case decreased. We conclude that the EQ-5D has shown itself to be responsive to differing degrees of HADS-assessed distress, although generalization beyond the UK context requires further investigation.

Publication of statistically significant research findings in prosthodontics & implant dentistry in the context of other dental specialties.

PubMed

Papageorgiou, Spyridon N; Kloukos, Dimitrios; Petridis, Haralampos; Pandis, Nikolaos

2015-10-01

To assess the hypothesis that there is excessive reporting of statistically significant studies published in prosthodontic and implantology journals, which could indicate selective publication. The last 30 issues of 9 journals in prosthodontics and implant dentistry were hand-searched for articles with statistical analyses. The percentages of significant and non-significant results were tabulated by parameter of interest. Univariable/multivariable logistic regression analyses were applied to identify possible predictors of reporting statistically significance findings. The results of this study were compared with similar studies in dentistry with random-effects meta-analyses. From the 2323 included studies 71% of them reported statistically significant results, with the significant results ranging from 47% to 86%. Multivariable modeling identified that geographical area and involvement of statistician were predictors of statistically significant results. Compared to interventional studies, the odds that in vitro and observational studies would report statistically significant results was increased by 1.20 times (OR: 2.20, 95% CI: 1.66-2.92) and 0.35 times (OR: 1.35, 95% CI: 1.05-1.73), respectively. The probability of statistically significant results from randomized controlled trials was significantly lower compared to various study designs (difference: 30%, 95% CI: 11-49%). Likewise the probability of statistically significant results in prosthodontics and implant dentistry was lower compared to other dental specialties, but this result did not reach statistical significant (P>0.05). The majority of studies identified in the fields of prosthodontics and implant dentistry presented statistically significant results. The same trend existed in publications of other specialties in dentistry. Copyright © 2015 Elsevier Ltd. All rights reserved.

Thyrotropin receptor autoantibodies (TSHRAbs): epitopes, origins and clinical significance.

PubMed

Kohn, Leonard D; Harii, Norikazu

2003-01-01

Epitopes for > 95% stimulating thyrotropin receptor autoantibodies (TSHRAbs) causally implicated in Graves' disease (Basedow's disease or primary hyperthyroidism) have been identified on on the N-terminal portion of the TSHR extracellular domain, residues 8-165. If the stimulating TSHRAb activity is solely dependent on this region, it is termed homogeneous; if its activity is only largely related to this region, it is termed heterogeneous. The presence of a heterogeneous stimulating TSHRAb in a patient is associated with rapid responses to propylthiouracil or methimazole and may be predictive of long term remission with these oral immunosuppressives. Epitopes for two different Graves' autoantibodies that inhibit TSH binding, TSH binding inhibition immunoglobulins or TBIIs, have also been identified on this region of the TSHR. They do not increase cAMP levels, although one may activate the inositol phosphate, Ca++, arachidonate release signal system. The epitope of blocking TSHRAbs with the ability to inhibit TSH binding (TBII activity), TSH activity, and stimulating TSHRAb activity, and that are causally implicated in the primary hypothyroidism of patients with idiopathic myxedema or some patients with Hashimoto's disease have, in contrast, been largely identified largely on the C-terminal portion of the TSHR extracellular domain, residues 270-395. They have been implicated as important in pregnancy where they attenuate the signs and symptoms of Graves' hyperthyroidism. The appearance of these blocking TSHRAbs during pregnancy in Graves' patients might cause overt or occult hypothyroidism, with resultant effects on fetal development and postnatal intelligence levels. The different TSHRAbs can exist in the same patient at any moment in time, potentially making disease expression a sum of their activities. Assays taking advantage of the epitope mapping findings enable us to detect individual TSHRAbs within a single patient and to better understand their clinical

The Clinician Perspective on Sex Differences in Autism Spectrum Disorders

ERIC Educational Resources Information Center

Jamison, Rene; Bishop, Somer L.; Huerta, Marisela; Halladay, Alycia K.

2017-01-01

Research studies using existing samples of individuals with autism spectrum disorders have identified differences in symptoms between males and females. Differences are typically reported in school age and adolescence, with similarities in symptom presentation at earlier ages. However, existing studies on sex differences are significantly limited,…

Contents of chemical elements in stomach during prenatal development: different age-dependent dynamical changes and their significance

PubMed Central

Hou, Shao-Fan; Li, Hai-Rong; Wang, Li-Zhen; Li, De-Zhu; Yang, Lin-Sheng; Li, Chong-Zheng

2003-01-01

AIM: To observe dynamic of different chemical elements in stomach tissue during fetal development. METHODS: To determine contents of the 21 chemical elements in each stomach samples from fetus aging four to ten months. The content values were compared to those from adult tissue samples, and the values for each month group were also analyzed for dynamic changes. RESULTS: Three representations were found regarding the relationship between contents of the elements and ages of the fetus, including the positive correlative (K), reversely correlative (Na, Ca, P, Al, Cu, Zn, Fe, Mn, Cr, Sr, Li, Cd, Ba, Se) and irrelevant groups (Mg, Co, Ni, V, Pb, Ti). CONCLUSION: The chemical elements’ contents in stomach tissues were found to change dynamically with the stomach weights. The age-dependent representations for different chemical elements during the prenatal development may be of some significance for assessing development of fetal stomach and some chemical elements. The data may be helpful for the nutritional balance of fetus and mothers during prenatal development and even the perinatal stages. PMID:12717857

Significant Wilderness Qualities: Can They Be Identified and Monitored? Proceedings of the Annual NOLS [National Outdoor Leadership School] Wilderness Research Colloquium (3rd, Shoshone National Forest, Wyoming, August 10-15, 1987).

ERIC Educational Resources Information Center

Cole, David N., Comp.; Lucas, Robert C., Comp.

This report is a compilation of the papers presented at a colloquium on wilderness management and a synopsis of discussions held during the conference. The conference theme was how to determine and monitor the most significant features and qualities of the wilderness resource. Generally, participants identify solitude; pollution-free air and…

Frequent Amyloid Deposition Without Significant Cognitive Impairment Among the Elderly

PubMed Central

Aizenstein, Howard Jay; Nebes, Robert D.; Saxton, Judith A.; Price, Julie C.; Mathis, Chester A.; Tsopelas, Nicholas D.; Ziolko, Scott K.; James, Jeffrey A.; Snitz, Beth E.; Houck, Patricia R.; Bi, Wenzhu; Cohen, Ann D.; Lopresti, Brian J.; DeKosky, Steven T.; Halligan, Edythe M.; Klunk, William E.

2009-01-01

Objective To characterize the prevalence of amyloid deposition in a clinically unimpaired elderly population, as assessed by Pittsburgh Compound B (PiB) positron emission tomography (PET) imaging, and its relationship to cognitive function, measured with a battery of neuropsychological tests. Design Subjects underwent cognitive testing and PiB PET imaging (15 mCi for 90 minutes with an ECAT HR + scanner). Logan graphical analysis was applied to estimate regional PiB retention distribution volume, normalized to a cerebellar reference region volume, to yield distribution volume ratios (DVRs). Setting University medical center. Participants From a community-based sample of volunteers, 43 participants aged 65 to 88 years who did not meet diagnostic criteria for Alzheimer disease or mild cognitive impairment were included. Main Outcome Measures Regional PiB retention and cognitive test performance. Results Of 43 clinically unimpaired elderly persons imaged, 9 (21%) showed evidence of early amyloid deposition in at least 1 brain area using an objectively determined DVR cutoff. Demographic characteristics did not differ significantly between amyloid-positive and amyloid-negative participants, and neurocognitive performance was not significantly worse among amyloid-positive compared with amyloid-negative participants. Conclusions Amyloid deposition can be identified among cognitively normal elderly persons during life, and the prevalence of asymptomatic amyloid deposition may be similar to that of symptomatic amyloid deposition. In this group of participants without clinically significant impairment, amyloid deposition was not associated with worse cognitive function, suggesting that an elderly person with a significant amyloid burden can remain cognitively normal. However, this finding is based on relatively small numbers and needs to be replicated in larger cohorts. Longitudinal follow-up of these subjects will be required to support the potential of PiB imaging to

Accuracy Rates of Ancestry Estimation by Forensic Anthropologists Using Identified Forensic Cases.

PubMed

Thomas, Richard M; Parks, Connie L; Richard, Adam H

2017-07-01

A common task in forensic anthropology involves the estimation of the ancestry of a decedent by comparing their skeletal morphology and measurements to skeletons of individuals from known geographic groups. However, the accuracy rates of ancestry estimation methods in actual forensic casework have rarely been studied. This article uses 99 forensic cases with identified skeletal remains to develop accuracy rates for ancestry estimations conducted by forensic anthropologists. The overall rate of correct ancestry estimation from these cases is 90.9%, which is comparable to most research-derived rates and those reported by individual practitioners. Statistical tests showed no significant difference in accuracy rates depending on examiner education level or on the estimated or identified ancestry. More recent cases showed a significantly higher accuracy rate. The incorporation of metric analyses into the ancestry estimate in these cases led to a higher accuracy rate. © 2017 American Academy of Forensic Sciences.

Reversal of Apixaban Induced Alterations in Hemostasis by Different Coagulation Factor Concentrates: Significance of Studies In Vitro with Circulating Human Blood

PubMed Central

Arellano-Rodrigo, Eduardo; Roquer, Jaume; Reverter, Joan Carles; Sanz, Victoria Veronica; Molina, Patricia; Lopez-Vilchez, Irene; Diaz-Ricart, Maribel; Galan, Ana Maria

2013-01-01

Apixaban is a new oral anticoagulant with a specific inhibitory action on FXa. No information is available on the reversal of the antihemostatic action of apixaban in experimental or clinical settings. We have evaluated the effectiveness of different factor concentrates at reversing modifications of hemostatic mechanisms induced by moderately elevated concentrations of apixaban (200 ng/ml) added in vitro to blood from healthy donors (n = 10). Effects on thrombin generation (TG) and thromboelastometry (TEM) parameters were assessed. Modifications in platelet adhesive, aggregating and procoagulant activities were evaluated in studies with blood circulating through damaged vascular surfaces, at a shear rate of 600 s−1. The potential of prothrombin complex concentrates (PCCs; 50 IU/kg), activated prothrombin complex concentrates (aPCCs; 75 IU/kg), or activated recombinant factor VII (rFVIIa; 270 μg/kg), at reversing the antihemostatic actions of apixaban, were investigated. Apixaban interfered with TG kinetics. Delayed lag phase, prolonged time to peak and reduced peak values, were improved by the different concentrates, though modifications in TG patterns were diversely affected depending on the activating reagents. Apixaban significantly prolonged clotting times (CTs) in TEM studies. Prolongations in CTs were corrected by the different concentrates with variable efficacies (rFVIIa≥aPCC>PCC). Apixaban significantly reduced fibrin and platelet interactions with damaged vascular surfaces in perfusion studies (p<0.05 and p<0.01, respectively). Impairments in fibrin formation were normalized by the different concentrates. Only rFVIIa significantly restored levels of platelet deposition. Alterations in hemostasis induced by apixaban were variably compensated by the different factor concentrates investigated. However, effects of these concentrates were not homogeneous in all the tests, with PCCs showing more efficacy in TG, and rFVIIa being more effective on TEM

Identifying potential engaging leaders within medical education: The role of positive influence on peers.

PubMed

Michalec, Barret; Veloski, J Jon; Hojat, Mohammadreza; Tykocinski, Mark L

2014-08-26

Abstract Background: Previous research has paid little to no attention towards exploring methods of identifying existing medical student leaders. Aim: Focusing on the role of influence and employing the tenets of the engaging leadership model, this study examines demographic and academic performance-related differences of positive influencers and if students who have been peer-identified as positive influencers also demonstrate high levels of genuine concern for others. Methods: Three separate fourth-year classes were asked to designate classmates that had significant positive influences on their professional and personal development. The top 10% of those students receiving positive influence nominations were compared with the other students on demographics, academic performance, and genuine concern for others. Results: Besides age, no demographic differences were found between positive influencers and other students. High positive influencers were not found to have higher standardized exam scores but did receive significantly higher clinical clerkship ratings. High positive influencers were found to possess a higher degree of genuine concern for others. Conclusion: The findings lend support to (a) utilizing the engaging model to explore leaders and leadership within medical education, (b) this particular method of identifying existing medical student leaders, and (c) return the focus of leadership research to the power of influence.

Identifying differences in early literacy skills across subgroups of language-minority children: A latent profile analysis.

PubMed

Lonigan, Christopher J; Goodrich, J Marc; Farver, JoAnn M

2018-04-01

Despite acknowledgment that language-minority children come from a wide variety of home language backgrounds and have a wide range of proficiency in their first (L1) and second (L2) languages, it is unknown whether differences across language-minority children in relative and absolute levels of proficiency in L1 and L2 predict subsequent development of literacy-related skills. The purpose of this study was to identify subgroups of language-minority children and evaluate whether differences in level and rate of growth of early literacy skills differed across subgroups. Five-hundred and twenty-six children completed measures of Spanish and English language and early literacy skills at the beginning, middle, and end of the preschool year. Latent growth models indicated that children's early literacy skills were increasing over the course of the preschool year. Latent profile analysis indicated that language-minority children could be classified into nine distinct groups, each with unique patterns of absolute and relative levels of proficiency in L1 and L2. Results of three-step mixture models indicated that profiles were closely associated with level of early literacy skills at the beginning of the preschool year. Initial level of early literacy skills was positively associated with growth in code-related skills (i.e., print knowledge, phonological awareness) and inversely associated with growth in language skills. These findings suggest that language-minority children are a diverse group with regard to their L1 and L2 proficiencies and that growth in early literacy skills is most associated with level of proficiency in the same language. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

Early onset prostate cancer has a significant genetic component.

PubMed

Lange, Ethan M; Salinas, Claudia A; Zuhlke, Kimberly A; Ray, Anna M; Wang, Yunfei; Lu, Yurong; Ho, Lindsey A; Luo, Jingchun; Cooney, Kathleen A

2012-02-01

Prostate cancer (PCa) affects more than 190,000 men each year with ∼10% of men diagnosed at ≤55 years, that is, early onset (EO) PCa. Based on historical findings for other cancers, EO PCa likely reflects a stronger underlying genetic etiology. We evaluated the association between EO PCa and previously identified single nucleotide polymorphisms (SNPs) in 754 Caucasian cases from the Michigan Prostate Cancer Genetics Project (mean 49.8 years at diagnosis), 2,713 Caucasian controls from Illumina's iControlDB database and 1,163 PCa cases diagnosed at >55 years from the Cancer Genetic Markers of Susceptibility Study (CGEMS). Significant associations existed for 13 of 14 SNPs (rs9364554 on 6q25, rs10486567 on 7p15, rs6465657 on 7q21, rs6983267 on 8q24, rs1447295 on 8q24, rs1571801 on 9q33, rs10993994 on 10q11, rs4962416 on 10q26, rs7931342 on 11q13, rs4430796 on 17q12, rs1859962 on 17q24.3, rs2735839 on 19q13, and rs5945619 on Xp11.22, but not rs2660753 on 3p12). EO PCa cases had a significantly greater cumulative number of risk alleles (mean 12.4) than iControlDB controls (mean 11.2; P = 2.1 × 10(-33)) or CGEMS cases (mean 11.9; P = 1.7 × 10(-5)). Notably, EO PCa cases had a higher frequency of the risk allele than CGEMS cases at 11 of 13 associated SNPs, with significant differences for five SNPs. EO PCa cases diagnosed at <50 (mean 12.8) also had significantly more risk alleles than those diagnosed at 50-55 years (mean 12.1; P = 0.0003). These results demonstrate the potential for identifying PCa-associated genetic variants by focusing on the subgroup of men diagnosed with EO disease. Copyright © 2011 Wiley Periodicals, Inc.

Early Onset Prostate Cancer Has A Significant Genetic Component

PubMed Central

Lange, Ethan M.; Salinas, Claudia A.; Zuhlke, Kimberly A.; Ray, Anna M.; Wang, Yunfei; Lu, Yurong; Ho, Lindsey A.; Luo, Jingchun; Cooney, Kathleen A.

2011-01-01

BACKGROUND Prostate cancer (PCa) affects more than 190,000 men each year with ~10% of men diagnosed at ≤ 55 years, i.e., early onset (EO) PCa. Based on historical findings for other cancers, EO PCa likely reflects a stronger underlying genetic etiology. METHODS We evaluated the association between EO PCa and previously identified single nucleotide polymorphisms (SNPs) in 754 Caucasian cases from the Michigan Prostate Cancer Genetics Project (mean 49.8 years at diagnosis), 2,713 Caucasian controls from Illumina’s iControlDB database and 1,163 PCa cases diagnosed at >55 years from the Cancer Genetic Markers of Susceptibility Study (CGEMS). RESULTS Significant associations existed for 13 of 14 SNPs (rs9364554 on 6q25, rs10486567 on 7p15, rs6465657 on 7q21, rs6983267 on 8q24, rs1447295 on 8q24, rs1571801 on 9q33, rs10993994 on 10q11, rs4962416 on 10q26, rs7931342 on 11q13, rs4430796 on 17q12, rs1859962 on 17q24.3, rs2735839 on 19q13, and rs5945619 on Xp11.22, but not rs2660753 on 3p12). EO PCa cases had a significantly greater cumulative number of risk alleles (mean 12.4) than iControlDB controls (mean 11.2; p=2.1×10−33) or CGEMS cases (mean 11.9; p=1.7 × 10−5). Notably, EO PCa cases had a higher frequency of the risk allele than CGEMS cases at 11 of13 associated SNPs, with significant differences for five SNPs. EO PCa cases diagnosed at <50 (mean 12.8) also had significantly more risk alleles than those diagnosed at 50–55 years (mean 12.1; p = 0.0003). CONCLUSIONS These results demonstrate the potential for identifying PCa-associated genetic variants by focusing on the subgroup of men diagnosed with EO disease. PMID:21538423

Identifying Key Flavors in Strawberries Driving Liking via Internal and External Preference Mapping.

PubMed

Oliver, Penelope; Cicerale, Sara; Pang, Edwin; Keast, Russell

2018-04-01

Australian consumers desire the development of a more flavorsome Australian strawberry cultivar. To aid in the development of well-liked strawberries, the attributes driving liking need to be identified. The objective of this research is to apply Preference Mapping (PM) techniques to the descriptive profile of commercial and newly bred strawberry cultivars, together with consumer preference data to determine the flavors contributing to liking. A trained sensory panel (n = 12) used Quantitative Descriptive Analysis (QDA®) methodology to evaluate two appearance, seven aroma, five texture, 10 flavor and 10 aftertaste attributes of three commercial strawberry cultivars and six elite breeding lines grown in Victoria, Australia. Strawberry consumers (n = 150) assessed their liking of the same strawberry cultivars. QDA® significantly discriminated strawberries on 28 of the 34 sensory attributes. There were significant differences in hedonic ratings of strawberries (F(8,714) = 11.5, P = 0.0001), with Hierarchical Cluster Analysis (HCA) identifying three consumer clusters each displaying differing patterns of preference. Internal and external PM techniques were applied to the data to identify the attributes driving consumer acceptability. Sweet, berry, caramel, fruity and floral attributes were identified as most contributing to liking. Sour, citrus, green, astringent, firm and gritty attributes were conversely associated with a reduction in consumer liking. Elite Lines 2 and 6 have been identified as having the broadest appeal, satisfying between 60% and 70% of consumers in the population assessed, thus the introduction of these cultivars should satisfy the largest group of consumers in the Australian market. The results of this research could be applied to breeding programs, to ensure newly bred cultivars express characteristics that were identified as well-liked amongst consumers. In addition, this research provides evidence for marketing strawberries by

Frameshift mutational target gene analysis identifies similarities and differences in constitutional mismatch repair-deficiency and Lynch syndrome.

PubMed

Maletzki, Claudia; Huehns, Maja; Bauer, Ingrid; Ripperger, Tim; Mork, Maureen M; Vilar, Eduardo; Klöcking, Sabine; Zettl, Heike; Prall, Friedrich; Linnebacher, Michael

2017-07-01

Mismatch-repair deficient (MMR-D) malignancies include Lynch Syndrome (LS), which is secondary to germline mutations in one of the MMR genes, and the rare childhood-form of constitutional mismatch repair-deficiency (CMMR-D); caused by bi-allelic MMR gene mutations. A hallmark of LS-associated cancers is microsatellite instability (MSI), characterized by coding frameshift mutations (cFSM) in target genes. By contrast, tumors arising in CMMR-D patients are thought to display a somatic mutation pattern differing from LS. This study has the main goal to identify cFSM in MSI target genes relevant in CMMR-D and to compare the spectrum of common somatic mutations, including alterations in DNA polymerases POLE and D1 between LS and CMMR-D. CMMR-D-associated tumors harbored more somatic mutations compared to LS cases, especially in the TP53 gene and in POLE and POLD1, where novel mutations were additionally identified. Strikingly, MSI in classical mononucleotide markers BAT40 and CAT25 was frequent in CMMR-D cases. MSI-target gene analysis revealed mutations in CMMR-D-associated tumors, some of them known to be frequently hit in LS, such as RNaseT2, HT001, and TGFβR2. Our results imply a general role for these cFSM as potential new drivers of MMR-D tumorigenesis. © 2017 Wiley Periodicals, Inc.

Genome-wide association study in Chinese identifies novel loci for blood pressure and hypertension

PubMed Central

Lu, Xiangfeng; Wang, Laiyuan; Lin, Xu; Huang, Jianfeng; Charles Gu, C.; He, Meian; Shen, Hongbing; He, Jiang; Zhu, Jingwen; Li, Huaixing; Hixson, James E.; Wu, Tangchun; Dai, Juncheng; Lu, Ling; Shen, Chong; Chen, Shufeng; He, Lin; Mo, Zengnan; Hao, Yongchen; Mo, Xingbo; Yang, Xueli; Li, Jianxin; Cao, Jie; Chen, Jichun; Fan, Zhongjie; Li, Ying; Zhao, Liancheng; Li, Hongfan; Lu, Fanghong; Yao, Cailiang; Yu, Lin; Xu, Lihua; Mu, Jianjun; Wu, Xianping; Deng, Ying; Hu, Dongsheng; Zhang, Weidong; Ji, Xu; Guo, Dongshuang; Guo, Zhirong; Zhou, Zhengyuan; Yang, Zili; Wang, Renping; Yang, Jun; Zhou, Xiaoyang; Yan, Weili; Sun, Ningling; Gao, Pingjin; Gu, Dongfeng

2015-01-01

Hypertension is a common disorder and the leading risk factor for cardiovascular disease and premature deaths worldwide. Genome-wide association studies (GWASs) in the European population have identified multiple chromosomal regions associated with blood pressure, and the identified loci altogether explain only a small fraction of the variance for blood pressure. The differences in environmental exposures and genetic background between Chinese and European populations might suggest potential different pathways of blood pressure regulation. To identify novel genetic variants affecting blood pressure variation, we conducted a meta-analysis of GWASs of blood pressure and hypertension in 11 816 subjects followed by replication studies including 69 146 additional individuals. We identified genome-wide significant (P < 5.0 × 10−8) associations with blood pressure, which included variants at three new loci (CACNA1D, CYP21A2, and MED13L) and a newly discovered variant near SLC4A7. We also replicated 14 previously reported loci, 8 (CASZ1, MOV10, FGF5, CYP17A1, SOX6, ATP2B1, ALDH2, and JAG1) at genome-wide significance, and 6 (FIGN, ULK4, GUCY1A3, HFE, TBX3-TBX5, and TBX3) at a suggestive level of P = 1.81 × 10−3 to 5.16 × 10−8. These findings provide new mechanistic insights into the regulation of blood pressure and potential targets for treatments. PMID:25249183

A new method to detect significant basal body temperature changes during a woman's menstrual cycle.

PubMed

Freundl, Günter; Frank-Herrmann, Petra; Brown, Simon; Blackwell, Leonard

2014-10-01

To compare the results of a computer programme based on the Trigg's tracking system (TTS) identification of the basal body temperature (BBT) shift day from daily records of BBT values (TTS transition day), with the BBT shift day identified from the same records using the Sensiplan(®) symptothermal method of natural family planning. A computer programme was written to display the daily BBT readings for 364 menstrual cycles from 51 women aged 24 to 35 years, obtained from the German Natural Family Planning (NFP) database. The TTS transition day so identified from each record was then compared with the BBT shift day estimated from the same record by the Sensiplan(®) method. Total agreement between the methods was obtained for 81% (294/364) of the cycles and 18% (67) cycles differed by ± 1 day. For the 364 pairs of values distributed among 51 women the medians of the differences between the TTS transition day and Sensiplan(®) initial day of the BBT rise (shift day) were not significantly different (χ(2) = 65.28, df = 50, p = 0.07205). The advantages of the tracking signal algorithm are that in many cases it was possible to identify the BBT shift day on that very day - rather than only some days later - and to estimate the probability that a transition had occurred from the different values of the tracking signal.

Identifying marine Important Bird Areas using at-sea survey data

USGS Publications Warehouse

Smith, Melanie A.; Walker, Nathan J.; Free, Christopher M.; Kirchhoff, Matthew J.; Drew, Gary S.; Warnock, Nils; Stenhouse, Iain J.

2014-01-01

Effective marine bird conservation requires identification of at-sea locations used by populations for foraging, staging, and migration. Using an extensive database of at-sea survey data spanning over 30 years, we developed a standardized and data-driven spatial method for identifying globally significant marine Important Bird Areas in Alaska. To delineate these areas we developed a six-step process: binning data and accounting for unequal survey effort, filtering input data for persistence of species use, using a moving window analysis to produce maps representing a gradient from low to high abundance, drawing core area boundaries around major concentrations based on abundance thresholds, validating the results, and combining overlapping boundaries into important areas for multiple species. We identified 126 bird core areas which were merged into 59 pelagic sites important to 45 out of 57 species assessed. The final areas included approximately 34–38% of all marine birds in Alaska waters, within just 6% of the total area. We identified globally significant Important Bird Areas spanning 20 degrees of latitude and 56 degrees of longitude, in two different oceans, with climates ranging from temperate to polar. Although our maps did suffer from some data gaps, these gaps did not preclude us from identifying sites that incorporated 13% of the assessed continental waterbird population and 9% of the assessed global seabird population. The application of this technique over a large and productive region worked well for a wide range of birds, exhibiting a variety of foraging strategies and occupying a variety of ecosystem types.

SPARQL-enabled identifier conversion with Identifiers.org

PubMed Central

Wimalaratne, Sarala M.; Bolleman, Jerven; Juty, Nick; Katayama, Toshiaki; Dumontier, Michel; Redaschi, Nicole; Le Novère, Nicolas; Hermjakob, Henning; Laibe, Camille

2015-01-01

Motivation: On the semantic web, in life sciences in particular, data is often distributed via multiple resources. Each of these sources is likely to use their own International Resource Identifier for conceptually the same resource or database record. The lack of correspondence between identifiers introduces a barrier when executing federated SPARQL queries across life science data. Results: We introduce a novel SPARQL-based service to enable on-the-fly integration of life science data. This service uses the identifier patterns defined in the Identifiers.org Registry to generate a plurality of identifier variants, which can then be used to match source identifiers with target identifiers. We demonstrate the utility of this identifier integration approach by answering queries across major producers of life science Linked Data. Availability and implementation: The SPARQL-based identifier conversion service is available without restriction at http://identifiers.org/services/sparql. Contact: sarala@ebi.ac.uk PMID:25638809

SPARQL-enabled identifier conversion with Identifiers.org.

PubMed

Wimalaratne, Sarala M; Bolleman, Jerven; Juty, Nick; Katayama, Toshiaki; Dumontier, Michel; Redaschi, Nicole; Le Novère, Nicolas; Hermjakob, Henning; Laibe, Camille

2015-06-01

On the semantic web, in life sciences in particular, data is often distributed via multiple resources. Each of these sources is likely to use their own International Resource Identifier for conceptually the same resource or database record. The lack of correspondence between identifiers introduces a barrier when executing federated SPARQL queries across life science data. We introduce a novel SPARQL-based service to enable on-the-fly integration of life science data. This service uses the identifier patterns defined in the Identifiers.org Registry to generate a plurality of identifier variants, which can then be used to match source identifiers with target identifiers. We demonstrate the utility of this identifier integration approach by answering queries across major producers of life science Linked Data. The SPARQL-based identifier conversion service is available without restriction at http://identifiers.org/services/sparql. © The Author 2015. Published by Oxford University Press.

Data Identifiers, Versioning, and Micro-citation

NASA Astrophysics Data System (ADS)

Parsons, M. A.; Duerr, R. E.

2012-12-01

Data citation, especially using Digital Object Identifiers (DOIs), is an increasingly accepted scientific practice. For example, the AGU Council asserts that data "publications" should "be credited and cited like the products of any other scientific activity," and Thomson Reuters has recently announced a data citation index built from DOIs assigned to data sets. Correspondingly, formal guidelines for how to cite a data set (using DOIs or similar identifiers/locators) have recently emerged, notably those from the international DataCite consortium, the UK Digital Curation Centre, and the US Federation of Earth Science Information Partners. These different data citation guidelines are largely congruent. They agree on the basic practice and elements of data citation, especially for relatively static, whole data collections. There is less agreement on some of the more subtle nuances of data citation. They define different methods for handling different data set versions, especially for the very dynamic, growing data sets that are common in Earth Sciences. They also differ in how people should cite specific, arbitrarily large elements, "passages," or subsets of a larger data collection, i.e., the precise data records actually used in a study. This detailed "micro-citation", and careful reference to exact versions of data are essential to ensure scientific reproducibility. Identifiers such as DOIs are necessary but not sufficient for the precise, detailed, references necessary. Careful practice must be coupled with the use of curated identifiers. In this paper we review the pros and cons of different approaches to versioning and micro-citation. We suggest a workable solution for most existing Earth science data and suggest a more rigorous path forward for the future.

Asymptomatic bacteriuria. Clinical significance and management.

PubMed

Raz, Raul

2003-10-01

The clinical significance and management of asymptomatic bacteriuria (ASB) differs according to different groups of patients. ASB requires antibiotic treatment in pregnant women, children aged 5-6 years and prior to invasive genitourinary procedures. However, there is a consensus that ASB in the elderly, healthy school girls and young women, diabetic women and patients with indwelling catheters or intermittent catheterization has no clinical significance and antibiotic prescription is not indicated.

A systems biology strategy to identify molecular mechanisms of action and protein indicators of traumatic brain injury.

PubMed

Yu, Chenggang; Boutté, Angela; Yu, Xueping; Dutta, Bhaskar; Feala, Jacob D; Schmid, Kara; Dave, Jitendra; Tawa, Gregory J; Wallqvist, Anders; Reifman, Jaques

2015-02-01

The multifactorial nature of traumatic brain injury (TBI), especially the complex secondary tissue injury involving intertwined networks of molecular pathways that mediate cellular behavior, has confounded attempts to elucidate the pathology underlying the progression of TBI. Here, systems biology strategies are exploited to identify novel molecular mechanisms and protein indicators of brain injury. To this end, we performed a meta-analysis of four distinct high-throughput gene expression studies involving different animal models of TBI. By using canonical pathways and a large human protein-interaction network as a scaffold, we separately overlaid the gene expression data from each study to identify molecular signatures that were conserved across the different studies. At 24 hr after injury, the significantly activated molecular signatures were nonspecific to TBI, whereas the significantly suppressed molecular signatures were specific to the nervous system. In particular, we identified a suppressed subnetwork consisting of 58 highly interacting, coregulated proteins associated with synaptic function. We selected three proteins from this subnetwork, postsynaptic density protein 95, nitric oxide synthase 1, and disrupted in schizophrenia 1, and hypothesized that their abundance would be significantly reduced after TBI. In a penetrating ballistic-like brain injury rat model of severe TBI, Western blot analysis confirmed our hypothesis. In addition, our analysis recovered 12 previously identified protein biomarkers of TBI. The results suggest that systems biology may provide an efficient, high-yield approach to generate testable hypotheses that can be experimentally validated to identify novel mechanisms of action and molecular indicators of TBI. © 2014 The Authors. Journal of Neuroscience Research Published by Wiley Periodicals, Inc.

A typology of vaping: Identifying differing beliefs, motivations for use, identity and political interest amongst e-cigarette users.

PubMed

Farrimond, Hannah

2017-10-01

The aim of this study was to identify and differentiate socially shared accounts of e-cigarette use (vaping) using Q-methodology, combining factor analysis with qualitative comments. Seventy statements on e-cigarettes, drawn from media, academic and online discussions, were sorted by participants along a continuum of agreement/disagreement, commenting on strongly ranked items. Each participant thus created their own 'account' of their vaping. A by-person correlation matrix of the sorts was conducted, then factor analysed, to identify similar accounts (p<0.01). Fifty-five UK vapers participated by post, 55% male, mean age of 46, 84% only vaping/16% vaping and smoking, 95% vaping daily. Three accounts of e-cigarettes were identified. The first two were associated with having quit smoking; the third with ongoing tobacco smoking and vaping. In Factor One, 'Vaping as Pleasure', vaping was characterized as enjoyable, with long-term use envisaged and a medical model of vaping rejected. Factor One participants also held a strong vaping identity and were politically motivated to maintain the rights of adults to vape. In Factor Two, 'Vaping as Medical Treatment', vaping was understood as a pragmatic choice about how to medicate one's smoking addiction, with the aim being to treat and ultimately reduce nicotine dependence. In Factor Three, 'Ambivalent E-Cigarette Use', participants reported fewer benefits and harboured more negative beliefs about e-cigarettes; they also strongly rejected a vaper identity, having no interest in online forums or being labelled a 'vaper' themselves. The UK e-cigarette users in this sample were not a homogeneous group; differing in their beliefs, motivations for use, identity and political interest. In particular they diverged on whether they accepted a medicalized account of vaping and identified as a vaper. Public health messages targeted to one group of e-cigarette users may not resonate with others. Crown Copyright © 2017. Published by

What difference reveals about similarity.

PubMed

Sagi, Eyal; Gentner, Dedre; Lovett, Andrew

2012-08-01

Detecting that two images are different is faster for highly dissimilar images than for highly similar images. Paradoxically, we showed that the reverse occurs when people are asked to describe how two images differ--that is, to state a difference between two images. Following structure-mapping theory, we propose that this disassociation arises from the multistage nature of the comparison process. Detecting that two images are different can be done in the initial (local-matching) stage, but only for pairs with low overlap; thus, "different" responses are faster for low-similarity than for high-similarity pairs. In contrast, identifying a specific difference generally requires a full structural alignment of the two images, and this alignment process is faster for high-similarity pairs. We described four experiments that demonstrate this dissociation and show that the results can be simulated using the Structure-Mapping Engine. These results pose a significant challenge for nonstructural accounts of similarity comparison and suggest that structural alignment processes play a significant role in visual comparison. Copyright © 2012 Cognitive Science Society, Inc.

Colonoscopy can miss diverticula of the left colon identified by barium enema

PubMed Central

Niikura, Ryota; Nagata, Naoyoshi; Shimbo, Takuro; Akiyama, Junichi; Uemura, Naomi

2013-01-01

AIM: To identify the diagnostic value of colonoscopy for diverticulosis as determined by barium enema. METHODS: A total of 65 patients with hematochezia who underwent colonoscopy and barium enema were analyzed, and the diagnostic value of colonoscopy for diverticula was assessed. The receiver operating characteristic area under the curve was compared in relation to age (< 70 or ≥ 70 years), sex, and colon location. The number of diverticula was counted, and the detection ratio was calculated. RESULTS: Colonic diverticula were observed in 46 patients with barium enema. Colonoscopy had a sensitivity of 91% and specificity of 90%. No significant differences were found in the receiver operating characteristic area under the curve (ROC-AUC) for age group or sex. The ROC-AUC of the left colon was significantly lower than that of the right colon (0.81 vs 0.96, P = 0.02). Colonoscopy identified 486 colonic diverticula, while barium enema identified 1186. The detection ratio for the entire colon was therefore 0.41 (486/1186). The detection ratio in the left colon (0.32, 189/588) was significantly lower than that of the right colon (0.50, 297/598) (P < 0.01). CONCLUSION: Compared with barium enema, only half the number of colonic diverticula can be detected by colonoscopy in the entire colon and even less in the left colon. PMID:23613630

Colonoscopy can miss diverticula of the left colon identified by barium enema.

PubMed

Niikura, Ryota; Nagata, Naoyoshi; Shimbo, Takuro; Akiyama, Junichi; Uemura, Naomi

2013-04-21

To identify the diagnostic value of colonoscopy for diverticulosis as determined by barium enema. A total of 65 patients with hematochezia who underwent colonoscopy and barium enema were analyzed, and the diagnostic value of colonoscopy for diverticula was assessed. The receiver operating characteristic area under the curve was compared in relation to age (< 70 or ≥ 70 years), sex, and colon location. The number of diverticula was counted, and the detection ratio was calculated. Colonic diverticula were observed in 46 patients with barium enema. Colonoscopy had a sensitivity of 91% and specificity of 90%. No significant differences were found in the receiver operating characteristic area under the curve (ROC-AUC) for age group or sex. The ROC-AUC of the left colon was significantly lower than that of the right colon (0.81 vs 0.96, P = 0.02). Colonoscopy identified 486 colonic diverticula, while barium enema identified 1186. The detection ratio for the entire colon was therefore 0.41 (486/1186). The detection ratio in the left colon (0.32, 189/588) was significantly lower than that of the right colon (0.50, 297/598) (P < 0.01). Compared with barium enema, only half the number of colonic diverticula can be detected by colonoscopy in the entire colon and even less in the left colon.

Identifying Stress Transcription Factors Using Gene Expression and TF-Gene Association Data

PubMed Central

Wu, Wei-Sheng; Chen, Bor-Sen

2007-01-01

Unicellular organisms such as yeasts have evolved to survive environmental stresses by rapidly reorganizing the genomic expression program to meet the challenges of harsh environments. The complex adaptation mechanisms to stress remain to be elucidated. In this study, we developed Stress Transcription Factor Identification Algorithm (STFIA), which integrates gene expression and TF-gene association data to identify the stress transcription factors (TFs) of six kinds of stresses. We identified some general stress TFs that are in response to various stresses, and some specific stress TFs that are in response to one specific stress. The biological significance of our findings is validated by the literature. We found that a small number of TFs may be sufficient to control a wide variety of expression patterns in yeast under different stresses. Two implications can be inferred from this observation. First, the adaptation mechanisms to different stresses may have a bow-tie structure. Second, there may exist extensive regulatory cross-talk among different stress responses. In conclusion, this study proposes a network of the regulators of stress responses and their mechanism of action. PMID:20066130

Genome-wide oxidative bisulfite sequencing identifies sex-specific methylation differences in the human placenta

PubMed Central

Johnson, Michelle D; Dopierala, Justyna

2018-01-01

ABSTRACT DNA methylation is an important regulator of gene function. Fetal sex is associated with the risk of several specific pregnancy complications related to placental function. However, the association between fetal sex and placental DNA methylation remains poorly understood. We carried out whole-genome oxidative bisulfite sequencing in the placentas of two healthy female and two healthy male pregnancies generating an average genome depth of coverage of 25x. Most highly ranked differentially methylated regions (DMRs) were located on the X chromosome but we identified a 225 kb sex-specific DMR in the body of the CUB and Sushi Multiple Domains 1 (CSMD1) gene on chromosome 8. The sex-specific differential methylation pattern observed in this region was validated in additional placentas using in-solution target capture. In a new RNA-seq data set from 64 female and 67 male placentas, CSMD1 mRNA was 1.8-fold higher in male than in female placentas (P value = 8.5 × 10−7, Mann-Whitney test). Exon-level quantification of CSMD1 mRNA from these 131 placentas suggested a likely placenta-specific CSMD1 isoform not detected in the 21 somatic tissues analyzed. We show that the gene body of an autosomal gene, CSMD1, is differentially methylated in a sex- and placental-specific manner, displaying sex-specific differences in placental transcript abundance. PMID:29376485

Risk of abnormal triple screen for Down syndrome is significantly higher in patients with female fetuses.

PubMed

Spong, C Y; Ghidini, A; Stanley-Christian, H; Meck, J M; Seydel, F D; Pezzullo, J C

1999-04-01

Previous studies have shown that mid-trimester maternal serum alpha-fetoprotein (AFP) levels are significantly higher and human chorionic gonadotrophin (hCG) levels significantly lower in women with male compared with female fetuses. We have evaluated whether triple-screen criteria are more likely to identify women with female fetuses as at risk for Down syndrome. From the Georgetown University genetics database we obtained the absolute values and corresponding multiples of the median (MoM) for AFP, hCG and unconjugated oestriol (uE3) in singleton gestations for the period database November 1992 July 1996. A Down syndrome risk of 1/270 or greater at mid-trimester was considered as high risk. A total of 977 patients with triple screen and outcome information were identified, including 502 female and 475 male fetuses. Patients with female fetuses were significantly more likely to have lower serum AFP (p=0.003) and a positive triple screen for Down syndrome (72 (14 per cent) versus 45 (9 per cent), p<0.02) than those with male fetuses. The gestational age at triple screen, maternal serum hCG and uE3, race and diabetes were not significantly different between the two groups. Since Down syndrome is less common in female than male fetuses, and the rates of female and male Down syndrome fetuses detected by triple screen and subsequent amniocentesis are not significantly different, the excess of positive mid-trimester maternal serum triple screen in women with female fetuses is likely due to false-positive results.

Altered Microbiome Leads to Significant Phenotypic and Transcriptomic Differences in a Lipid Accumulating Chlorophyte.

PubMed

Richter, Lubna V; Mansfeldt, Cresten B; Kuan, Michael M; Cesare, Alexandra E; Menefee, Stephen T; Richardson, Ruth E; Ahner, Beth A

2018-06-19

Given the challenges facing the economically favorable production of products from microalgae, understanding factors that might impact productivity rates including growth rates and accumulation of desired products, for example, triacylglycerols (TAG) for biodiesel feedstock, remains critical. Although operational parameters such as media composition and reactor design can clearly effect growth rates, the role of microbe-microbe interactions is just beginning to be elucidated. In this study an oleaginous marine algae Chlorella spp. C596 culture is shown to be better described as a microbial community. Perturbations to this microbial community showed a significant impact on phenotypes including sustained differences in growth rate and TAG accumulation of 2.4 and 2.5 fold, respectively. Characterization of the associated community using Illumina 16S rRNA amplicon and random shotgun transcriptomic analyses showed that the fast growth rate correlated with two specific bacterial species ( Ruegeria and Rhodobacter spp). The transcriptomic response of the Chlorella species revealed that the slower growing algal consortium C596-S1 upregulated genes associated with photosynthesis and resource scavenging and decreased the expression of genes associated with transcription and translation relative to the initial C596-R1. Our studies advance the appreciation of the effects microbiomes can have on algal growth in bioreactors and suggest that symbiotic interactions are involved in a range of critical processes including nitrogen, carbon cycling, and oxidative stress.

Large-scale integrative network-based analysis identifies common pathways disrupted by copy number alterations across cancers

PubMed Central

2013-01-01

Background Many large-scale studies analyzed high-throughput genomic data to identify altered pathways essential to the development and progression of specific types of cancer. However, no previous study has been extended to provide a comprehensive analysis of pathways disrupted by copy number alterations across different human cancers. Towards this goal, we propose a network-based method to integrate copy number alteration data with human protein-protein interaction networks and pathway databases to identify pathways that are commonly disrupted in many different types of cancer. Results We applied our approach to a data set of 2,172 cancer patients across 16 different types of cancers, and discovered a set of commonly disrupted pathways, which are likely essential for tumor formation in majority of the cancers. We also identified pathways that are only disrupted in specific cancer types, providing molecular markers for different human cancers. Analysis with independent microarray gene expression datasets confirms that the commonly disrupted pathways can be used to identify patient subgroups with significantly different survival outcomes. We also provide a network view of disrupted pathways to explain how copy number alterations affect pathways that regulate cell growth, cycle, and differentiation for tumorigenesis. Conclusions In this work, we demonstrated that the network-based integrative analysis can help to identify pathways disrupted by copy number alterations across 16 types of human cancers, which are not readily identifiable by conventional overrepresentation-based and other pathway-based methods. All the results and source code are available at http://compbio.cs.umn.edu/NetPathID/. PMID:23822816

Detecting significant change in stream benthic macroinvertebrate communities in wilderness areas

USGS Publications Warehouse

Milner, Alexander M.; Woodward, Andrea; Freilich, Jerome E.; Black, Robert W.; Resh, Vincent H.

2016-01-01

Within a region, both MDS analyses typically identified similar years as exceeding reference condition variation, illustrating the utility of the approach for identifying wider spatial scale effects that influence more than one stream. MDS responded to both simulated water temperature stress and a pollutant event, and generally outlying years on MDS plots could be explained by environmental variables, particularly higher precipitation. Multivariate control charts successfully identified whether shifts in community structure identified by MDS were significant and whether the shift represented a press disturbance (long-term change) or a pulse disturbance. We consider a combination of TD and MDS with control charts to be a potentially powerful tool for determining years significantly outside of a reference condition variation.

Dictionary Pruning with Visual Word Significance for Medical Image Retrieval

PubMed Central

Zhang, Fan; Song, Yang; Cai, Weidong; Hauptmann, Alexander G.; Liu, Sidong; Pujol, Sonia; Kikinis, Ron; Fulham, Michael J; Feng, David Dagan; Chen, Mei

2016-01-01

Content-based medical image retrieval (CBMIR) is an active research area for disease diagnosis and treatment but it can be problematic given the small visual variations between anatomical structures. We propose a retrieval method based on a bag-of-visual-words (BoVW) to identify discriminative characteristics between different medical images with Pruned Dictionary based on Latent Semantic Topic description. We refer to this as the PD-LST retrieval. Our method has two main components. First, we calculate a topic-word significance value for each visual word given a certain latent topic to evaluate how the word is connected to this latent topic. The latent topics are learnt, based on the relationship between the images and words, and are employed to bridge the gap between low-level visual features and high-level semantics. These latent topics describe the images and words semantically and can thus facilitate more meaningful comparisons between the words. Second, we compute an overall-word significance value to evaluate the significance of a visual word within the entire dictionary. We designed an iterative ranking method to measure overall-word significance by considering the relationship between all latent topics and words. The words with higher values are considered meaningful with more significant discriminative power in differentiating medical images. We evaluated our method on two public medical imaging datasets and it showed improved retrieval accuracy and efficiency. PMID:27688597

Dictionary Pruning with Visual Word Significance for Medical Image Retrieval.

PubMed

Zhang, Fan; Song, Yang; Cai, Weidong; Hauptmann, Alexander G; Liu, Sidong; Pujol, Sonia; Kikinis, Ron; Fulham, Michael J; Feng, David Dagan; Chen, Mei

2016-02-12

Content-based medical image retrieval (CBMIR) is an active research area for disease diagnosis and treatment but it can be problematic given the small visual variations between anatomical structures. We propose a retrieval method based on a bag-of-visual-words (BoVW) to identify discriminative characteristics between different medical images with Pruned Dictionary based on Latent Semantic Topic description. We refer to this as the PD-LST retrieval. Our method has two main components. First, we calculate a topic-word significance value for each visual word given a certain latent topic to evaluate how the word is connected to this latent topic. The latent topics are learnt, based on the relationship between the images and words, and are employed to bridge the gap between low-level visual features and high-level semantics. These latent topics describe the images and words semantically and can thus facilitate more meaningful comparisons between the words. Second, we compute an overall-word significance value to evaluate the significance of a visual word within the entire dictionary. We designed an iterative ranking method to measure overall-word significance by considering the relationship between all latent topics and words. The words with higher values are considered meaningful with more significant discriminative power in differentiating medical images. We evaluated our method on two public medical imaging datasets and it showed improved retrieval accuracy and efficiency.

Distributed design approach in persistent identifiers systems

NASA Astrophysics Data System (ADS)

Golodoniuc, Pavel; Car, Nicholas; Klump, Jens

2017-04-01

The need to identify both digital and physical objects is ubiquitous in our society. Past and present persistent identifier (PID) systems, of which there is a great variety in terms of technical and social implementations, have evolved with the advent of the Internet, which has allowed for globally unique and globally resolvable identifiers. PID systems have catered for identifier uniqueness, integrity, persistence, and trustworthiness, regardless of the identifier's application domain, the scope of which has expanded significantly in the past two decades. Since many PID systems have been largely conceived and developed by small communities, or even a single organisation, they have faced challenges in gaining widespread adoption and, most importantly, the ability to survive change of technology. This has left a legacy of identifiers that still exist and are being used but which have lost their resolution service. We believe that one of the causes of once successful PID systems fading is their reliance on a centralised technical infrastructure or a governing authority. Golodoniuc et al. (2016) proposed an approach to the development of PID systems that combines the use of (a) the Handle system, as a distributed system for the registration and first-degree resolution of persistent identifiers, and (b) the PID Service (Golodoniuc et al., 2015), to enable fine-grained resolution to different information object representations. The proposed approach solved the problem of guaranteed first-degree resolution of identifiers, but left fine-grained resolution and information delivery under the control of a single authoritative source, posing risk to the long-term availability of information resources. Herein, we develop these approaches further and explore the potential of large-scale decentralisation at all levels: (i) persistent identifiers and information resources registration; (ii) identifier resolution; and (iii) data delivery. To achieve large-scale decentralisation

Investigation of Current Methods to Identify Helicopter Gear Health

NASA Technical Reports Server (NTRS)

Dempsey, Paula J.; Lewicki, David G.; Le, Dy D.

2007-01-01

This paper provides an overview of current vibration methods used to identify the health of helicopter transmission gears. The gears are critical to the transmission system that provides propulsion, lift and maneuvering of the helicopter. This paper reviews techniques used to process vibration data to calculate conditions indicators (CI's), guidelines used by the government aviation authorities in developing and certifying the Health and Usage Monitoring System (HUMS), condition and health indicators used in commercial HUMS, and different methods used to set thresholds to detect damage. Initial assessment of a method to set thresholds for vibration based condition indicators applied to flight and test rig data by evaluating differences in distributions between comparable transmissions are also discussed. Gear condition indicator FM4 values are compared on an OH58 helicopter during 14 maneuvers and an OH58 transmission test stand during crack propagation tests. Preliminary results show the distributions between healthy helicopter and rig data are comparable and distributions between healthy and damaged gears show significant differences.

Investigation of Current Methods to Identify Helicopter Gear Health

NASA Technical Reports Server (NTRS)

Dempsey, Paula J.; Lewicki, David G.; Le, Dy D.

2007-01-01

This paper provides an overview of current vibration methods used to identify the health of helicopter transmission gears. The gears are critical to the transmission system that provides propulsion, lift and maneuvering of the helicopter. This paper reviews techniques used to process vibration data to calculate conditions indicators (CI s), guidelines used by the government aviation authorities in developing and certifying the Health and Usage Monitoring System (HUMS), condition and health indicators used in commercial HUMS, and different methods used to set thresholds to detect damage. Initial assessment of a method to set thresholds for vibration based condition indicators applied to flight and test rig data by evaluating differences in distributions between comparable transmissions are also discussed. Gear condition indicator FM4 values are compared on an OH58 helicopter during 14 maneuvers and an OH58 transmission test stand during crack propagation tests. Preliminary results show the distributions between healthy helicopter and rig data are comparable and distributions between healthy and damaged gears show significant differences.

The use of a responder analysis to identify clinically meaningful differences in chronic urticaria patients following placebo- controlled treatment with rupatadine 10 and 20 mg.

PubMed

Giménez-Arnau, A; Izquierdo, I; Maurer, M

2009-09-01

According to the EAACI/GA(2)LEN/EDF guidelines for urticaria management, modern non-sedating H1-antihistamines are the first-line symptomatic treatment for chronic urticaria. Two previous randomized clinical trials demonstrated rupatadine efficacy and safety in chronic urticaria treatment. However, a responder analysis to identify clinically meaningful differences in patients with chronic urticaria has not yet been performed. This analysis includes the pooled data from two randomized, double-blind, placebo-controlled, multicentre studies in which chronic urticaria patients were treated with rupatadine at different doses. Responder rates were defined as the percentage of patients after 4 weeks of treatment who exhibited a reduction of symptoms by at least 50% or 75% as compared to baseline. The variables analysed were as follows: Mean Pruritus Score (MPS), Mean Number of Wheals (MNW), and Mean Urticaria Activity Score (UAS). A total of 538 patients were included. This responder analysis, using different response levels, shows that the efficacy of rupatadine 10 mg and 20 mg is significantly better as compared to placebo in the treatment of chronic urticaria patients. Notably, treatment with rupatadine 20 mg daily resulted in a higher percentage of patients with response of 75% symptom reduction or better than rupatadine 10 mg. Our results support the use of higher than standard doses of non sedating antihistamines in chronic urticaria. We strongly recommend performing and reporting responder analyses for established and new drugs used by patients with chronic urticaria.

Analysis of endoscopic brush samples identified mucosa-associated dysbiosis in inflammatory bowel disease.

PubMed

Nishino, Kyohei; Nishida, Atsushi; Inoue, Ryo; Kawada, Yuki; Ohno, Masashi; Sakai, Shigeki; Inatomi, Osamu; Bamba, Shigeki; Sugimoto, Mitsushige; Kawahara, Masahiro; Naito, Yuji; Andoh, Akira

2018-01-01

The mucosa-associated gut microbiota directly modulates epithelial and mucosal function. In this study, we investigated the mucosa-associated microbial community in patients with inflammatory bowel disease (IBD), using endoscopic brush samples. A total of 174 mucus samples from 43 patients with ulcerative colitis (UC), 26 with Crohn's disease (CD) and 14 non-IBD controls were obtained by gentle brushing of mucosal surfaces using endoscopic cytology brushes. The gut microbiome was analyzed using 16S rRNA gene sequencing. There were no significant differences in microbial structure among different anatomical sites (the ileum, cecum and sigmoid colon) within individuals. There was, however, a significant difference in microbial structure between CD, UC and non-IBD controls. The difference between CD and non-IBD controls was more marked than that between UC patients and non-IBD controls. α-Diversity was significantly lower in UC and CD patients than non-IBD controls. When comparing CD patients with non-IBD controls, the phylum Proteobacteria was significantly increased and the phyla Firmicutes and Bacteroidetes were significantly reduced. These included a significant increase in the genera Escherichia, Ruminococcus (R. gnavus), Cetobacterium, Actinobacillus and Enterococcus, and a significant decrease in the genera Faecalibacterium, Coprococcus, Prevotella and Roseburia. Comparisons between CD and UC patients revealed a greater abundance of the genera Escherichia, Ruminococcus (R. gnavus), Clostridium, Cetobacterium, Peptostreptococcus in CD patients, and the genera Faecalibacterium, Blautia, Bifidobacterium, Roseburia and Citrobacter in UC patients. Mucosa-associated dysbiosis was identified in IBD patients. CD and UC may be distinguishable from the mucosa-associated microbial community structure.

Gender Differences in Academic Self-Efficacy: A Meta-Analysis

ERIC Educational Resources Information Center

Huang, Chiungjung

2013-01-01

A meta-analysis of 187 studies containing 247 independent studies (N = 68,429) on gender differences in academic self-efficacy identified an overall effect size of 0.08, with a small difference favoring males. Moderator analysis demonstrated that content domain was a significant moderator in explaining effect size variation. Females displayed…

A Comparison of Multiple Facets of Self-Concept in Gifted vs. Non-Identified Israeli Students

ERIC Educational Resources Information Center

Zeidner, Moshe; Shani-Zinovich, Inbal

2015-01-01

This study compares facets of self-concept in gifted and non-identified Israeli adolescent students. The self-concept mean score profile of gifted vs. non-selected Israeli students was significantly different, with gifted students reporting higher mean levels of academic self-concept, but lower mean levels of social, personal, and physical…

Creating Significant Learning Experiences across Disciplines

ERIC Educational Resources Information Center

Levine, Laura E.; Fallahi, Carolyn R.; Nicoll-Senft, Joan M.; Tessier, Jack T.; Watson, Cheryl L.; Wood, Rebecca M.

2008-01-01

The purpose of this study was to use Fink's (2003) taxonomy of significant learning to redesign courses and assess student learning. Significant improvements were found across the semester for students in the six courses, but there were differences in which taxa showed improvement in each course. The meta-analysis showed significant, positive…

Hematological and plasma biochemical reference ranges of Alaskan seabirds: Their ecological significance and clinical importance

USGS Publications Warehouse

Newman, S.H.; Piatt, John F.; White, J.

1997-01-01

Blood was analyzed from 151 pelagic marine birds to establish reference ranges for hematological and plasma biochemical parameters from healthy, wild populations of Pacific seabirds. Of the 13 species examined, 9 were from the Family Alcidae (N = 122 individuals) and the remainder (N = 29) from the Families Phalacrocoracidae, Laridae, and Procellariidae. Three of 8 hematological parameters (total white blood cell count, lymphocyte count and eosinophil count) differed significantly among species, as did 9 of 13 plasma biochemical parameters (alkaline phosphatase, aspartate aminotransferase, creatine kinase, cholesterol, glucose, lactate dehydrogenase, total bilirubin, total protein and field total protein). There were no differences among species for packed cell volume, buffy coat, cell counts of heterophils, monocytes and basophils, or for concentrations of alanine aminotransferase, triglycerides, uric acid and calcium. Plasma calcium concentration, triglyceride levels and field total protein varied significantly between sexes, with females having higher mean concentrations of all 3 parameters. However, no significant relationships between measures of breeding condition (brood patch size, subcutaneous and mesenteric fat deposits, or ovarian follicle size and ovary weight) and calcium or alkaline phosphatase concentrations in female birds could be identified. Alanine aminotransferase and uric acid were the only analytes which did not differ significantly between species or sexes.

Multiplatform serum metabolic phenotyping combined with pathway mapping to identify biochemical differences in smokers.

PubMed

Kaluarachchi, Manuja R; Boulangé, Claire L; Garcia-Perez, Isabel; Lindon, John C; Minet, Emmanuel F

2016-10-01

Determining perturbed biochemical functions associated with tobacco smoking should be helpful for establishing causal relationships between exposure and adverse events. A multiplatform comparison of serum of smokers (n = 55) and never-smokers (n = 57) using nuclear magnetic resonance spectroscopy, UPLC-MS and statistical modeling revealed clustering of the classes, distinguished by metabolic biomarkers. The identified metabolites were subjected to metabolic pathway enrichment, modeling adverse biological events using available databases. Perturbation of metabolites involved in chronic obstructive pulmonary disease, cardiovascular diseases and cancer were identified and discussed. Combining multiplatform metabolic phenotyping with knowledge-based mapping gives mechanistic insights into disease development, which can be applied to next-generation tobacco and nicotine products for comparative risk assessment.

Optical techniques for biological triggers and identifiers

NASA Astrophysics Data System (ADS)

Grant, Bruce A. C.

2004-12-01

Optical techniques for the classification and identification of biological particles provide a number of advantages over traditional 'Wet Chemistry" methods, amongst which are speed of response and the reduction/elimination of consumables. These techniques can be employed in both 'Trigger" and 'Identifier" systems. Trigger systems monitor environmental particulates with the aim of detecting 'unusual" changes in the overall environmental composition and providing an indication of threat. At the present time there is no single optical measurement that can distinguish between benign and hostile events. Therefore, in order to distinguish between these 2 classifications, a number of different measurements must be effected and a decision made on the basis of the 'integrated" data. Smiths Detection have developed a data gathering platform capable of measuring multiple optical, physical and electrical parameters of individual airborne biological particles. The data from all these measurements are combined in a hazard classification algorithm based on Bayesian Inference techniques. Identifier systems give a greater level of information and confidence than triggers, -- although they require reagents and are therefore much more expensive to operate -- and typically take upwards of 20 minutes to respond. Ideally, in a continuous flow mode, identifier systems would respond in real-time, and identify a range of pathogens specifically and simultaneously. The results of recent development work -- carried out by Smiths Detection and its collaborators -- to develop an optical device that meets most of these requirements, and has the stretch potential to meet all of the requirements in a 3-5 year time frame will be presented. This technology enables continuous stand-alone operation for both civil and military defense applications and significant miniaturisation can be achieved with further development.

Interactive cervical motion kinematics: sensitivity, specificity and clinically significant values for identifying kinematic impairments in patients with chronic neck pain.

PubMed

Sarig Bahat, Hilla; Chen, Xiaoqi; Reznik, David; Kodesh, Einat; Treleaven, Julia

2015-04-01

Chronic neck pain has been consistently shown to be associated with impaired kinematic control including reduced range, velocity and smoothness of cervical motion, that seem relevant to daily function as in quick neck motion in response to surrounding stimuli. The objectives of this study were: to compare interactive cervical kinematics in patients with neck pain and controls; to explore the new measures of cervical motion accuracy; and to find the sensitivity, specificity, and optimal cutoff values for defining impaired kinematics in those with neck pain. In this cross-section study, 33 patients with chronic neck pain and 22 asymptomatic controls were assessed for their cervical kinematic control using interactive virtual reality hardware and customized software utilizing a head mounted display with built-in head tracking. Outcome measures included peak and mean velocity, smoothness (represented by number of velocity peaks (NVP)), symmetry (represented by time to peak velocity percentage (TTPP)), and accuracy of cervical motion. Results demonstrated significant and strong effect-size differences in peak and mean velocities, NVP and TTPP in all directions excluding TTPP in left rotation, and good effect-size group differences in 5/8 accuracy measures. Regression results emphasized the high clinical value of neck motion velocity, with very high sensitivity and specificity (85%-100%), followed by motion smoothness, symmetry and accuracy. These finding suggest cervical kinematics should be evaluated clinically, and screened by the provided cut off values for identification of relevant impairments in those with neck pain. Such identification of presence or absence of kinematic impairments may direct treatment strategies and additional evaluation when needed. Copyright © 2014 Elsevier Ltd. All rights reserved.

Identifying a system of predominant negative symptoms: Network analysis of three randomized clinical trials.

PubMed

Levine, Stephen Z; Leucht, Stefan

2016-12-01

Reasons for the recent mixed success of research into negative symptoms may be informed by conceptualizing negative symptoms as a system that is identifiable from network analysis. We aimed to identify: (I) negative symptom systems; (I) central negative symptoms within each system; and (III) differences between the systems, based on network analysis of negative symptoms for baseline, endpoint and change. Patients with chronic schizophrenia and predominant negative symptoms participated in three clinical trials that compared placebo and amisulpride to 60days (n=487). Networks analyses were computed from the Scale for the Assessment of Negative Symptoms (SANS) scores for baseline and endpoint for severity, and estimated change based on mixed models. Central symptoms to each network were identified. The networks were contrasted for connectivity with permutation tests. Network analysis showed that the baseline and endpoint symptom severity systems formed symptom groups of Affect, Poor responsiveness, Lack of interest, and Apathy-inattentiveness. The baseline and endpoint networks did not significantly differ in terms of connectivity, but both significantly (P<0.05) differed to the change network. In the change network the apathy-inattentiveness symptom group split into three other groups. The most central symptoms were Decreased Spontaneous Movements at baseline and endpoint, and Poverty of Speech for estimated change. Results provide preliminary evidence for: (I) a replicable negative symptom severity system; and (II) symptoms with high centrality (e.g., Decreased Spontaneous Movement), that may be future treatment targets following replication to ensure the curent results generalize to other samples. Copyright © 2016 Elsevier B.V. All rights reserved.

[Impedance characteristics of ear acupoints in identifying excess or deficiency syndrome of stroke].

PubMed

Wang, Pin; Yang, Hua-Yuan; Wang, Yi-Qin

2010-06-01

To explore the impedance characteristics of ear acupoints in stroke patients with excess or deficiency syndrome, and to provide basis data for objective study of the syndromes of stroke. The data of electrical characteristics of ear acupoints in stroke patients and healthy people were collected, and excess syndrome and deficiency syndrome of stroke were identified by quantifying the syndromes of stroke using scales. The differences in impedance characteristics of ear acupoints between stroke patients and healthy people were analyzed, and the differences in impedance characteristics of ear acupoints between stroke patients with excess syndrome and stroke patients with deficiency syndrome were analyzed too. The correlation among impedance characteristics of ear acupoints, stroke and the syndromes was also analyzed. There were significant differences in impedance characteristics of ear acupoints between stroke patients and healthy people (P<0.05,P<0.01). The ear acupoints CO12 (Gan) and CO13 (Pi) had a significant role in diagnosing stroke as compared with CO18 (Neifenmi), AT3.4.AH12i (Naogan), CO10 (Shen), TG2p (Shenshangxian), AH6a (Jiaogan), AT4 (Pizhixia), and CO15 (Xin). There were significant differences in impedance characteristics of ear acupoints between stroke patients with excess syndrome and stroke patients with deficiency syndrome (P<0.05, P<0.01). The ear acupoints AH6a (Jiaogan) and CO10 (Shen) played an important role in differentiation diagnosis of excess syndrome and deficiency syndrome of stroke, followed by CO18 (Neifenmi), TF4 (Shenmen) and TG2p (Shenshangxian). Some ear acupoints with diagnostic value for stroke may provide basis of objective research for stroke diagnosis as well as identifying excess syndrome and deficiency syndrome of stroke.

The Role of Curriculum in Organizational Significant Change Planning

ERIC Educational Resources Information Center

Chrusciel, Don

2006-01-01

Purpose: With significant change as an ongoing challenge, the development and use of a flexible change curriculum is identified as a success factor that will allow an organization to optimize the outcome from change transformations. Design/methodology/approach: After discussing significant change, this paper will contrast two organizations in…

Significant difference in active metabolite levels of ginseng in humans consuming Asian or Western diet: The link with enteric microbiota.

PubMed

Wan, Jin-Yi; Wang, Chong-Zhi; Zhang, Qi-Hui; Liu, Zhi; Musch, Mark W; Bissonnette, Marc; Chang, Eugene B; Li, Ping; Qi, Lian-Wen; Yuan, Chun-Su

2017-04-01

After ingestion of ginseng, the bioavailability of its parent compounds is low and enteric microbiota plays an important role in parent compound biotransformation to their metabolites. Diet type can influence the enteric microbiota profile. When human subjects on different diets ingest ginseng, their different gut microbiota profiles may influence the metabolism of ginseng parent compounds. In this study, the effects of different diet type on gut microbiota metabolism of American ginseng saponins were investigated. We recruited six healthy adults who regularly consumed different diet types. These subjects received 7 days' oral American ginseng, and their biological samples were collected for LC-Q-TOF-MS analysis. We observed significant ginsenoside Rb 1 (a major parent compound) and compound K (a major active metabolite) level differences in the samples from the subjects consuming different diets. Subjects on an Asian diet had much higher Rb 1 levels but much lower compound K levels compared with those on a Western diet. Since compound K possesses much better cancer chemoprevention potential, our data suggested that consumers on a Western diet should obtain better cancer prevention effects with American ginseng intake compared with those on an Asian diet. Ginseng compound levels could be enhanced or reduced via gut microbiota manipulation for clinical utility. Copyright © 2016 John Wiley & Sons, Ltd.

Mutation screening of the HGD gene identifies a novel alkaptonuria mutation with significant founder effect and high prevalence.

PubMed

Sakthivel, Srinivasan; Zatkova, Andrea; Nemethova, Martina; Surovy, Milan; Kadasi, Ludevit; Saravanan, Madurai P

2014-05-01

Alkaptonuria (AKU) is an autosomal recessive disorder; caused by the mutations in the homogentisate 1, 2-dioxygenase (HGD) gene located on Chromosome 3q13.33. AKU is a rare disorder with an incidence of 1: 250,000 to 1: 1,000,000, but Slovakia and the Dominican Republic have a relatively higher incidence of 1: 19,000. Our study focused on studying the frequency of AKU and identification of HGD gene mutations in nomads. HGD gene sequencing was used to identify the mutations in alkaptonurics. For the past four years, from subjects suspected to be clinically affected, we found 16 positive cases among a randomly selected cohort of 41 Indian nomads (Narikuravar) settled in the specific area of Tamil Nadu, India. HGD gene mutation analysis showed that 11 of these patients carry the same homozygous splicing mutation c.87 + 1G > A; in five cases, this mutation was found to be heterozygous, while the second AKU-causing mutation was not identified in these patients. This result indicates that the founder effect and high degree of consanguineous marriages have contributed to AKU among nomads. Eleven positive samples were homozygous for a novel mutation c.87 + 1G > A, that abolishes an intron 2 donor splice site and most likely causes skipping of exon 2. The prevalence of AKU observed earlier seems to be highly increased in people of nomadic origin. © 2014 John Wiley & Sons Ltd/University College London.

Primary and acquired EGFR T790M-mutant NSCLC patients identified by routine mutation testing show different characteristics but may both respond to osimertinib treatment.

PubMed

Li, Weihua; Qiu, Tian; Guo, Lei; Ling, Yun; Gao, Yibo; Ying, Jianming; He, Jie

2018-06-01

Primary EGFR T790M mutation is occasionally identified by routine mutation testing in tyrosine kinase inhibitor (TKI)-naive patients with non-small cell lung cancer (NSCLC). We herein aimed to compare the characteristics of primary and acquired T790M mutations in NSCLC patients, and their response to osimertinib. Using amplification refractory mutation system (ARMS) detection, primary T790M was identified in 0.5% (46/8723) of TKI-naive patients, whereas acquired T790M was detected in 49.7% (71/143) of TKI-relapsed patients. T790M always coexisted with a sensitizing EGFR mutation. Primary T790M more commonly coexisted with L858R, whereas acquired T790M was more likely to coexist with exon 19 deletions. Moreover, next-generation sequencing (NGS) showed that concomitant sensitizing EGFR and primary T790M mutant allele frequencies (MAFs) were highly concordant, but acquired T790M MAFs were significantly lower than the sensitizing EGFR MAFs. Sixteen acquired T790M-mutant patients received osimertinib. The median progression-free survival (PFS) was 8.1 months. Four primary T790M-mutant patients received osimertinib and the median PFS was 8.0 months. Together, our study demonstrates that primary and acquired T790M-mutant patients show distinct differences in some clinical and molecular characteristics, but may both respond to osimertinib treatment. Copyright © 2018 Elsevier B.V. All rights reserved.

Seizure semiology identifies patients with bilateral temporal lobe epilepsy.

PubMed

Loesch, Anna Mira; Feddersen, Berend; Tezer, F Irsel; Hartl, Elisabeth; Rémi, Jan; Vollmar, Christian; Noachtar, Soheyl

2015-01-01

Laterality in temporal lobe epilepsy is usually defined by EEG and imaging results. We investigated whether the analysis of seizure semiology including lateralizing seizure phenomena identifies bilateral independent temporal lobe seizure onset. We investigated the seizure semiology in 17 patients in whom invasive EEG-video-monitoring documented bilateral temporal seizure onset. The results were compared to 20 left and 20 right consecutive temporal lobe epilepsy (TLE) patients who were seizure free after anterior temporal lobe resection. The seizure semiology was analyzed using the semiological seizure classification with particular emphasis on the sequence of seizure phenomena over time and lateralizing seizure phenomena. Statistical analysis included chi-square test or Fisher's exact test. Bitemporal lobe epilepsy patients had more frequently different seizure semiology (100% vs. 40%; p<0.001) and significantly more often lateralizing seizure phenomena pointing to bilateral seizure onset compared to patients with unilateral TLE (67% vs. 11%; p<0.001). The sensitivity of identical vs. different seizure semiology for the identification of bilateral TLE was high (100%) with a specificity of 60%. Lateralizing seizure phenomena had a low sensitivity (59%) but a high specificity (89%). The combination of lateralizing seizure phenomena and different seizure semiology showed a high specificity (94%) but a low sensitivity (59%). The analysis of seizure semiology including lateralizing seizure phenomena adds important clinical information to identify patients with bilateral TLE. Copyright © 2014 Elsevier B.V. All rights reserved.

Identifying key genes associated with acute myocardial infarction.

PubMed

Cheng, Ming; An, Shoukuan; Li, Junquan

2017-10-01

This study aimed to identify key genes associated with acute myocardial infarction (AMI) by reanalyzing microarray data. Three gene expression profile datasets GSE66360, GSE34198, and GSE48060 were downloaded from GEO database. After data preprocessing, genes without heterogeneity across different platforms were subjected to differential expression analysis between the AMI group and the control group using metaDE package. P < .05 was used as the cutoff for a differentially expressed gene (DEG). The expression data matrices of DEGs were imported in ReactomeFIViz to construct a gene functional interaction (FI) network. Then, DEGs in each module were subjected to pathway enrichment analysis using DAVID. MiRNAs and transcription factors predicted to regulate target DEGs were identified. Quantitative real-time polymerase chain reaction (RT-PCR) was applied to verify the expression of genes. A total of 913 upregulated genes and 1060 downregulated genes were identified in the AMI group. A FI network consists of 21 modules and DEGs in 12 modules were significantly enriched in pathways. The transcription factor-miRNA-gene network contains 2 transcription factors FOXO3 and MYBL2, and 2 miRNAs hsa-miR-21-5p and hsa-miR-30c-5p. RT-PCR validations showed that expression levels of FOXO3 and MYBL2 were significantly increased in AMI, and expression levels of hsa-miR-21-5p and hsa-miR-30c-5p were obviously decreased in AMI. A total of 41 DEGs, such as SOCS3, VAPA, and COL5A2, are speculated to have roles in the pathogenesis of AMI; 2 transcription factors FOXO3 and MYBL2, and 2 miRNAs hsa-miR-21-5p and hsa-miR-30c-5p may be involved in the regulation of the expression of these DEGs.

An investigation into drug-related problems identifiable by commercial medication review software.

PubMed

Curtain, Colin; Bindoff, Ivan; Westbury, Juanita; Peterson, Gregory

2013-01-01

Accredited pharmacists conduct home medicines reviews (HMRs) to detect and resolve potential drug-related problems (DRPs). A commercial expert system, Medscope Review Mentor (MRM), has been developed to assist pharmacists in the detection and resolution of potential DRPs. This study compares types of DRPs identified with the commercial system which uses multiple classification ripple down rules (MCRDR) with the findings of pharmacists. HMR data from 570 reviews collected from accredited pharmacists was entered into MRM and the DRPs were identified. A list of themes describing the main concept of each DRP identified by MRM was developed to allow comparison with pharmacists. Theme types, frequencies, similarity and dissimilarity were explored. The expert system was capable of detecting a wide range of potential DRPs: 2854 themes; compared to pharmacists: 1680 themes. The system identified the same problems as pharmacists in many patient cases. Ninety of 119 types of themes identifiable by pharmacists were also identifiable by software. MRM could identify the same problems in the same patients as pharmacists for 389 problems, resulting in a low overlap of similarity with an averaged Jaccard Index of 0.09. MRM found significantly more potential DRPs than pharmacists. MRM identified a wide scope of DRPs approaching the range of DRPs that were identified by pharmacists. Differences may be associated with system consistency and perhaps human oversight or human selective prioritisation. DRPs identified by the system were still considered relevant even though the system identified a larger number of problems.

Gender differences in identifying emotions from auditory and visual stimuli.

PubMed

Waaramaa, Teija

2017-12-01

The present study focused on gender differences in emotion identification from auditory and visual stimuli produced by two male and two female actors. Differences in emotion identification from nonsense samples, language samples and prolonged vowels were investigated. It was also studied whether auditory stimuli can convey the emotional content of speech without visual stimuli, and whether visual stimuli can convey the emotional content of speech without auditory stimuli. The aim was to get a better knowledge of vocal attributes and a more holistic understanding of the nonverbal communication of emotion. Females tended to be more accurate in emotion identification than males. Voice quality parameters played a role in emotion identification in both genders. The emotional content of the samples was best conveyed by nonsense sentences, better than by prolonged vowels or shared native language of the speakers and participants. Thus, vocal non-verbal communication tends to affect the interpretation of emotion even in the absence of language. The emotional stimuli were better recognized from visual stimuli than auditory stimuli by both genders. Visual information about speech may not be connected to the language; instead, it may be based on the human ability to understand the kinetic movements in speech production more readily than the characteristics of the acoustic cues.

No Differences in Achieving Hepatitis C Virus Care Milestones Between Patients Identified by Birth Cohort or Risk-Based Screening.

PubMed

Norton, Brianna L; Southern, William N; Steinman, Meredith; Smith, Bryce D; Deluca, Joseph; Rosner, Zachary; Litwin, Alain H

2016-09-01

National hepatitis C virus (HCV) screening guidelines recommended 1-time testing of persons born between 1945 and 1965. We performed a retrospective study to compare care milestones achieved by HCV-infected patients identified by birth cohort versus risk-based screens. We determined the proportions of patients newly identified with HCV infection who met care milestones (viral load, referral to and evaluation by a specialist, offer of treatment, initiation of treatment, and sustained viral response) and the time it took to reach them. We found no differences in HCV care milestones for patients identified via birth cohort testing versus risk-based screening. Overall, only 43% of HCV antibody-positive patients were referred to care, and less than 4% started treatment. The time to each care milestone was lengthy and varied greatly; treatment was initiated in a median of 308 days. Although birth cohort testing will likely increase identification of patients with HCV infection, it does not seem to increase the number of patients that meet management milestones. New methods are needed to increase access to care and establish efficient models of health care delivery. Copyright © 2016 AGA Institute. Published by Elsevier Inc. All rights reserved.

Admixture Mapping of African-American Women in the AMBER Consortium Identifies New Loci for Breast Cancer and Estrogen-Receptor Subtypes.

PubMed

Ruiz-Narváez, Edward A; Sucheston-Campbell, Lara; Bensen, Jeannette T; Yao, Song; Haddad, Stephen; Haiman, Christopher A; Bandera, Elisa V; John, Esther M; Bernstein, Leslie; Hu, Jennifer J; Ziegler, Regina G; Deming, Sandra L; Olshan, Andrew F; Ambrosone, Christine B; Palmer, Julie R; Lunetta, Kathryn L

2016-01-01

Recent genetic admixture coupled with striking differences in incidence of estrogen receptor (ER) breast cancer subtypes, as well as severity, between women of African and European ancestry, provides an excellent rationale for performing admixture mapping in African American women with breast cancer risk. We performed the largest breast cancer admixture mapping study with in African American women to identify novel genomic regions associated with the disease. We conducted a genome-wide admixture scan using 2,624 autosomal ancestry informative markers (AIMs) in 3,629 breast cancer cases (including 1,968 ER-positive, 1093 ER-negative, and 601 triple-negative) and 4,658 controls from the African American Breast Cancer Epidemiology and Risk (AMBER) Consortium, a collaborative study of four large geographically different epidemiological studies of breast cancer in African American women. We used an independent case-control study to test for SNP association in regions with genome-wide significant admixture signals. We found two novel genome-wide significant regions of excess African ancestry, 4p16.1 and 17q25.1, associated with ER-positive breast cancer. Two regions known to harbor breast cancer variants, 10q26 and 11q13, were also identified with excess of African ancestry. Fine-mapping of the identified genome-wide significant regions suggests the presence of significant genetic associations with ER-positive breast cancer in 4p16.1 and 11q13. In summary, we identified three novel genomic regions associated with breast cancer risk by ER status, suggesting that additional previously unidentified variants may contribute to the racial differences in breast cancer risk in the African American population.

Epigenetic differences in normal colon mucosa of cancer patients suggests altered dietary metabolic pathways

PubMed Central

Silviera, Matthew L.; Smith, Brian P.; Powell, Jasmine; Sapienza, Carmen

2012-01-01

We have compared DNA methylation in normal colon mucosa between colon cancer patients and patients without cancer. We identified significant differences in methylation between the two groups at 114 – 874 genes. The majority of the differences are in pathways involved in the metabolism of carbohydrates, lipids and amino acids. We also compared transcript levels of genes in the insulin-signaling pathway. We found that the mucosa of cancer patients had significantly higher transcript levels of several hormones regulating glucose metabolism and significantly lower transcript levels of a glycolytic enzyme and a key regulator of glucose and lipid homeostasis. The se differences suggest that the normal colon mucosa of cancer patients metabolizes dietary components differently than the colon mucosa of controls. Because the differences identified are present in morphologically normal tissue, they may be diagnostic of colon cancer and/or prognostic of colon cancer susceptibility. PMID:22300984

Solid tags for identifying failed reactor components

DOEpatents

Bunch, Wilbur L.; Schenter, Robert E.

1987-01-01

A solid tag material which generates stable detectable, identifiable, and measurable isotopic gases on exposure to a neutron flux to be placed in a nuclear reactor component, particularly a fuel element, in order to identify the reactor component in event of its failure. Several tag materials consisting of salts which generate a multiplicity of gaseous isotopes in predetermined ratios are used to identify different reactor components.

A Noise Trimming and Positional Significance of Transposon Insertion System to Identify Essential Genes in Yersinia pestis

NASA Astrophysics Data System (ADS)

Yang, Zheng Rong; Bullifent, Helen L.; Moore, Karen; Paszkiewicz, Konrad; Saint, Richard J.; Southern, Stephanie J.; Champion, Olivia L.; Senior, Nicola J.; Sarkar-Tyson, Mitali; Oyston, Petra C. F.; Atkins, Timothy P.; Titball, Richard W.

2017-02-01

Massively parallel sequencing technology coupled with saturation mutagenesis has provided new and global insights into gene functions and roles. At a simplistic level, the frequency of mutations within genes can indicate the degree of essentiality. However, this approach neglects to take account of the positional significance of mutations - the function of a gene is less likely to be disrupted by a mutation close to the distal ends. Therefore, a systematic bioinformatics approach to improve the reliability of essential gene identification is desirable. We report here a parametric model which introduces a novel mutation feature together with a noise trimming approach to predict the biological significance of Tn5 mutations. We show improved performance of essential gene prediction in the bacterium Yersinia pestis, the causative agent of plague. This method would have broad applicability to other organisms and to the identification of genes which are essential for competitiveness or survival under a broad range of stresses.

A Noise Trimming and Positional Significance of Transposon Insertion System to Identify Essential Genes in Yersinia pestis

PubMed Central

Yang, Zheng Rong; Bullifent, Helen L.; Moore, Karen; Paszkiewicz, Konrad; Saint, Richard J.; Southern, Stephanie J.; Champion, Olivia L.; Senior, Nicola J.; Sarkar-Tyson, Mitali; Oyston, Petra C. F.; Atkins, Timothy P.; Titball, Richard W.

2017-01-01

Massively parallel sequencing technology coupled with saturation mutagenesis has provided new and global insights into gene functions and roles. At a simplistic level, the frequency of mutations within genes can indicate the degree of essentiality. However, this approach neglects to take account of the positional significance of mutations - the function of a gene is less likely to be disrupted by a mutation close to the distal ends. Therefore, a systematic bioinformatics approach to improve the reliability of essential gene identification is desirable. We report here a parametric model which introduces a novel mutation feature together with a noise trimming approach to predict the biological significance of Tn5 mutations. We show improved performance of essential gene prediction in the bacterium Yersinia pestis, the causative agent of plague. This method would have broad applicability to other organisms and to the identification of genes which are essential for competitiveness or survival under a broad range of stresses. PMID:28165493

Identifying Breast Cancer Oncogenes

DTIC Science & Technology

2011-10-01

antibodies . Analytes considered positive (>10) and showing significant (1.5) fold increase in signal are shown as black diamonds. All labeled analytes...Curto et al., 2007). Using a general phospho-tyrosine antibody (4G10) we determined that overexpression of PAK1 indeed upregulates phospho-tyrosine...PAK1. Remarkably, three distinct antibodies identified MET as highly phosphorylated specifically in HMLE-PAK1 cells strongly suggesting that MET could

Deciphering life history transcriptomes in different environments

PubMed Central

Etges, William J.; Trotter, Meredith V.; de Oliveira, Cássia C.; Rajpurohit, Subhash; Gibbs, Allen G.; Tuljapurkar, Shripad

2014-01-01

We compared whole transcriptome variation in six preadult stages and seven adult female ages in two populations of cactophilic Drosophila mojavensis reared on two host plants in order to understand how differences in gene expression influence standing life history variation. We used Singular Value Decomposition (SVD) to identify dominant trajectories of life cycle gene expression variation, performed pair-wise comparisons of stage and age differences in gene expression across the life cycle, identified when genes exhibited maximum levels of life cycle gene expression, and assessed population and host cactus effects on gene expression. Life cycle SVD analysis returned four significant components of transcriptional variation, revealing functional enrichment of genes responsible for growth, metabolic function, sensory perception, neural function, translation and aging. Host cactus effects on female gene expression revealed population and stage specific differences, including significant host plant effects on larval metabolism and development, as well as adult neurotransmitter binding and courtship behavior gene expression levels. In 3 - 6 day old virgin females, significant up-regulation of genes associated with meiosis and oogenesis was accompanied by down-regulation of genes associated with somatic maintenance, evidence for a life history tradeoff. The transcriptome of D. mojavensis reared in natural environments throughout its life cycle revealed core developmental transitions and genome wide influences on life history variation in natural populations. PMID:25442828

Cultural significance of wild mammals in Mayan and mestizo communities of the Lacandon Rainforest, Chiapas, Mexico.

PubMed

García Del Valle, Yasminda; Naranjo, Eduardo J; Caballero, Javier; Martorell, Carlos; Ruan-Soto, Felipe; Enríquez, Paula L

2015-05-07

Several ethnobiology studies evaluate the cultural significance (CS) of plants and mushrooms. However, this is not the case for mammals. It is important to make studies of CS allowing the comparison of cultural groups because the value given to groups of organisms may be based on different criteria. Such information would be valuable for wildlife preservation plans. In this study, the most culturally significant species of mammals from the Lacandon Rainforest (Chiapas, Mexico) for people from two Mayan-Lacandon and mestizo communities were identified. The reasons behind the CS of the studied species were explored and the existence of differences among the cultural groups was evaluated. One hundred ninety-eight semi-structured and structured interviews were applied to compile socio-demographic information, qualitative data on CS categories, and free listings. Frequency of mention was a relative indicator to evaluate the CS of each species of mammal. Comparison of responses between communities was carried out through multivariate analyses. The non-parametric Mann-Whitney U test was used to compare the number of mentioned species by Lacandons and mestizos as well as different responses in the qualitative categories. A χ2 test was used to compare frequency of categories. 38 wild mammal species were identified. The classification and Principal Components Analyses show an apparent separation between Lacandon and mestizo sites based on the relative importance of species. All four communities mentioned the lowland paca the most, followed by peccary, white-tailed deer, armadillo, and jaguar. No significant difference was found in the number of mentioned species between the two groups. Eight CS categories were identified. The most important category was "harmful mammals", which included 28 species. Other relevant categories were edible, medicinal, and appearing in narratives. The data obtained in this study demonstrates the existence of differential cultural patterns in the

Identifying resistance gene analogs associated with resistances to different pathogens in common bean.

PubMed

López, Camilo E; Acosta, Iván F; Jara, Carlos; Pedraza, Fabio; Gaitán-Solís, Eliana; Gallego, Gerardo; Beebe, Steve; Tohme, Joe

2003-01-01

ABSTRACT A polymerase chain reaction approach using degenerate primers that targeted the conserved domains of cloned plant disease resistance genes (R genes) was used to isolate a set of 15 resistance gene analogs (RGAs) from common bean (Phaseolus vulgaris). Eight different classes of RGAs were obtained from nucleotide binding site (NBS)-based primers and seven from not previously described Toll/Interleukin-1 receptor-like (TIR)-based primers. Putative amino acid sequences of RGAs were significantly similar to R genes and contained additional conserved motifs. The NBS-type RGAs were classified in two subgroups according to the expected final residue in the kinase-2 motif. Eleven RGAs were mapped at 19 loci on eight linkage groups of the common bean genetic map constructed at Centro Internacional de Agricultura Tropical. Genetic linkage was shown for eight RGAs with partial resistance to anthracnose, angular leaf spot (ALS) and Bean golden yellow mosaic virus (BGYMV). RGA1 and RGA2 were associated with resistance loci to anthracnose and BGYMV and were part of two clusters of R genes previously described. A new major cluster was detected by RGA7 and explained up to 63.9% of resistance to ALS and has a putative contribution to anthracnose resistance. These results show the usefulness of RGAs as candidate genes to detect and eventually isolate numerous R genes in common bean.

Genome-wide significant loci for addiction and anxiety.

PubMed

Hodgson, K; Almasy, L; Knowles, E E M; Kent, J W; Curran, J E; Dyer, T D; Göring, H H H; Olvera, R L; Fox, P T; Pearlson, G D; Krystal, J H; Duggirala, R; Blangero, J; Glahn, D C

2016-08-01

Psychiatric comorbidity is common among individuals with addictive disorders, with patients frequently suffering from anxiety disorders. While the genetic architecture of comorbid addictive and anxiety disorders remains unclear, elucidating the genes involved could provide important insights into the underlying etiology. Here we examine a sample of 1284 Mexican-Americans from randomly selected extended pedigrees. Variance decomposition methods were used to examine the role of genetics in addiction phenotypes (lifetime history of alcohol dependence, drug dependence or chronic smoking) and various forms of clinically relevant anxiety. Genome-wide univariate and bivariate linkage scans were conducted to localize the chromosomal regions influencing these traits. Addiction phenotypes and anxiety were shown to be heritable and univariate genome-wide linkage scans revealed significant quantitative trait loci for drug dependence (14q13.2-q21.2, LOD=3.322) and a broad anxiety phenotype (12q24.32-q24.33, LOD=2.918). Significant positive genetic correlations were observed between anxiety and each of the addiction subtypes (ρg=0.550-0.655) and further investigation with bivariate linkage analyses identified significant pleiotropic signals for alcohol dependence-anxiety (9q33.1-q33.2, LOD=3.054) and drug dependence-anxiety (18p11.23-p11.22, LOD=3.425). This study confirms the shared genetic underpinnings of addiction and anxiety and identifies genomic loci involved in the etiology of these comorbid disorders. The linkage signal for anxiety on 12q24 spans the location of TMEM132D, an emerging gene of interest from previous GWAS of anxiety traits, whilst the bivariate linkage signal identified for anxiety-alcohol on 9q33 peak coincides with a region where rare CNVs have been associated with psychiatric disorders. Other signals identified implicate novel regions of the genome in addiction genetics. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

Changes in snoring during natural sleep identified by acoustic crest factor analysis at different times of night.

PubMed

Hill, P D; Osman, E Z; Osborne, J E; Lee, B W

2000-12-01

Sleep nasendoscopy can be used to identify the site of snoring but questions remain about how well a short assessment during drug-induced sleep reflects the natural condition. To investigate the uniformity of snoring during natural sleep we studied five patients (three men, two women) referred by their GPs for treatment of their snoring. A digital audio tape recorder captured the free-field snore sound at different times of night in hospital. Acoustic Crest Factor values were calculated on the 15 recordings made, having previously demonstrated that high crest factor values distinguish palatal from non-palatal snoring at sleep nasendoscopy. Some recordings showed reproducibility, but others showed substantial changes between recordings an hour apart. We infer that the snoring mechanism may change in some individuals during the night, with or without a change of snore site. We conclude a single recording, as in sleep nasendoscopy, may not be representative.

Method and device for identifying different species of honeybees

DOEpatents

Kerr, Howard T.; Buchanan, Michael E.; Valentine, Kenneth H.

1989-01-01

A method and device have been provided for distinguishing Africanized honeybees from European honeybees. The method is based on the discovery of a distinct difference in the acoustical signatures of these two species of honeybees in flight. The European honeybee signature has a fundamental power peak in the 210 to 240 Hz range while the Africanized honeybee signature has a fundamental power peak in the 260 to 290 Hz range. The acoustic signal produced by honeybees is analyzed by means of a detecting device to quickly determine the honeybee species through the detection of the presence of frequencies in one of these distinct ranges. The device includes a microphone for acoustical signal detection which feeds the detected signal into a frequency analyzer which is designed to detect the presence of either of the known fundamental wingbeat frequencies unique to the acoustical signatures of these species as an indication of the identity of the species and indicate the species identity on a readout device.

Objective measurements of the penile angulation are significantly different than self-estimated magnitude among patients with penile curvature.

PubMed

Liguori, Giovanni; Salonia, Andrea; Garaffa, Giulio; Chiriacò, Giovanni; Pavan, Nicola; Cavallini, Giorgio; Trombetta, Carlo

2018-01-01

The study was aimed to assess the presence of actual differences between the objective and the perceived magnitude of a curvature between patients affected by Peyronie's disease (PD) and congenital penile curvature (CPC). Wee analysed a cohort of 88 consecutive patients seeking medical help for either CPC or PD. All patients were invited to provide a self-made drawing of their penis in erection in order to obtain self-provided description of the deformity. An objective measurement of the deformity was also performed drawing two intersecting lines through the center of the distal and proximal straight section of the penile shaft. Our findings showed significant differences between patient self-estimation and the objective measurements of the penile angulation performed by trained experts, with only 32% of patients correctly assessing their own curvature. Overall, patients tended to overestimate (56%) their degree of curvature, but the results are different in patients with PD than those with CPC. In the 60 men (68%) who did not accurately assess their curvature, PD patients generally overestimated their curvature versus CPC patients (67% vs 16%). On the contrary CPC patients underestimated their curvature compared to PD (42% vs. 4%). In order to improve patients' satisfaction rates, the surgeon needs to take into consideration the patient's perception of the deformity when planning the type of surgical correction. Copyright® by the International Brazilian Journal of Urology.

Textual Analysis of General Surgery Residency Personal Statements: Topics and Gender Differences.

PubMed

Ostapenko, Laura; Schonhardt-Bailey, Cheryl; Sublette, Jessica Walling; Smink, Douglas S; Osman, Nora Y

Applicants to US general surgery residency training programs submit standardized applications. Applicants use the personal statement to express their individual rationale for a career in surgery. Our research explores common topics and gender differences within the personal statements of general surgery applicants. We analyzed the electronic residency application service personal statements of 578 applicants (containing 3,82,405 words) from Liaison Committee on Medical Education-accredited medical schools to a single ACGME-accredited general surgery program using an automated textual analysis program to identify common topics and gender differences. Using a recursive algorithm, the program identified common words and clusters, grouping them into topic classes, which are internally validated. We identified and labeled 8 statistically significant topic classes through independent review: "my story," "the art of surgery," "clinical vignettes," "why I love surgery," "residency program characteristics," "working as a team," "academics and research," and "global health and policy." Although some classes were common to all applications, we also identified gender-specific differences. Notably, women were significantly more likely than men to be represented within the class of "working as a team." (p < 0.01) Furthermore, men were significantly more likely than women to be represented within the class of "clinical vignettes" (p < 0.01). Applying textual analysis to a national cohort, we identified common narrative topics in the personal statements of aspiring general surgeons, noting differences between the statements of men and women. Women were more likely to discuss surgery as a team endeavor while men were more likely to focus on the details of their surgical experiences. Our work mirrors what has been found in social psychology research on gender-based differences in how men and women communicate their career goals and aspirations in other competitive professional

Statistical Analysis of Demographic and Temporal Differences in LANL's 2014 Voluntary Protection Program Survey

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

Davis, Adam Christopher; Booth, Steven Richard

2015-08-20

Voluntary Protection Program (VPP) surveys were conducted in 2013 and 2014 to assess the degree to which workers at Los Alamos National Laboratory feel that their safety is valued by their management and peers. The goal of this analysis is to determine whether the difference between the VPP survey scores in 2013 and 2014 is significant, and to present the data in a way such that it can help identify either positive changes or potential opportunities for improvement. Data for several questions intended to identify the demographic groups of the respondent are included in both the 2013 and 2014 VPPmore » survey results. These can be used to identify any significant differences among groups of employees as well as to identify any temporal trends in these cohorts.« less

Cost Minimization Analysis of Different Strategies of Management of Clinically Significant Scorpion Envenomation Among Pediatric Patients.

PubMed

Sinha, Madhumita; Quan, Dan; McDonald, Fred W; Valdez, André

2016-12-01

Scorpion antivenom was recently approved for use in patients with clinically significant scorpion envenomation in the United States; no formal economic analysis on its impact on cost of management has been performed. Three different strategies of management of scorpion envenomation with systemic neurotoxic symptoms in children were compared for cost minimization from a societal perspective. In strategy I, patients were managed with supportive care only without antivenom. In strategy II, an aggressive strategy of full-dose antivenom (initial dose of 3 vials with the use of additional vials administered 1 vial at a time) was considered. In strategy III, a single-vial serial antivenom dosing strategy titrated to clinical response was considered. Clinical probabilities for the different strategies were obtained from retrospective review of medical records of patients with scorpion envenomation over a 10-year period at our institution. Baseline cost values were obtained from patient reimbursement data from our institution. In baseline analysis, strategy I of supportive care only with no antivenom was least costly at US $3466.50/patient. Strategy III of single-vial serial dosing was intermediate but less expensive than strategy II of full-dose antivenom, with an incremental cost of US $3171.08 per patient. In a 1-way sensitivity analysis, at a threshold antivenom cost of US $1577.87, strategy III of single-vial serial dosing became the least costly strategy. For children with scorpion envenomation, use of a management strategy based on serial dosing of antivenom titrated to clinical response is less costly than a strategy of initial use of full-dose antivenom.

Identifying key nodes in multilayer networks based on tensor decomposition.

PubMed

Wang, Dingjie; Wang, Haitao; Zou, Xiufen

2017-06-01

The identification of essential agents in multilayer networks characterized by different types of interactions is a crucial and challenging topic, one that is essential for understanding the topological structure and dynamic processes of multilayer networks. In this paper, we use the fourth-order tensor to represent multilayer networks and propose a novel method to identify essential nodes based on CANDECOMP/PARAFAC (CP) tensor decomposition, referred to as the EDCPTD centrality. This method is based on the perspective of multilayer networked structures, which integrate the information of edges among nodes and links between different layers to quantify the importance of nodes in multilayer networks. Three real-world multilayer biological networks are used to evaluate the performance of the EDCPTD centrality. The bar chart and ROC curves of these multilayer networks indicate that the proposed approach is a good alternative index to identify real important nodes. Meanwhile, by comparing the behavior of both the proposed method and the aggregated single-layer methods, we demonstrate that neglecting the multiple relationships between nodes may lead to incorrect identification of the most versatile nodes. Furthermore, the Gene Ontology functional annotation demonstrates that the identified top nodes based on the proposed approach play a significant role in many vital biological processes. Finally, we have implemented many centrality methods of multilayer networks (including our method and the published methods) and created a visual software based on the MATLAB GUI, called ENMNFinder, which can be used by other researchers.

Identifying key nodes in multilayer networks based on tensor decomposition

NASA Astrophysics Data System (ADS)

Wang, Dingjie; Wang, Haitao; Zou, Xiufen

2017-06-01

The identification of essential agents in multilayer networks characterized by different types of interactions is a crucial and challenging topic, one that is essential for understanding the topological structure and dynamic processes of multilayer networks. In this paper, we use the fourth-order tensor to represent multilayer networks and propose a novel method to identify essential nodes based on CANDECOMP/PARAFAC (CP) tensor decomposition, referred to as the EDCPTD centrality. This method is based on the perspective of multilayer networked structures, which integrate the information of edges among nodes and links between different layers to quantify the importance of nodes in multilayer networks. Three real-world multilayer biological networks are used to evaluate the performance of the EDCPTD centrality. The bar chart and ROC curves of these multilayer networks indicate that the proposed approach is a good alternative index to identify real important nodes. Meanwhile, by comparing the behavior of both the proposed method and the aggregated single-layer methods, we demonstrate that neglecting the multiple relationships between nodes may lead to incorrect identification of the most versatile nodes. Furthermore, the Gene Ontology functional annotation demonstrates that the identified top nodes based on the proposed approach play a significant role in many vital biological processes. Finally, we have implemented many centrality methods of multilayer networks (including our method and the published methods) and created a visual software based on the MATLAB GUI, called ENMNFinder, which can be used by other researchers.

An integrative somatic mutation analysis to identify pathways linked with survival outcomes across 19 cancer types

PubMed Central

Park, Sunho; Kim, Seung-Jun; Yu, Donghyeon; Peña-Llopis, Samuel; Gao, Jianjiong; Park, Jin Suk; Chen, Beibei; Norris, Jessie; Wang, Xinlei; Chen, Min; Kim, Minsoo; Yong, Jeongsik; Wardak, Zabi; Choe, Kevin; Story, Michael; Starr, Timothy; Cheong, Jae-Ho; Hwang, Tae Hyun

2016-01-01

Motivation: Identification of altered pathways that are clinically relevant across human cancers is a key challenge in cancer genomics. Precise identification and understanding of these altered pathways may provide novel insights into patient stratification, therapeutic strategies and the development of new drugs. However, a challenge remains in accurately identifying pathways altered by somatic mutations across human cancers, due to the diverse mutation spectrum. We developed an innovative approach to integrate somatic mutation data with gene networks and pathways, in order to identify pathways altered by somatic mutations across cancers. Results: We applied our approach to The Cancer Genome Atlas (TCGA) dataset of somatic mutations in 4790 cancer patients with 19 different types of tumors. Our analysis identified cancer-type-specific altered pathways enriched with known cancer-relevant genes and targets of currently available drugs. To investigate the clinical significance of these altered pathways, we performed consensus clustering for patient stratification using member genes in the altered pathways coupled with gene expression datasets from 4870 patients from TCGA, and multiple independent cohorts confirmed that the altered pathways could be used to stratify patients into subgroups with significantly different clinical outcomes. Of particular significance, certain patient subpopulations with poor prognosis were identified because they had specific altered pathways for which there are available targeted therapies. These findings could be used to tailor and intensify therapy in these patients, for whom current therapy is suboptimal. Availability and implementation: The code is available at: http://www.taehyunlab.org. Contact: jhcheong@yuhs.ac or taehyun.hwang@utsouthwestern.edu or taehyun.cs@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online. PMID:26635139

Differences in Poor Readers' Abilities to Identify High-Frequency Words in Isolation and Context.

ERIC Educational Resources Information Center

Krieger, Veronica K.

1981-01-01

Reports that fourth-grade poor readers were able to identify more high-frequency words in context than in isolation. Discusses the findings in terms of a context-oriented approach of word identification instruction and assessment. (FL)

Salivary Concentration of Progesterone and Cortisol Significantly Differs Across Individuals After Correcting for Blood Hormone Values

PubMed Central

Konishi, Shoko; Brindle, Eleanor; Guyton, Amanda; O’Connor, Kathleen A.

2014-01-01

Between-individual variation of salivary progesterone (P4) and cortisol levels does not always closely reflect blood hormone concentrations. This may be partly a function of individual differences in salivary hormone excretion. We tested whether time of day at sampling and ethnicity contributed to individual variation in salivary hormones after adjusting for blood hormone levels. Forty-three Caucasian and 15 Japanese women (18–34 years) collected four sets of matched dried blood spot (DBS) and saliva specimens across a menstrual cycle (N = 232 specimen sets). Linear fixed-effects (LFE) models were used to estimate the effects of diurnal variation and ethnicity on salivary P4 and cortisol while adjusting for DBS levels. For each hormone, women with exclusively positive or negative residuals (unexplained variance) from the LFE models were categorized as high- or low-saliva-to-DBS hormone ratio (SDR; high or low salivary secretors), respectively. We found that salivary P4 (P < 0.05) was significantly higher in early morning compared to the afternoon, after controlling for DBS levels, ethnicity, and BMI. After further adjusting for this diurnal effect, significant individual variation in salivary P4 and cortisol remained: sixteen and nine women, respectively were categorized as low or high salivary secretors for both hormones (P < 0.001), suggesting systematic individual-specific variation of salivary hormonal concentration. We conclude that when saliva is used to quantify P4 or cortisol levels, time of day at sampling should be controlled. Even with this adjustment, salivary P4 and cortisol do not closely mirror between-individual variation of serum P4 and cortisol in a substantial proportion of individuals. PMID:22826025

"Clinical" Significance: "Clinical" Significance and "Practical" Significance are NOT the Same Things

ERIC Educational Resources Information Center

Peterson, Lisa S.

2008-01-01

Clinical significance is an important concept in research, particularly in education and the social sciences. The present article first compares clinical significance to other measures of "significance" in statistics. The major methods used to determine clinical significance are explained and the strengths and weaknesses of clinical significance…

A probabilistic approach to identify putative drug targets in biochemical networks.

PubMed

Murabito, Ettore; Smallbone, Kieran; Swinton, Jonathan; Westerhoff, Hans V; Steuer, Ralf

2011-06-06

Network-based drug design holds great promise in clinical research as a way to overcome the limitations of traditional approaches in the development of drugs with high efficacy and low toxicity. This novel strategy aims to study how a biochemical network as a whole, rather than its individual components, responds to specific perturbations in different physiological conditions. Proteins exerting little control over normal cells and larger control over altered cells may be considered as good candidates for drug targets. The application of network-based drug design would greatly benefit from using an explicit computational model describing the dynamics of the system under investigation. However, creating a fully characterized kinetic model is not an easy task, even for relatively small networks, as it is still significantly hampered by the lack of data about kinetic mechanisms and parameters values. Here, we propose a Monte Carlo approach to identify the differences between flux control profiles of a metabolic network in different physiological states, when information about the kinetics of the system is partially or totally missing. Based on experimentally accessible information on metabolic phenotypes, we develop a novel method to determine probabilistic differences in the flux control coefficients between the two observable phenotypes. Knowledge of how differences in flux control are distributed among the different enzymatic steps is exploited to identify points of fragility in one of the phenotypes. Using a prototypical cancerous phenotype as an example, we demonstrate how our approach can assist researchers in developing compounds with high efficacy and low toxicity. © 2010 The Royal Society

Microbiological investigation and clinical significance of Corynebacterium spp. in respiratory specimens.

PubMed

Nhan, Tu-Xuan; Parienti, Jean-Jacques; Badiou, Guillaume; Leclercq, Roland; Cattoir, Vincent

2012-11-01

The purpose of this retrospective study was to evaluate the pathogenic role of Corynebacterium species in lower respiratory tract infections as well as their routine laboratory investigation. From April 2007 to August 2009, 27 clinical isolates were significantly recovered from respiratory specimens of 27 different patients clinically suspected of having lower respiratory tract infections. The average age of patients was 65 years, while 22 (81%) patients presented at least 1 predisposing condition. Of the 27 patients, 15 (56%) were classified as infected according to Centers for Disease Control and Prevention/National Healthcare Safety Network criteria, with 93% of infections being hospital acquired. All isolates were accurately identified to the species level using molecular methods (i.e., 17 Corynebacterium pseudodiphtheriticum, 7 Corynebacterium striatum, and 3 Corynebacterium accolens), whereas phenotypic methods remained frequently unreliable for identifying C. striatum and C. accolens strains. All tested isolates were susceptible to amoxicillin, imipenem, vancomycin, linezolid, and tigecycline, whereas most of them were resistant to erythromycin. Copyright © 2012 Elsevier Inc. All rights reserved.

The Impact of Significant Other Expressed Emotion on Patient Outcomes in Chronic Fatigue Syndrome

PubMed Central

2014-01-01

Objective: Previous literature has identified the importance of interpersonal processes for patient outcomes in chronic fatigue syndrome/myalgic encephalomyelitis (CFS/ME), particularly in the context of significant other relationships. The current study investigated expressed emotion (EE), examining the independent effects of critical comments and emotional overinvolvement (EOI) in association with patient outcomes. Method: Fifty-five patients with CFS/ME and their significant others were recruited from specialist CFS/ME services. Significant other EE status was coded from a modified Camberwell Family Interview. Patient outcomes (fatigue severity, disability, and depression) were derived from questionnaire measures. Forty-four patients (80%) completed follow-up questionnaires 6-months after recruitment. Results: Significant other high-EE categorized by both high levels of critical comments and high EOI was predictive of worse fatigue severity at follow-up. High-critical EE was associated with higher levels of patient depressive symptoms longitudinally; depressive symptoms were observed to mediate the relationship between high critical comments and fatigue severity reported at follow-up. There were higher rates of high-EE in parents than in partners, and this was because of higher rates of EOI in parents. Conclusions: Patients with high-EE significant others demonstrated poorer outcomes at follow-up compared with patients in low-EE dyads. One mechanism for this appears to be as a result of increased patient depression. Future research should seek to further clarify whether the role of interpersonal processes in CFS/ME differs across different patient-significant other relationships. The development of significant other-focused treatment interventions may be particularly beneficial for both patients and significant others. PMID:25180548

Comparative genomic analysis of Helicobacter pylori from Malaysia identifies three distinct lineages suggestive of differential evolution

PubMed Central

Kumar, Narender; Mariappan, Vanitha; Baddam, Ramani; Lankapalli, Aditya K.; Shaik, Sabiha; Goh, Khean-Lee; Loke, Mun Fai; Perkins, Tim; Benghezal, Mohammed; Hasnain, Seyed E.; Vadivelu, Jamuna; Marshall, Barry J.; Ahmed, Niyaz

2015-01-01

The discordant prevalence of Helicobacter pylori and its related diseases, for a long time, fostered certain enigmatic situations observed in the countries of the southern world. Variation in H. pylori infection rates and disease outcomes among different populations in multi-ethnic Malaysia provides a unique opportunity to understand dynamics of host–pathogen interaction and genome evolution. In this study, we extensively analyzed and compared genomes of 27 Malaysian H. pylori isolates and identified three major phylogeographic lineages: hspEastAsia, hpEurope and hpSouthIndia. The analysis of the virulence genes within the core genome, however, revealed a comparable pathogenic potential of the strains. In addition, we identified four genes limited to strains of East-Asian lineage. Our analyses identified a few strain-specific genes encoding restriction modification systems and outlined 311 core genes possibly under differential evolutionary constraints, among the strains representing different ethnic groups. The cagA and vacA genes also showed variations in accordance with the host genetic background of the strains. Moreover, restriction modification genes were found to be significantly enriched in East-Asian strains. An understanding of these variations in the genome content would provide significant insights into various adaptive and host modulation strategies harnessed by H. pylori to effectively persist in a host-specific manner. PMID:25452339

Identifying molecular subtypes related to clinicopathologic factors in pancreatic cancer

PubMed Central

2014-01-01

Background Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal tumors and usually presented with locally advanced and distant metastasis disease, which prevent curative resection or treatments. In this regard, we considered identifying molecular subtypes associated with clinicopathological factor as prognosis factors to stratify PDAC for appropriate treatment of patients. Results In this study, we identified three molecular subtypes which were significant on survival time and metastasis. We also identified significant genes and enriched pathways represented for each molecular subtype. Considering R0 resection patients included in each subtype, metastasis and survival times are significantly associated with subtype 1 and subtype 2. Conclusions We observed three PDAC molecular subtypes and demonstrated that those subtypes were significantly related with metastasis and survival time. The study may have utility in stratifying patients for cancer treatment. PMID:25560450

Expression of HOXB genes is significantly different in acute myeloid leukemia with a partial tandem duplication of MLL vs. a MLL translocation: a cross-laboratory study.

PubMed

Liu, Hsi-Che; Shih, Lee-Yung; May Chen, Mei-Ju; Wang, Chien-Chih; Yeh, Ting-Chi; Lin, Tung-Huei; Chen, Chien-Yu; Lin, Chih-Jen; Liang, Der-Cherng

2011-05-01

In acute myeloid leukemia (AML), the mixed lineage leukemia (MLL) gene may be rearranged to generate a partial tandem duplication (PTD), or fused to partner genes through a chromosomal translocation (tMLL). In this study, we first explored the differentially expressed genes between MLL-PTD and tMLL using gene expression profiling of our cohort (15 MLL-PTD and 10 tMLL) and one published data set. The top 250 probes were chosen from each set, resulting in 29 common probes (21 unique genes) to both sets. The selected genes include four HOXB genes, HOXB2, B3, B5, and B6. The expression values of these HOXB genes significantly differ between MLL-PTD and tMLL cases. Clustering and classification analyses were thoroughly conducted to support our gene selection results. Second, as MLL-PTD, FLT3-ITD, and NPM1 mutations are identified in AML with normal karyotypes, we briefly studied their impact on the HOXB genes. Another contribution of this study is to demonstrate that using public data from other studies enriches samples for analysis and yields more conclusive results. 2011 Elsevier Inc. All rights reserved.

Physical and genetic-interaction density reveals functional organization and informs significance cutoffs in genome-wide screens

PubMed Central

Dittmar, John C.; Pierce, Steven; Rothstein, Rodney; Reid, Robert J. D.

2013-01-01

Genome-wide experiments often measure quantitative differences between treated and untreated cells to identify affected strains. For these studies, statistical models are typically used to determine significance cutoffs. We developed a method termed “CLIK” (Cutoff Linked to Interaction Knowledge) that overlays biological knowledge from the interactome on screen results to derive a cutoff. The method takes advantage of the fact that groups of functionally related interacting genes often respond similarly to experimental conditions and, thus, cluster in a ranked list of screen results. We applied CLIK analysis to five screens of the yeast gene disruption library and found that it defined a significance cutoff that differed from traditional statistics. Importantly, verification experiments revealed that the CLIK cutoff correlated with the position in the rank order where the rate of true positives drops off significantly. In addition, the gene sets defined by CLIK analysis often provide further biological perspectives. For example, applying CLIK analysis retrospectively to a screen for cisplatin sensitivity allowed us to identify the importance of the Hrq1 helicase in DNA crosslink repair. Furthermore, we demonstrate the utility of CLIK to determine optimal treatment conditions by analyzing genome-wide screens at multiple rapamycin concentrations. We show that CLIK is an extremely useful tool for evaluating screen quality, determining screen cutoffs, and comparing results between screens. Furthermore, because CLIK uses previously annotated interaction data to determine biologically informed cutoffs, it provides additional insights into screen results, which supplement traditional statistical approaches. PMID:23589890

SEQUOIA: significance enhanced network querying through context-sensitive random walk and minimization of network conductance.

PubMed

Jeong, Hyundoo; Yoon, Byung-Jun

2017-03-14

Network querying algorithms provide computational means to identify conserved network modules in large-scale biological networks that are similar to known functional modules, such as pathways or molecular complexes. Two main challenges for network querying algorithms are the high computational complexity of detecting potential isomorphism between the query and the target graphs and ensuring the biological significance of the query results. In this paper, we propose SEQUOIA, a novel network querying algorithm that effectively addresses these issues by utilizing a context-sensitive random walk (CSRW) model for network comparison and minimizing the network conductance of potential matches in the target network. The CSRW model, inspired by the pair hidden Markov model (pair-HMM) that has been widely used for sequence comparison and alignment, can accurately assess the node-to-node correspondence between different graphs by accounting for node insertions and deletions. The proposed algorithm identifies high-scoring network regions based on the CSRW scores, which are subsequently extended by maximally reducing the network conductance of the identified subnetworks. Performance assessment based on real PPI networks and known molecular complexes show that SEQUOIA outperforms existing methods and clearly enhances the biological significance of the query results. The source code and datasets can be downloaded from http://www.ece.tamu.edu/~bjyoon/SEQUOIA .

Identifying important motivational factors for professionals in Greek hospitals

PubMed Central

Kontodimopoulos, Nick; Paleologou, Victoria; Niakas, Dimitris

2009-01-01

Background The purpose of this study was to identify important motivational factors according to the views of health-care professionals in Greek hospitals and particularly to determine if these might differ in the public and private sectors. Methods A previously developed -and validated- instrument addressing four work-related motivators (job attributes, remuneration, co-workers and achievements) was used. Three categories of health care professionals, doctors (N = 354), nurses (N = 581) and office workers (N = 418), working in public and private hospitals, participated and motivation was compared across socio-demographic and occupational variables. Results The range of reported motivational factors was mixed and Maslow's conclusions that lower level motivational factors must be met before ascending to the next level were not confirmed. The highest ranked motivator for the entire sample, and by professional subgroup, was achievements (P < 0.001). Within subgroups, motivators were similar, and only one significant difference was observed, namely between doctors and nurses in respect to co-workers (P < 0.05). Remuneration (and salary in particular) was reported as a significant incentive only for professionals in managerial positions. Health professionals in private hospitals were motivated by all factors significantly more than their public-hospital counterparts. Conclusion The results are in agreement with the literature which focuses attention to management approaches employing both monetary and non-monetary incentives to motivate health care workers. This study showed that intrinsic factors are particularly important and should become a target for effective employee motivation. PMID:19754968

The profiles of students with significant cognitive disabilities and complex communication needs.

PubMed

Erickson, Karen A; Geist, Lori A

2016-09-01

Understanding the characteristics of students with complex communication needs and significant cognitive disabilities is an important first step toward creating the kinds of supports and services required to help them successfully access the general education curriculum, achieve grade-level standards, and improve overall communication competence. The First Contact Survey was designed to collect important information about students with significant cognitive disabilities who were eligible to take the Dynamic Learning Maps™ (DLM(®)) alternate assessment based on alternate achievement standards. From November 2012-May 2013, the survey was used to gather information regarding more than 44,787 students. At that time, the goal was to use the data to inform the development of the DLM assessment. Although the survey includes a wealth of information regarding this large sample of students, the reanalysis of the data reported in the current study focused on the motor, sensory, language, reading, and writing skills of students with significant cognitive disabilities, based on their speech production abilities. Significant differences were identified across each of the domains between students who do and do not use speech with or without aided augmentative and alternative communication.

Identifying Predictors, Moderators, and Mediators of Antidepressant Response in Major Depressive Disorder: Neuroimaging Approaches

PubMed Central

Phillips, Mary L.; Chase, Henry W.; Sheline, Yvette I.; Etkin, Amit; Almeida, Jorge R.C.; Deckersbach, Thilo; Trivedi, Madhukar H.

2015-01-01

Objective Despite significant advances in neuroscience and treatment development, no widely accepted biomarkers are available to inform diagnostics or identify preferred treatments for individuals with major depressive disorder. Method In this critical review, the authors examine the extent to which multimodal neuroimaging techniques can identify biomarkers reflecting key pathophysiologic processes in depression and whether such biomarkers may act as predictors, moderators, and mediators of treatment response that might facilitate development of personalized treatments based on a better understanding of these processes. Results The authors first highlight the most consistent findings from neuroimaging studies using different techniques in depression, including structural and functional abnormalities in two parallel neural circuits: serotonergically modulated implicit emotion regulation circuitry, centered on the amygdala and different regions in the medial prefrontal cortex; and dopaminergically modulated reward neural circuitry, centered on the ventral striatum and medial prefrontal cortex. They then describe key findings from the relatively small number of studies indicating that specific measures of regional function and, to a lesser extent, structure in these neural circuits predict treatment response in depression. Conclusions Limitations of existing studies include small sample sizes, use of only one neuroimaging modality, and a focus on identifying predictors rather than moderators and mediators of differential treatment response. By addressing these limitations and, most importantly, capitalizing on the benefits of multimodal neuroimaging, future studies can yield moderators and mediators of treatment response in depression to facilitate significant improvements in shorter- and longer-term clinical and functional outcomes. PMID:25640931

Genetic analysis of atherosclerosis identifies a major susceptibility locus in the major histocompatibility complex of mice.

PubMed

Grainger, Andrew T; Jones, Michael B; Li, Jing; Chen, Mei-Hua; Manichaikul, Ani; Shi, Weibin

2016-11-01

Recent genome-wide association studies (GWAS) have identified over 50 significant loci containing common variants associated with coronary artery disease. However, these variants explain only 26% of the genetic heritability of the disease, suggesting that many more variants remain to be discovered. Here, we examined the genetic basis underlying the marked difference between SM/J-Apoe -/- and BALB/cJ-Apoe -/- mice in atherosclerotic lesion formation. 206 female F 2 mice generated from an intercross between the two Apoe -/- strains were fed 12 weeks of western diet. Atherosclerotic lesion sizes in the aortic root were measured and 149 genetic markers genotyped across the entire genome. A significant locus, named Ath49 (LOD score: 4.18), for atherosclerosis was mapped to the H2 complex [mouse major histocompatibility complex (MHC)] on chromosome 17. Bioinformatic analysis identified 12 probable candidate genes, including Tnfrsf21, Adgrf1, Adgrf5, Mep1a, and Pla2g7. Corresponding human genomic regions of Ath49 showed significant association with coronary heart disease. Five suggestive loci on chromosomes 1, 4, 5, and 8 for atherosclerosis were also identified. Atherosclerotic lesion sizes were significantly correlated with HDL but not with non-HDL cholesterol, triglyceride or glucose levels in the F 2 cohort. We have identified the MHC as a major genetic determinant of atherosclerosis, highlighting the importance of inflammation in atherogenesis. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Significantly Increased Odds of Reporting Previous Shoulder Injuries in Female Marines Based on Larger Magnitude Shoulder Rotator Bilateral Strength Differences

PubMed Central

Eagle, Shawn R.; Connaboy, Chris; Nindl, Bradley C.; Allison, Katelyn F.

2018-01-01

Background: Musculoskeletal injuries to the extremities are a primary concern for the United States (US) military. One possible injury risk factor in this population is side-to-side strength imbalance. Purpose: To examine the odds of reporting a previous shoulder injury in US Marine Corps Ground Combat Element Integrated Task Force volunteers based on side-to-side strength differences in isokinetic shoulder strength. Study Design: Cohort study; Level of evidence, 3. Methods: Male (n = 219) and female (n = 91) Marines were included in this analysis. Peak torque values from 5 shoulder internal/external rotation repetitions were averaged and normalized to body weight. The difference in side-to-side strength measurements was calculated as the absolute value of the limb difference divided by the mean peak torque of the dominant limb. Participants were placed into groups based on the magnitude of these differences: <10%, 10% to 20%, and >20%. Odds ratios (ORs) and 95% CIs were calculated. Results: When separated by sex, 13.2% of men reported an injury, while 5.5% of women reported an injury. Female Marines with >20% internal rotation side-to-side strength differences demonstrated increased odds of reporting a previous shoulder injury compared with female Marines with <10% strength differences (OR, 15.4; 95% CI, 1.4-167.2; P = .03 ) and female Marines with 10% to 20% strength differences (OR, 13.9; 95% CI, 1.3-151.2; P = .04). No significant ORs were demonstrated in male Marines. Conclusion: Marines with larger magnitude internal rotation strength differences demonstrated increased odds of reporting a previous shoulder injury compared with those with lesser magnitude differences. Additionally, female sex appears to drastically affect the increased odds of reporting shoulder injuries (OR, 13.9-15.4) with larger magnitude differences (ie, >20%) compared with those with lesser magnitude differences (ie, <10% and 10%-20%). The retrospective cohort design of this study cannot

Significantly Increased Odds of Reporting Previous Shoulder Injuries in Female Marines Based on Larger Magnitude Shoulder Rotator Bilateral Strength Differences.

PubMed

Eagle, Shawn R; Connaboy, Chris; Nindl, Bradley C; Allison, Katelyn F

2018-02-01

Musculoskeletal injuries to the extremities are a primary concern for the United States (US) military. One possible injury risk factor in this population is side-to-side strength imbalance. To examine the odds of reporting a previous shoulder injury in US Marine Corps Ground Combat Element Integrated Task Force volunteers based on side-to-side strength differences in isokinetic shoulder strength. Cohort study; Level of evidence, 3. Male (n = 219) and female (n = 91) Marines were included in this analysis. Peak torque values from 5 shoulder internal/external rotation repetitions were averaged and normalized to body weight. The difference in side-to-side strength measurements was calculated as the absolute value of the limb difference divided by the mean peak torque of the dominant limb. Participants were placed into groups based on the magnitude of these differences: <10%, 10% to 20%, and >20%. Odds ratios (ORs) and 95% CIs were calculated. When separated by sex, 13.2% of men reported an injury, while 5.5% of women reported an injury. Female Marines with >20% internal rotation side-to-side strength differences demonstrated increased odds of reporting a previous shoulder injury compared with female Marines with <10% strength differences (OR, 15.4; 95% CI, 1.4-167.2; P = .03 ) and female Marines with 10% to 20% strength differences (OR, 13.9; 95% CI, 1.3-151.2; P = .04). No significant ORs were demonstrated in male Marines. Marines with larger magnitude internal rotation strength differences demonstrated increased odds of reporting a previous shoulder injury compared with those with lesser magnitude differences. Additionally, female sex appears to drastically affect the increased odds of reporting shoulder injuries (OR, 13.9-15.4) with larger magnitude differences (ie, >20%) compared with those with lesser magnitude differences (ie, <10% and 10%-20%). The retrospective cohort design of this study cannot delineate cause and effect but establishes a relationship between

Self-efficacy difference among patients with cancer with different socioeconomic status: application of latent class analysis and standardization and decomposition analysis.

PubMed

Yuan, Changrong; Wei, Chunlan; Wang, Jichuan; Qian, Huijuan; Ye, Xianghong; Liu, Yingyan; Hinds, Pamela S

2014-06-01

Although the relationship between partial socioeconomic status (SES) and self-efficacy has been studied in previous studies, few research have examined self-efficacy difference among patients with cancer with different SES. A cross-sectional survey involving 764 patients with cancer was completed. Latent class analysis (LCA) was applied to identify distinct groups of patients with cancer using four SES indicators (education, income, employment status and health insurance status). Standardization and decomposition analysis (SDA) was then used to examine differences in patients' self-efficacy among SES groups and the components of the differences attributed to confounding factors, such as gender, age, anxiety, depression and social support. Participants were classified into four distinctive SES groups via using LCA method, and the observed self-efficacy level significantly varied by SES groups; as theorized, higher self-efficacy was associated with higher SES. The self-efficacy differences by SES groups were decomposed into "real" group differences and factor component effects that are attributed to group differences in confounding factor compositions. Self-efficacy significantly varies by SES. Social support significantly confounded the observed differences in self-efficacy between different SES groups among Chinese patients with cancer. Copyright © 2014 Elsevier Ltd. All rights reserved.

Optimal screening of children with acute malnutrition requires a change in current WHO guidelines as MUAC and WHZ identify different patient groups.

PubMed

Laillou, Arnaud; Prak, Sophonneary; de Groot, Richard; Whitney, Sophie; Conkle, Joel; Horton, Lindsey; Un, Sam Oeurn; Dijkhuizen, Marjoleine A; Wieringa, Frank T

2014-01-01

Timely treatment of acute malnutrition in children <5 years of age could prevent >500,000 deaths annually. Screening at community level is essential to identify children with malnutrition. Current WHO guidelines for community screening for malnutrition recommend a Mid Upper Arm Circumference (MUAC) of <115 mm to identify severe acute malnutrition (SAM). However, it is currently unclear how MUAC relates to the other indicator used to define acute malnutrition: weight-for-height Z-score (WHZ). Secondary data from >11,000 Cambodian children, obtained by different surveys between 2010 and 2012, was used to calculate sensitivity and ROC curves for MUAC and WHZ. The secondary analysis showed that using the current WHO cut-off of 115 mm for screening for severe acute malnutrition over 90% of children with a weight-for-height z-score (WHZ) <-3 would have been missed. Reversely, WHZ<-3 missed 80% of the children with a MUAC<115 mm. The current WHO cut-off for screening for SAM should be changed upwards from the current 115 mm. In the Cambodian data-set, a cut-off of 133 mm would allow inclusion of >65% of children with a WHZ<-3. Importantly, MUAC and WHZ identified different sub-groups of children with acute malnutrition, therefore these 2 indicators should be regarded as independent from each other. We suggest a 2-step model with MUAC used a screening at community level, followed by MUAC and WHZ measured at a primary health care unit, with both indicators used independently to diagnose severe acute malnutrition. Current guidelines should be changed to reflect this, with treatment initiated when either MUAC <115 mm or WHZ<-3.