Sample records for profile analysis identified

  1. Further Examining Berry's Model: The Applicability of Latent Profile Analysis to Acculturation

    ERIC Educational Resources Information Center

    Fox, Rina S.; Merz, Erin L.; Solórzano, Martha T.; Roesch, Scott C.

    2013-01-01

    This study used latent profile analysis (LPA) to identify acculturation profiles. A three-profile solution fit the data best, and comparisons on demographic and psychosocial outcomes as a function of profile yielded expected results. The findings support using LPA as a parsimonious way to model acculturation without anticipating profiles in…

  2. Identification of (R)-selective ω-aminotransferases by exploring evolutionary sequence space.

    PubMed

    Kim, Eun-Mi; Park, Joon Ho; Kim, Byung-Gee; Seo, Joo-Hyun

    2018-03-01

    Several (R)-selective ω-aminotransferases (R-ωATs) have been reported. The existence of additional R-ωATs having different sequence characteristics from previous ones is highly expected. In addition, it is generally accepted that R-ωATs are variants of aminotransferase group III. Based on these backgrounds, sequences in RefSeq database were scored using family profiles of branched-chain amino acid aminotransferase (BCAT) and d-alanine aminotransferase (DAT) to predict and identify putative R-ωATs. Sequences with two profile analysis scores were plotted on two-dimensional score space. Candidates with relatively similar scores in both BCAT and DAT profiles (i.e., profile analysis score using BCAT profile was similar to profile analysis score using DAT profile) were selected. Experimental results for selected candidates showed that putative R-ωATs from Saccharopolyspora erythraea (R-ωAT_Sery), Bacillus cellulosilyticus (R-ωAT_Bcel), and Bacillus thuringiensis (R-ωAT_Bthu) had R-ωAT activity. Additional experiments revealed that R-ωAT_Sery also possessed DAT activity while R-ωAT_Bcel and R-ωAT_Bthu had BCAT activity. Selecting putative R-ωATs from regions with similar profile analysis scores identified potential R-ωATs. Therefore, R-ωATs could be efficiently identified by using simple family profile analysis and exploring evolutionary sequence space. Copyright © 2017 Elsevier Inc. All rights reserved.

  3. Latent profile analysis of students' motivation and outcomes in mathematics: an organismic integration theory perspective.

    PubMed

    Wang, Chee Keng John; Liu, Woon Chia; Nie, Youyan; Chye, Yen Leng Stefanie; Lim, Boon San Coral; Liem, Gregory Arief; Tay, Eng Guan; Hong, Ying-Yi; Chiu, Chi-Yue

    2017-05-01

    The purpose of the current study was to identify the motivation profiles at the intraindividual level using a latent profile analyses (LPA) approach. A total of 1151 secondary school students aged 13 to 17 years old from Singapore took part in the study. Using LPA, four distinct motivational profiles were identified based on four motivation regulations. Profile 1 has very low introjected and low autonomous motivation (6% of sample). Profile 2 had high external and identified regulations and very low intrinsic regulation (10%). Profile 3 consisted of students with high identified and intrinsic regulations (51%). Profile 4 had moderately low identified and intrinsic regulations (33%). The results showed that the four profiles differed significantly in terms of effort, competence, value, and time spent on math beyond homework. The best profile (Profile 3) reported highest scores in effort, value, competence and time spent on Math beyond homework. The worst profile (Profile 1) reported lowest scores in all the four outcome variables.

  4. Determination of antibiotic resistance and high-performance liquid chromatography profiles for Mycobacterium species.

    PubMed

    Toka Özer, Türkan; Yula, Erkan; Doğan, Metin; Baskın, Hüseyin

    2018-04-27

    Incidence of mycobacterial infections has been increasing. However, diagnosis and treatment of mycobacterial infections can be difficult. The aim of this study was to investigate high-performance liquid chromatography (HPLC) analysis of the mycolic acids for rapid identification and dendrogram cluster analysis of mycobacterium species. Clinical specimens received for mycobacterial culture and antimicrobial susceptibility test were processed by standard laboratory protocols. Positive cultures were analyzed with HPLC method. Mycolic acid analysis with HPLC was used for diagnosis of tuberculosis and other mycobacterial infections. These reports were compared with Sherlock Library mycobacterial species, and the similarity index was analyzed. This value was formed by a software in multidimensional space that was the calculation of the average distance between the nearest library profile and unknown profile. The ninety-two samples were identified as M. tuberculosis. (similarity index between 0.593 and 0.994). One of the other strains was identified as M. avium intracellulare (strain No. 82) (SI = 0.906); one of them was identified as M. interjectum (strain no. 89) (SI = 0.644). Total 94 samples were identified, and dendrogram was applied to these samples. Profile A (10.6%), profile B (59.6%), profile C (11.7%), profile D (3.2%), and other profiles as single different profiles were identified. Rates for each as 1% (89, 94, 1, 82, 26, 42, 32, 41, 100, 43, 47, 44, 40, 35). High-performance liquid chromatography is a useful, rapid, reliable, and practical method for diagnosis of mycobacterium species. © 2018 Wiley Periodicals, Inc.

  5. Analysis of motivational profiles of satisfaction and importance of physical education in high school adolescents.

    PubMed

    Granero-Gallegos, Antonio; Baena-Extremera, Antonio; Pérez-Quero, Francisco J; Ortiz-Camacho, Maria M; Bracho-Amador, Clara

    2012-01-01

    The purpose of this study was to analyze the motivational profiles of satisfaction with and importance of physical education in high school students and its relation with gender and the practice of sport. The sample comprised 2002 students aged from 12 to 19 who completed the Sport Motivation Scale (Núñez et al., 2006), the Sport Satisfaction Instrument (Baena-Extremera et al., 2012) and the Importance of Physical Education Scale (Moreno et al., 2009). Descriptive analyzes, correlations between the scales, a cluster analysis for profiles, and a MANOVA were conducted to examine differences by gender. Three clusters (profiles) were identified. The first profile identified was "moderate" motivation (n = 463) and was associated with boys who practice physical activity for less than 3 hours per week. The second profile identified was "low" motivation (n = 545) and was associated mainly with girls who practice physical activity for less than 3 hours per week. And lastly the third profile identified was "high" motivation (n = 910), which was found to be greater in boys who practiced physical exercise for more than 3 hours a week.

  6. Classroom Behaviour and Academic Achievement: How Classroom Behaviour Categories Relate to Gender and Academic Performance

    ERIC Educational Resources Information Center

    Borg, Elin

    2015-01-01

    Latent profile analysis was used to identify different categories of students having different "profiles" using self-reported classroom behaviour. Four categories of students with unique classroom behaviour profiles were identified among secondary school students in Oslo, Norway (n = 1570). Analyses examined how classroom behaviour…

  7. Profiles of Reactivity in Cocaine-Exposed Children

    ERIC Educational Resources Information Center

    Schuetze, Pamela; Molnar, Danielle S.; Eiden, Rina D.

    2012-01-01

    This study explored the possibility that specific, theoretically consistent profiles of reactivity could be identified in a sample of cocaine-exposed infants and whether these profiles were associated with a range of infant and/or maternal characteristics. Cluster analysis was used to identify distinct groups of infants based on physiological,…

  8. The Role of Religiousness/Spirituality in Health-Related Quality of Life Among Adolescents with HIV: A Latent Profile Analysis

    PubMed Central

    Kimmel, Allison L.; Cheng, Yao Iris; Wang, Jichuan

    2016-01-01

    The purpose of this study was to determine whether distinct latent profiles of religiousness/spirituality exist for ALWH, and if so, are latent profile memberships associated with health-related quality of life (HRQoL). Latent profile analysis of religiosity identified four profiles/groups. Compared to the other three groups, higher levels of emotional well-being were found among young perinatally infected adolescents who attended religious services, but who did not pray privately, feel God's presence or identify as religious or spiritual. Social HRQoL was significantly higher among the highest overall religious/spiritual group. Understanding adolescent profiles of religiousness/spirituality on HRQoL could inform faith-based interventions. PMID:27071797

  9. The Role of Religiousness/Spirituality in Health-Related Quality of Life Among Adolescents with HIV: A Latent Profile Analysis.

    PubMed

    Lyon, Maureen E; Kimmel, Allison L; Cheng, Yao Iris; Wang, Jichuan

    2016-10-01

    The purpose of this study was to determine whether distinct latent profiles of religiousness/spirituality exist for ALWH, and if so, are latent profile memberships associated with health-related quality of life (HRQoL). Latent profile analysis of religiosity identified four profiles/groups. Compared to the other three groups, higher levels of emotional well-being were found among young perinatally infected adolescents who attended religious services, but who did not pray privately, feel God's presence or identify as religious or spiritual. Social HRQoL was significantly higher among the highest overall religious/spiritual group. Understanding adolescent profiles of religiousness/spirituality on HRQoL could inform faith-based interventions. Trial registration NCT01289444.

  10. Examining Combinations of Social Physique Anxiety and Motivation Regulations Using Latent Profile Analysis

    ERIC Educational Resources Information Center

    Ullrich-French, Sarah; Cox, Anne E.; Cooper, Brittany Rhoades

    2016-01-01

    Previous research has used cluster analysis to examine how social physique anxiety (SPA) combines with motivation in physical education. This study utilized a more advanced analytic approach, latent profile analysis (LPA), to identify profiles of SPA and motivation regulations. Students in grades 9-12 (N = 298) completed questionnaires at two time…

  11. Psychological profiling of offender characteristics from crime behaviors in serial rape offences.

    PubMed

    Kocsis, Richard N; Cooksey, Ray W; Irwin, Harvey J

    2002-04-01

    Criminal psychological profiling has progressively been incorporated into police procedures despite a dearth of empirical research. Indeed, in the study of serial violent crimes for the purpose of psychological profiling, very few original, quantitative, academically reviewed studies actually exist. This article reports on the analysis of 62 incidents of serial sexual assault. The statistical procedure of multidimensional scaling was employed in the analysis of this data, which in turn produced a five-cluster model of serial rapist behavior. First, a central cluster of behaviors were identified that represent common behaviors to all patterns of serial rape. Second, four distinct outlying patterns were identified as demonstrating distinct offence styles, these being assigned the following descriptive labels brutality, intercourse, chaotic, and ritual. Furthermore, analysis of these patterns also identified distinct offender characteristics that allow for the use of empirically robust offender profiles in future serial rape investigations.

  12. Student Engagement and School Burnout in Finnish Lower-Secondary Schools: Latent Profile Analysis

    ERIC Educational Resources Information Center

    Virtanen, T. E.; Lerkkanen, M.-K.; Poikkeus, A.-M.; Kuorelahti, M.

    2018-01-01

    Self-ratings of behavioural engagement, cognitive engagement and school burnout were used in person-centred analyses to identify latent profiles among 2,485 Finnish lower-secondary school students. Three profiles were identified: high-engagement/low-burnout (40.6% of the sample), average-engagement/average-burnout (53.9%), and…

  13. Cell Painting, a high-content image-based assay for morphological profiling using multiplexed fluorescent dyes

    PubMed Central

    Bray, Mark-Anthony; Singh, Shantanu; Han, Han; Davis, Chadwick T.; Borgeson, Blake; Hartland, Cathy; Kost-Alimova, Maria; Gustafsdottir, Sigrun M.; Gibson, Christopher C.; Carpenter, Anne E.

    2016-01-01

    In morphological profiling, quantitative data are extracted from microscopy images of cells to identify biologically relevant similarities and differences among samples based on these profiles. This protocol describes the design and execution of experiments using Cell Painting, a morphological profiling assay multiplexing six fluorescent dyes imaged in five channels, to reveal eight broadly relevant cellular components or organelles. Cells are plated in multi-well plates, perturbed with the treatments to be tested, stained, fixed, and imaged on a high-throughput microscope. Then, automated image analysis software identifies individual cells and measures ~1,500 morphological features (various measures of size, shape, texture, intensity, etc.) to produce a rich profile suitable for detecting subtle phenotypes. Profiles of cell populations treated with different experimental perturbations can be compared to suit many goals, such as identifying the phenotypic impact of chemical or genetic perturbations, grouping compounds and/or genes into functional pathways, and identifying signatures of disease. Cell culture and image acquisition takes two weeks; feature extraction and data analysis take an additional 1-2 weeks. PMID:27560178

  14. Characterization and expression analysis of two cDNAs encoding Xa1 and oxysterol binding proteins in sorghum (Sorghum bicolor)

    USDA-ARS?s Scientific Manuscript database

    Using suppression subtractive hybridization (SSH) and subsequent microarray analysis, expression profiles of sorghum genes responsive to greenbug phloem-feeding were obtained and identified. Among the profiles, two cDNAs designated to MM73 and MM95 were identified to encode Xa1 (Xa1) and oxysterol ...

  15. Community Violence, Protective Factors, and Adolescent Mental Health: A Profile Analysis

    ERIC Educational Resources Information Center

    Copeland-Linder, Nikeea; Lambert, Sharon F.; Ialongo, Nicholas S.

    2010-01-01

    This study examined interrelationships among community violence exposure, protective factors, and mental health in a sample of urban, predominantly African American adolescents (N = 504). Latent Profile Analysis was conducted to identify profiles of adolescents based on a combination of community violence exposure, self-worth, parental monitoring,…

  16. 41 CFR 60-2.1 - Scope and application.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... employees are located, the organizational profile and job group analysis of the affirmative action program... program, the organizational profile and job group analysis of that program must be annotated to identify...

  17. A new method to identify the foot of continental slope based on an integrated profile analysis

    NASA Astrophysics Data System (ADS)

    Wu, Ziyin; Li, Jiabiao; Li, Shoujun; Shang, Jihong; Jin, Xiaobin

    2017-06-01

    A new method is proposed to identify automatically the foot of the continental slope (FOS) based on the integrated analysis of topographic profiles. Based on the extremum points of the second derivative and the Douglas-Peucker algorithm, it simplifies the topographic profiles, then calculates the second derivative of the original profiles and the D-P profiles. Seven steps are proposed to simplify the original profiles. Meanwhile, multiple identification methods are proposed to determine the FOS points, including gradient, water depth and second derivative values of data points, as well as the concave and convex, continuity and segmentation of the topographic profiles. This method can comprehensively and intelligently analyze the topographic profiles and their derived slopes, second derivatives and D-P profiles, based on which, it is capable to analyze the essential properties of every single data point in the profile. Furthermore, it is proposed to remove the concave points of the curve and in addition, to implement six FOS judgment criteria.

  18. Latent profile analysis of regression-based norms demonstrates relationship of compounding MS symptom burden and negative work events.

    PubMed

    Frndak, Seth E; Smerbeck, Audrey M; Irwin, Lauren N; Drake, Allison S; Kordovski, Victoria M; Kunker, Katrina A; Khan, Anjum L; Benedict, Ralph H B

    2016-10-01

    We endeavored to clarify how distinct co-occurring symptoms relate to the presence of negative work events in employed multiple sclerosis (MS) patients. Latent profile analysis (LPA) was utilized to elucidate common disability patterns by isolating patient subpopulations. Samples of 272 employed MS patients and 209 healthy controls (HC) were administered neuroperformance tests of ambulation, hand dexterity, processing speed, and memory. Regression-based norms were created from the HC sample. LPA identified latent profiles using the regression-based z-scores. Finally, multinomial logistic regression tested for negative work event differences among the latent profiles. Four profiles were identified via LPA: a common profile (55%) characterized by slightly below average performance in all domains, a broadly low-performing profile (18%), a poor motor abilities profile with average cognition (17%), and a generally high-functioning profile (9%). Multinomial regression analysis revealed that the uniformly low-performing profile demonstrated a higher likelihood of reported negative work events. Employed MS patients with co-occurring motor, memory and processing speed impairments were most likely to report a negative work event, classifying them as uniquely at risk for job loss.

  19. Beyond the average marital communication: Latent profiles of the observed interactions among Chinese newlywed couples.

    PubMed

    Cao, Hongjian; Fang, Xiaoyi; Fine, Mark A; Ju, Xiaoyan; Lan, Jing; Liu, Xuanwen

    2015-12-01

    Employing a multicontext observational design, using a person-centered approach, and treating the marital dyad as the unit of analysis, this study examined the within-couple communication patterning of 144 Chinese newlywed couples and its association with relationship satisfaction. Latent profile analysis consistently revealed 3 profiles of spouses' interactive behaviors across contexts differing in both topic nature (i.e., problem-solving vs. social support) and initiator (i.e., husbands vs. wives): (a) traditionally undemonstrative profile, (b) emotionally quarrelling profile, and (c) warmly supportive profile. The prevalence of communication profiles changed markedly with the nature of the discussion topic and the topic initiator. Further, using latent class analysis, we classified couples into subgroups based on their identified profile memberships across contexts (i.e., consistency of interaction mode across contexts). Three classes were identified: (a) consistently quarrelling class, (b) consistently supportive class, and (c) modestly traditional class. Both the consistently supportive class and the modestly traditional class reported significantly higher levels of marital satisfaction than did the consistently quarrelling class. (c) 2015 APA, all rights reserved).

  20. Three subgroups of pain profiles identified in 227 women with arthritis: a latent class analysis.

    PubMed

    de Luca, Katie; Parkinson, Lynne; Downie, Aron; Blyth, Fiona; Byles, Julie

    2017-03-01

    The objectives were to identify subgroups of women with arthritis based upon the multi-dimensional nature of their pain experience and to compare health and socio-demographic variables between subgroups. A latent class analysis of 227 women with self-reported arthritis was used to identify clusters of women based upon the sensory, affective, and cognitive dimensions of the pain experience. Multivariate multinomial logistic regression analysis was used to determine the relationship between cluster membership and health and sociodemographic characteristics. A three-class cluster model was most parsimonious. 39.5 % of women had a unidimensional pain profile; 38.6 % of women had moderate multidimensional pain profile that included additional pain symptomatology such as sensory qualities and pain catastrophizing; and 21.9 % of women had severe multidimensional pain profile that included prominent pain symptomatology such as sensory and affective qualities of pain, pain catastrophizing, and neuropathic pain. Women with severe multidimensional pain profile have a 30.5 % higher risk of poorer quality of life and a 7.3 % higher risk of suffering depression, and women with moderate multidimensional pain profile have a 6.4 % higher risk of poorer quality of life when compared to women with unidimensional pain. This study identified three distinct subgroups of pain profiles in older women with arthritis. Women had very different experiences of pain, and cluster membership impacted significantly on health-related quality of life. These preliminary findings provide a stronger understanding of profiles of pain and may contribute to the development of tailored treatment options in arthritis.

  1. Drafting. Occupational Competency Analysis Profile.

    ERIC Educational Resources Information Center

    Ohio State Univ., Columbus. Vocational Instructional Materials Lab.

    This Drafting Occupational Competency Analysis Profile (OCAP) is one of a series of competency lists, verified by expert workers, that have evolved from a modified DACUM (Developing a Curriculum) job analysis process involving business, industry, labor, and community agency representatives from throughout Ohio. This OCAP identifies the…

  2. Accounting. Occupational Competency Analysis Profile.

    ERIC Educational Resources Information Center

    Ohio State Univ., Columbus. Vocational Instructional Materials Lab.

    This Accounting Occupational Competency Analysis Profile (OCAP) is one of a series of competency lists, verified by expert workers, that have evolved from a modified DACUM (Developing a Curriculum) job analysis process involving business, industry, labor, and community agency representatives from throughout Ohio. This OCAP identifies the…

  3. Quality Control of True Height Profiles Obtained Automatically from Digital Ionograms.

    DTIC Science & Technology

    1982-05-01

    nece.,ssary and Identify by block number) Ionosphere Digisonde Electron Density Profile Ionogram Autoscaling ARTIST 2 , ABSTRACT (Continue on reverae...analysis technique currently used with the ionogram traces scaled automatically by the ARTIST software [Reinisch and Huang, 1983; Reinisch et al...19841, and the generalized polynomial analysis technique POLAN [Titheridge, 1985], using the same ARTIST -identified ionogram traces. 2. To determine how

  4. Animal Management Technician. Occupational Competency Analysis Profile.

    ERIC Educational Resources Information Center

    Ohio State Univ., Columbus. Vocational Instructional Materials Lab.

    This Occupational Competency Analysis Profile (OCAP) for animal management technician (AMT) is a competency list verified by expert workers that evolved from a job analysis. It identifies occupational, academic, and employability competencies needed to enter the occupation; lists and clusters them into broader units; and details the competency…

  5. General Marketing. Occupational Competency Analysis Profile.

    ERIC Educational Resources Information Center

    Ohio State Univ., Columbus. Vocational Instructional Materials Lab.

    This General Marketing Occupational Competency Analysis Profile (OCAP) is one of a series of competency lists, verified by expert workers, that have evolved from a modified DACUM (Developing a Curriculum) job analysis process involving business, industry, labor, and community agency representatives from throughout Ohio. This OCAP identifies the…

  6. Community violence, protective factors, and adolescent mental health: a profile analysis.

    PubMed

    Copeland-Linder, Nikeea; Lambert, Sharon F; Ialongo, Nicholas S

    2010-01-01

    This study examined interrelationships among community violence exposure, protective factors, and mental health in a sample of urban, predominantly African American adolescents (N = 504). Latent Profile Analysis was conducted to identify profiles of adolescents based on a combination of community violence exposure, self-worth, parental monitoring, and parental involvement and to examine whether these profiles differentially predict adolescents' depressive symptoms and aggressive behavior. Three classes were identified-a vulnerable class, a moderate risk/medium protection class, and a moderate risk/high protection class. The classes differentially predicted depressive symptoms but not aggressive behavior for boys and girls. The class with the highest community violence exposure also had the lowest self-worth.

  7. Nurse Aide. Occupational Competency Analysis Profile.

    ERIC Educational Resources Information Center

    Ohio State Univ., Columbus. Vocational Instructional Materials Lab.

    This Occupational Competency Analysis Profile (OCAP) for nurse aide (NA) is a competency list verified by expert workers that evolved from a job analysis. It identifies occupational, academic, and employability competencies needed to enter the occupation; lists and clusters them into broader units; and details the competency builders needed to…

  8. Coping flexibility and eudaimonic well-being in university students.

    PubMed

    Freire, Carlos; Ferradás, María Del Mar; Núñez, José Carlos; Valle, Antonio

    2018-05-31

    Despite the growing interest in the relationship between coping strategies and eudaimonic well-being, few studies have examined this issue from the perspective of coping flexibility. Therefore, the present study aimed to: (1) identify approach coping profiles in the university context and (2) analyze the differences between these profiles in terms of eudaimonic well-being. A prospective ex post facto design was used and 1,402 university students were selected through convenience sampling. Data were collected using validated self-reported instruments. A latent profile analysis was conducted to identify the participants' coping profiles. The relationship between profiles and eudaimonic well-being was determined using a multivariate analysis of covariance (MANCOVA), with gender, age, and university degree as covariates. Six student profiles were identified based on the degree to which they combined positive reappraisal, support seeking, and planning strategies. The profiles that involved the use of these three strategies to a greater extent experienced more eudaimonic well-being, and vice versa. To analyze the impact of coping on eudaimonic well-being, it is necessary to consider students' ability to combine different approach coping strategies. © 2018 Scandinavian Psychological Associations and John Wiley & Sons Ltd.

  9. Electronics. Occupational Competency Analysis Profile.

    ERIC Educational Resources Information Center

    Ohio State Univ., Columbus. Vocational Instructional Materials Lab.

    This Occupational Competency Analysis Profile (OCAP) contains a competency list verified by expert workers and developed through a modified DACUM (Developing a Curriculum) involving business, industry, labor, and community agency representatives from Ohio. This OCAP identifies the occupational, academic, and employability skills (competencies)…

  10. Masonry. Occupational Competency Analysis Profile.

    ERIC Educational Resources Information Center

    Ohio State Univ., Columbus. Vocational Instructional Materials Lab.

    This Occupational Competency Analysis Profile (OCAP) for masonry occupations contains a competency list verified by expert workers and developed through a modified DACUM (Developing a Curriculum) involving business, industry, labor, and community agency representatives from Ohio. This OCAP identifies the occupational, academic, and employability…

  11. Horticulture. Occupational Competency Analysis Profile.

    ERIC Educational Resources Information Center

    Ohio State Univ., Columbus. Vocational Instructional Materials Lab.

    This Occupational Competency Analysis Profile (OCAP) contains a competency list verified by expert workers and developed through a modified DACUM (Developing a Curriculum) involving business, industry, labor, and community agency representatives from Ohio. This OCAP identifies the occupational, academic, and employability skills (competencies)…

  12. Carpentry. Occupational Competency Analysis Profile.

    ERIC Educational Resources Information Center

    Ohio State Univ., Columbus. Vocational Instructional Materials Lab.

    This Occupational Competency Analysis Profile (OCAP) contains a competency list verified by expert workers and developed through a modified DACUM (Developing a Curriculum) involving business, industry, labor, and community agency representatives from Ohio. This OCAP identifies the occupational, academic, and employability skills (competencies)…

  13. Environmental Management. Occupational Competency Analysis Profile.

    ERIC Educational Resources Information Center

    Ohio State Univ., Columbus. Vocational Instructional Materials Lab.

    This Occupational Competency Analysis Profile (OCAP) contains a competency list verified by expert workers and developed through a modified DACUM (Developing a Curriculum) involving business, industry, labor, and community agency representatives from Ohio. This OCAP identifies the occupational, academic, and employability skills (competencies)…

  14. Marketing Management. Occupational Competency Analysis Profile.

    ERIC Educational Resources Information Center

    Ohio State Univ., Columbus. Vocational Instructional Materials Lab.

    This Occupational Competency Analysis Profile (OCAP) contains a competency list verified by expert workers and developed through a modified DACUM (Developing a Curriculum) involving business, industry, labor, and community agency representatives from Ohio. This OCAP identifies the occupational, academic, and employability skills (competencies)…

  15. Agriculture Products Processing. Occupational Competency Analysis Profile.

    ERIC Educational Resources Information Center

    Ohio State Univ., Columbus. Vocational Instructional Materials Lab.

    This Occupational Competency Analysis Profile (OCAP) contains a competency list verified by expert workers and developed through a modified DACUM (Developing a Curriculum) involving business, industry, labor, and community agency representatives from Ohio. This OCAP identifies the occupational, academic, and employability skills (competencies)…

  16. Integrated analysis of long noncoding RNA and mRNA expression profile in children with obesity by microarray analysis.

    PubMed

    Liu, Yuesheng; Ji, Yuqiang; Li, Min; Wang, Min; Yi, Xiaoqing; Yin, Chunyan; Wang, Sisi; Zhang, Meizhen; Zhao, Zhao; Xiao, Yanfeng

    2018-06-08

    Long noncoding RNAs (lncRNAs) have an important role in adipose tissue function and energy metabolism homeostasis, and abnormalities may lead to obesity. To investigate whether lncRNAs are involved in childhood obesity, we investigated the differential expression profile of lncRNAs in obese children compared with non-obese children. A total number of 1268 differentially expressed lncRNAs and 1085 differentially expressed mRNAs were identified. Gene Ontology (GO) and pathway analysis revealed that these lncRNAs were involved in varied biological processes, including the inflammatory response, lipid metabolic process, osteoclast differentiation and fatty acid metabolism. In addition, the lncRNA-mRNA co-expression network and the protein-protein interaction (PPI) network were constructed to identify hub regulatory lncRNAs and genes based on the microarray expression profiles. This study for the first time identifies an expression profile of differentially expressed lncRNAs in obese children and indicated hub lncRNA RP11-20G13.3 attenuated adipogenesis of preadipocytes, which is conducive to the search for new diagnostic and therapeutic strategies of childhood obesity.

  17. Graphic Communications--Commercial Photography. Ohio's Competency Analysis Profile.

    ERIC Educational Resources Information Center

    Ohio State Univ., Columbus. Vocational Instructional Materials Lab.

    This Ohio Competency Analysis Profile (OCAP), derived from a modified Developing a Curriculum (DACUM) process, is a current comprehensive and verified employer competency program list for graphic communications--commercial photography. Each unit (with or without subunits) contains competencies and competency builders that identify the…

  18. Machine Trades. Ohio's Competency Analysis Profile.

    ERIC Educational Resources Information Center

    Ohio State Univ., Columbus. Vocational Instructional Materials Lab.

    This Ohio Competency Analysis Profile (OCAP), derived from a modified Developing a Curriculum (DACUM) process, is a current comprehensive and verified employer competency program list for machine trades. Each unit (with or without subunits) contains competencies and competency builders that identify the occupational, academic, and employability…

  19. Welding. Ohio's Competency Analysis Profile.

    ERIC Educational Resources Information Center

    Ohio State Univ., Columbus. Vocational Instructional Materials Lab.

    This Ohio Competency Analysis Profile (OCAP), derived from a modified Developing a Curriculum (DACUM) process, is a comprehensive and verified employer competency list for a welding program. It contains units (with or without subunits), competencies, and competency builders that identify the occupational, academic, and employability skills needed…

  20. Dairy Producer. Ohio's Competency Analysis Profile.

    ERIC Educational Resources Information Center

    Ohio State Univ., Columbus. Vocational Instructional Materials Lab.

    This Ohio Competency Analysis Profile (OCAP), derived from a modified Developing a Curriculum (DACUM) process, is a current comprehensive and verified employer competency program list for dairy producers. Each unit (with or without subunits) contains competencies and competency builders that identify the occupational, academic, and employability…

  1. Law Enforcement. Ohio's Competency Analysis Profile.

    ERIC Educational Resources Information Center

    Ohio State Univ., Columbus. Vocational Instructional Materials Lab.

    This Ohio Competency Analysis Profile (OCAP), derived from a modified Developing a Curriculum (DACUM) process, is a current comprehensive and verified employer competency program list for law enforcement. Each unit (with or without subunits) contains competencies and competency builders that identify the occupational, academic, and employability…

  2. Poultry Producer. Ohio's Competency Analysis Profile.

    ERIC Educational Resources Information Center

    Ohio State Univ., Columbus. Vocational Instructional Materials Lab.

    This Ohio Competency Analysis Profile (OCAP), derived from a modified Developing a Curriculum (DACUM) process, is a comprehensive and verified employer competency list for a poultry producer program. It contains units (with or without subunits), competencies, and competency builders that identify the occupational, academic, and employability…

  3. Swine Producer. Ohio's Competency Analysis Profile.

    ERIC Educational Resources Information Center

    Ohio State Univ., Columbus. Vocational Instructional Materials Lab.

    This Ohio Competency Analysis Profile (OCAP), derived from a modified Developing a Curriculum (DACUM) process, is a comprehensive and verified employer competency list for a swine producer program. It contains units (with or without subunits), competencies, and competency builders that identify the occupational, academic, and employability skills…

  4. Diesel Mechanics. Ohio's Competency Analysis Profile.

    ERIC Educational Resources Information Center

    Ohio State Univ., Columbus. Vocational Instructional Materials Lab.

    This Ohio Competency Analysis Profile (OCAP), derived from a modified Developing a Curriculum (DACUM) process, is a current comprehensive and verified employer competency program list for diesel mechanics. Each unit (with or without subunits) contains competencies and competency builders that identify the occupational, academic, and employability…

  5. Building and Property Maintenance. Occupational Competency Analysis Profile.

    ERIC Educational Resources Information Center

    Ohio State Univ., Columbus. Vocational Instructional Materials Lab.

    This Occupational Competency Analysis Profile (OCAP) contains a competency list verified by expert workers and developed through a modified DACUM (Developing a Curriculum) involving business, industry, labor, and community agency representatives from Ohio. This OCAP identifies the occupational, academic, and employability skills (competencies)…

  6. Graphic Communications. Occupational Competency Analysis Profile.

    ERIC Educational Resources Information Center

    Ohio State Univ., Columbus. Vocational Instructional Materials Lab.

    This Occupational Competency Analysis Profile (OCAP), which is one of a series of OCAPs developed to identify the skills that Ohio employers deem necessary to entering a given occupation/occupational area, lists the occupational, academic, and employability skills required of individuals entering graphic communications occupations. The…

  7. Functional Status, Quality of Life, and Costs Associated With Fibromyalgia Subgroups: A Latent Profile Analysis.

    PubMed

    Luciano, Juan V; Forero, Carlos G; Cerdà-Lafont, Marta; Peñarrubia-María, María Teresa; Fernández-Vergel, Rita; Cuesta-Vargas, Antonio I; Ruíz, José M; Rozadilla-Sacanell, Antoni; Sirvent-Alierta, Elena; Santo-Panero, Pilar; García-Campayo, Javier; Serrano-Blanco, Antoni; Pérez-Aranda, Adrián; Rubio-Valera, María

    2016-10-01

    Although fibromyalgia syndrome (FM) is considered a heterogeneous condition, there is no generally accepted subgroup typology. We used hierarchical cluster analysis and latent profile analysis to replicate Giesecke's classification in Spanish FM patients. The second aim was to examine whether the subgroups differed in sociodemographic characteristics, functional status, quality of life, and in direct and indirect costs. A total of 160 FM patients completed the following measures for cluster derivation: the Center for Epidemiological Studies-Depression Scale, the Trait Anxiety Inventory, the Pain Catastrophizing Scale, and the Control over Pain subscale. Pain threshold was measured with a sphygmomanometer. In addition, the Fibromyalgia Impact Questionnaire-Revised, the EuroQoL-5D-3L, and the Client Service Receipt Inventory were administered for cluster validation. Two distinct clusters were identified using hierarchical cluster analysis ("hypersensitive" group, 69.8% and "functional" group, 30.2%). In contrast, the latent profile analysis goodness-of-fit indices supported the existence of 3 FM patient profiles: (1) a "functional" profile (28.1%) defined as moderate tenderness, distress, and pain catastrophizing; (2) a "dysfunctional" profile (45.6%) defined by elevated tenderness, distress, and pain catastrophizing; and (3) a "highly dysfunctional and distressed" profile (26.3%) characterized by elevated tenderness and extremely high distress and catastrophizing. We did not find significant differences in sociodemographic characteristics between the 2 clusters or among the 3 profiles. The functional profile was associated with less impairment, greater quality of life, and lower health care costs. We identified 3 distinct profiles which accounted for the heterogeneity of FM patients. Our findings might help to design tailored interventions for FM patients.

  8. Profiles of Nature Exposure and Outdoor Activities Associated With Occupational Well-Being Among Employees

    PubMed Central

    Hyvönen, Katriina; Törnroos, Kaisa; Salonen, Kirsi; Korpela, Kalevi; Feldt, Taru; Kinnunen, Ulla

    2018-01-01

    This research addresses the profiles of nature exposure and outdoor activities in nature among Finnish employees (N = 783). The profiles were formed on the bases of nature exposure at work and the frequency and type of outdoor activities in nature engaged in during leisure time. The profiles were investigated in relation to work engagement and burnout. The latent profile analysis identified a five-class solution as the best model: High exposure (8%), Versatile exposure (22%), Unilateral exposure (38%), Average exposure (13%), and Low exposure (19%). An Analysis of Covariance (ANCOVA) was conducted for each well-being outcome in order to evaluate how the identified profiles related to occupational well-being. Participants with a High, Versatile, or Unilateral exposure profile reported significantly higher work engagement in the dimensions of vigor and dedication than did the participants with a Low exposure profile. The participants with the High exposure profile also reported lower burnout in the dimensions of cynicism and professional inadequacy than the participants with the Low exposure profile. Nature exposure during the workday and leisure time is an under researched but important aspect in promoting occupational well-being. PMID:29867699

  9. Mathematics. Ohio's Competency Analysis Profile.

    ERIC Educational Resources Information Center

    Ohio State Univ., Columbus. Vocational Instructional Materials Lab.

    This competency analysis profile contains eight lists of mathematics skills that have been identified by employers and verified by math-certified instructors as being core competencies for eight groups of occupational areas. Each list is organized into subsections dealing with the following: numbers and number relations, measurement, data analysis…

  10. Precision Machining Technologies. Occupational Competency Analysis Profile.

    ERIC Educational Resources Information Center

    Ohio State Univ., Columbus. Vocational Instructional Materials Lab.

    This Occupational Competency Analysis Profile (OCAP), which is one of a series of OCAPs developed to identify the skills that Ohio employers deem necessary to entering a given occupation/occupational area, lists the occupational, academic, and employability skills required of individuals entering the occupation of precision machinist. The…

  11. Welding. Occupational Competency Analysis Profile.

    ERIC Educational Resources Information Center

    Ohio State Univ., Columbus. Vocational Instructional Materials Lab.

    This Occupational Competency Analysis Profile (OCAP), which is one of a series of OCAPs developed to identify the skills that Ohio employers deem necessary to entering a given occupation/occupational area, lists the occupational, academic, and employability skills required of individuals entering the occupation of welder. The introduction explains…

  12. A Latent Profile Analysis of University Students' Self-Regulated Learning Strategies

    ERIC Educational Resources Information Center

    Ning, Hoi Kwan; Downing, Kevin

    2015-01-01

    Based on self-reported cognitive, metacognitive, and behavioural strategy measures obtained from 828 final-year students from a university in Hong Kong, latent profile analysis (LPA) identified four distinct types of students with differential self-regulated learning strategy orientations: "competent self-regulated learners",…

  13. Heating, Ventilation, Air-Conditioning, and Refrigeration. Occupational Competency Analysis Profile.

    ERIC Educational Resources Information Center

    Ohio State Univ., Columbus. Vocational Instructional Materials Lab.

    This Occupational Competency Analysis Profile (OCAP) contains a competency list verified by expert workers and developed through a modified DACUM (Developing a Curriculum) involving business, industry, labor, and community agency representatives from Ohio. This OCAP identifies the occupational, academic, and employability skills (competencies)…

  14. 41 CFR 60-2.1 - Scope and application.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... action program other than by establishment, the contractor may reach agreement with OFCCP on the... employees are located, the organizational profile and job group analysis of the affirmative action program... program, the organizational profile and job group analysis of that program must be annotated to identify...

  15. Integrated analysis of rice transcriptomic and metabolomic responses to elevated night temperatures identifies sensitivity- and tolerance-related profiles.

    PubMed

    Glaubitz, Ulrike; Li, Xia; Schaedel, Sandra; Erban, Alexander; Sulpice, Ronan; Kopka, Joachim; Hincha, Dirk K; Zuther, Ellen

    2017-01-01

    Transcript and metabolite profiling were performed on leaves from six rice cultivars under high night temperature (HNT) condition. Six genes were identified as central for HNT response encoding proteins involved in transcription regulation, signal transduction, protein-protein interactions, jasmonate response and the biosynthesis of secondary metabolites. Sensitive cultivars showed specific changes in transcript abundance including abiotic stress responses, changes of cell wall-related genes, of ABA signaling and secondary metabolism. Additionally, metabolite profiles revealed a highly activated TCA cycle under HNT and concomitantly increased levels in pathways branching off that could be corroborated by enzyme activity measurements. Integrated data analysis using clustering based on one-dimensional self-organizing maps identified two profiles highly correlated with HNT sensitivity. The sensitivity profile included genes of the functional bins abiotic stress, hormone metabolism, cell wall, signaling, redox state, transcription factors, secondary metabolites and defence genes. In the tolerance profile, similar bins were affected with slight differences in hormone metabolism and transcription factor responses. Metabolites of the two profiles revealed involvement of GABA signaling, thus providing a link to the TCA cycle status in sensitive cultivars and of myo-inositol as precursor for inositol phosphates linking jasmonate signaling to the HNT response specifically in tolerant cultivars. © 2016 John Wiley & Sons Ltd.

  16. Viscous-Inviscid Interactions over Transonic Tangentially Blown Airfoils.

    DTIC Science & Technology

    1982-04-01

    analysis, computational fluid dynamics, asymptotic analysis. 20. RSTRACT fContinue on reverse side if neceseery and Identify by block number) A viscous...development of boundary layer and wall jet velocity profiles over airfoil. Profiles for upper surface shown in upper part of figure; lower surface values in...lower part of figure .......................... 33 6. Streanwise development of velocity profiles in wake for M = 0.75, a = 1, CJ = 0.055

  17. The Fukuyama Profile: A Vocational Guidance Philosophy and Instrument.

    ERIC Educational Resources Information Center

    Inaba, Lawrence A.

    1990-01-01

    Describes the Fukuyama Profile, which helps identify students' ability to choose an occupation through a process of self-analysis, job analysis, occupational tryouts, and matching of personality and interests with appropriate occupations. Gives examples of its use in Hawaii, New York, Germany, France, Switzerland, Japan, England, and the Soviet…

  18. Natural Resources. Ohio's Competency Analysis Profile. Forest Industry Worker. Resource Conservation.

    ERIC Educational Resources Information Center

    Ohio State Univ., Columbus. Vocational Instructional Materials Lab.

    This competency analysis profile lists 155 competencies that have been identified by employers as core competencies for inclusion in programs to train forest industry and resource conservation workers. The core competencies are organized into 10 units dealing the following: general safety precautions, natural resource industry operations, soil…

  19. Fertilizer/Chemical Sales and Service Worker. Ohio's Competency Analysis Profile.

    ERIC Educational Resources Information Center

    Ohio State Univ., Columbus. Vocational Instructional Materials Lab.

    This Ohio Competency Analysis Profile (OCAP), derived from a modified Developing a Curriculum (DACUM) process, is a current comprehensive and verified employer competency program list for fertilizer/chemical sales and service workers. Each unit (with or without subunits) contains competencies and competency builders that identify the occupational,…

  20. Multidimensional profiles of health locus of control in Hispanic Americans

    PubMed Central

    Champagne, Brian R; Fox, Rina S; Mills, Sarah D; Sadler, Georgia Robins; Malcarne, Vanessa L

    2016-01-01

    Latent profile analysis identified health locus of control profiles among 436 Hispanic Americans who completed the Multidimensional Health Locus of Control scales. Results revealed four profiles: Internally Oriented-Weak, -Moderate, -Strong, and Externally Oriented. The profile groups were compared on sociocultural and demographic characteristics, health beliefs and behaviors, and physical and mental health outcomes. The Internally Oriented-Strong group had less cancer fatalism, religiosity, and equity health attributions, and more alcohol consumption than the other three groups; the Externally Oriented group had stronger equity health attributions and less alcohol consumption. Deriving multidimensional health locus of control profiles through latent profile analysis allows examination of the relationships of health locus of control subtypes to health variables. PMID:25855212

  1. Metabolite profiling and associated gene expression reveal two metabolic shifts during the seed-to-seedling transition in Arabidopsis thaliana.

    PubMed

    Silva, Anderson Tadeu; Ligterink, Wilco; Hilhorst, Henk W M

    2017-11-01

    Metabolic and transcriptomic correlation analysis identified two distinctive profiles involved in the metabolic preparation for seed germination and seedling establishment, respectively. Transcripts were identified that may control metabolic fluxes. The transition from a quiescent metabolic state (dry seed) to the active state of a vigorous seedling is crucial in the plant's life cycle. We analysed this complex physiological trait by measuring the changes in primary metabolism that occur during the transition in order to determine which metabolic networks are operational. The transition involves several developmental stages from seed germination to seedling establishment, i.e. between imbibition of the mature dry seed and opening of the cotyledons, the final stage of seedling establishment. We hypothesized that the advancement of growth is associated with certain signature metabolite profiles. Metabolite-metabolite correlation analysis underlined two specific profiles which appear to be involved in the metabolic preparation for seed germination and efficient seedling establishment, respectively. Metabolite profiles were also compared to transcript profiles and although transcriptional changes did not always equate to a proportional metabolic response, in depth correlation analysis identified several transcripts that may directly influence the flux through metabolic pathways during the seed-to-seedling transition. This correlation analysis also pinpointed metabolic pathways which are significant for the seed-to-seedling transition, and metabolite contents that appeared to be controlled directly by transcript abundance. This global view of the transcriptional and metabolic changes during the seed-to-seedling transition in Arabidopsis opens up new perspectives for understanding the complex regulatory mechanism underlying this transition.

  2. Dynamic transcriptomic analysis in hircine longissimus dorsi muscle from fetal to neonatal development stages.

    PubMed

    Zhan, Siyuan; Zhao, Wei; Song, Tianzeng; Dong, Yao; Guo, Jiazhong; Cao, Jiaxue; Zhong, Tao; Wang, Linjie; Li, Li; Zhang, Hongping

    2018-01-01

    Muscle growth and development from fetal to neonatal stages consist of a series of delicately regulated and orchestrated changes in expression of genes. In this study, we performed whole transcriptome profiling based on RNA-Seq of caprine longissimus dorsi muscle tissue obtained from prenatal stages (days 45, 60, and 105 of gestation) and neonatal stage (the 3-day-old newborn) to identify genes that are differentially expressed and investigate their temporal expression profiles. A total of 3276 differentially expressed genes (DEGs) were identified (Q value < 0.01). Time-series expression profile clustering analysis indicated that DEGs were significantly clustered into eight clusters which can be divided into two classes (Q value < 0.05), class I profiles with downregulated patterns and class II profiles with upregulated patterns. Based on cluster analysis, GO enrichment analysis found that 75, 25, and 8 terms to be significantly enriched in biological process (BP), cellular component (CC), and molecular function (MF) categories in class I profiles, while 35, 21, and 8 terms to be significantly enriched in BP, CC, and MF in class II profiles. KEGG pathway analysis revealed that DEGs from class I profiles were significantly enriched in 22 pathways and the most enriched pathway was Rap1 signaling pathway. DEGs from class II profiles were significantly enriched in 17 pathways and the mainly enriched pathway was AMPK signaling pathway. Finally, six selected DEGs from our sequencing results were confirmed by qPCR. Our study provides a comprehensive understanding of the molecular mechanisms during goat skeletal muscle development from fetal to neonatal stages and valuable information for future studies of muscle development in goats.

  3. Profiles of Social and Coping Resources in Families of Children with Autism Spectrum Disorder: Relations to Parent and Child Outcomes

    ERIC Educational Resources Information Center

    Zaidman-Zait, Anat; Mirenda, Pat; Szatmari, Peter; Duku, Eric; Smith, Isabel M.; Vaillancourt, Tracy; Volden, Joanne; Waddell, Charlotte; Bennett, Teresa; Zwaigenbaum, Lonnie; Elsabaggh, Mayada; Georgiades, Stelios

    2018-01-01

    This study described empirically derived profiles of parents' personal and social coping resources in a sample of 207 families of children diagnosed with autism spectrum disorder. Latent Profile Analysis identified four family profiles based on socieoeconomic risk, coping strategy utilization, family functioning, available social supports, and…

  4. Profiles of childhood adversities in pathological gamblers - A latent class analysis.

    PubMed

    Lotzin, Annett; Ulas, Mehmet; Buth, Sven; Milin, Sascha; Kalke, Jens; Schäfer, Ingo

    2018-06-01

    Despite of high rates of adverse childhood experiences (ACEs) in pathological gamblers, researchers have rarely studied which types of ACEs often co-occur and how these profiles of ACEs are related to current psychopathology. We aimed to identify profiles of ACEs in pathological gamblers and examined how these profiles were related to gambling-related characteristics and current general psychopathology. In 329 current or lifetime pathological gamblers, diagnosed with the Composite Diagnostic Interview for DSM-IV, 10 types of ACEs were measured using the Adverse Childhood Experiences Questionnaire. Global psychopathology was assessed using the Symptom Checklist SCL-27. ACE profiles were identified using latent class analysis. Differences between ACE profiles in gambling-related characteristics and global psychopathology were analyzed using MANOVA. We found that four out of five gamblers (n=257, 78.1%) reported at least one ACE. Four distinct ACE profiles were identified: 'Low ACE', 'High ACE', 'Physical and emotional abuse', and 'Neglect'. The number of the fulfilled pathological gambling criteria and the severity of current global psychopathology differed between the ACE profiles: Gamblers with a 'High ACE' profile fulfilled more pathological gambling criteria and showed a more severe current psychopathology than gamblers of the 'Low ACE' profile. Gamblers with a 'Physical and emotional abuse' or an 'Emotion neglect' profile showed an intermediate severity of psychopathology. Our findings indicate that four different ACE profiles can be distinguished in pathological gamblers that differed in their gambling-related characteristics and current psychopathology. Systematic assessment of profiles of ACEs in pathological gamblers may inform about the severity of current global psychopathology that might be important to be addressed in addition to gambling-specific treatment. Copyright © 2018 Elsevier Ltd. All rights reserved.

  5. Latino Adolescent Educational Affiliation Profiles

    ERIC Educational Resources Information Center

    Gonzalez, Laura M.; Cavanaugh, Alyson M.; Taylor, Laura K.; Stein, Gabriela L.; Mayton, Heather N.

    2017-01-01

    Supporting postsecondary access for Latino adolescents is important due to the size of the population and mixed evidence of progress. In order to better understand the college-going and school belonging attitudes of Latinos, we used an exploratory latent profile analysis to identify the "educational affiliation" profiles present in a…

  6. Protein profiles associated with survival in lung adenocarcinoma

    PubMed Central

    Chen, Guoan; Gharib, Tarek G; Wang, Hong; Huang, Chiang-Ching; Kuick, Rork; Thomas, Dafydd G.; Shedden, Kerby A.; Misek, David E.; Taylor, Jeremy M. G.; Giordano, Thomas J.; Kardia, Sharon L. R.; Iannettoni, Mark D.; Yee, John; Hogg, Philip J.; Orringer, Mark B.; Hanash, Samir M.; Beer, David G.

    2003-01-01

    Morphologic assessment of lung tumors is informative but insufficient to adequately predict patient outcome. We previously identified transcriptional profiles that predict patient survival, and here we identify proteins associated with patient survival in lung adenocarcinoma. A total of 682 individual protein spots were quantified in 90 lung adenocarcinomas by using quantitative two-dimensional polyacrylamide gel electrophoresis analysis. A leave-one-out cross-validation procedure using the top 20 survival-associated proteins identified by Cox modeling indicated that protein profiles as a whole can predict survival in stage I tumor patients (P = 0.01). Thirty-three of 46 survival-associated proteins were identified by using mass spectrometry. Expression of 12 candidate proteins was confirmed as tumor-derived with immunohistochemical analysis and tissue microarrays. Oligonucleotide microarray results from both the same tumors and from an independent study showed mRNAs associated with survival for 11 of 27 encoded genes. Combined analysis of protein and mRNA data revealed 11 components of the glycolysis pathway as associated with poor survival. Among these candidates, phosphoglycerate kinase 1 was associated with survival in the protein study, in both mRNA studies and in an independent validation set of 117 adenocarcinomas and squamous lung tumors using tissue microarrays. Elevated levels of phosphoglycerate kinase 1 in the serum were also significantly correlated with poor outcome in a validation set of 107 patients with lung adenocarcinomas using ELISA analysis. These studies identify new prognostic biomarkers and indicate that protein expression profiles can predict the outcome of patients with early-stage lung cancer. PMID:14573703

  7. Utilization of ACL Injury Biomechanical and Neuromuscular Risk Profile Analysis to Determine the Effectiveness of Neuromuscular Training.

    PubMed

    Hewett, Timothy E; Ford, Kevin R; Xu, Yingying Y; Khoury, Jane; Myer, Gregory D

    2016-12-01

    The widespread use of anterior cruciate ligament (ACL) injury prevention interventions has not been effective in reducing the injury incidence among female athletes who participate in high-risk sports. The purpose of this study was to determine if biomechanical and neuromuscular factors that contribute to the knee abduction moment (KAM), a predictor of future ACL injuries, could be used to characterize athletes by a distinct factor. Specifically, we hypothesized that a priori selected biomechanical and neuromuscular factors would characterize participants into distinct at-risk profiles. Controlled laboratory study. A total of 624 female athletes who participated in jumping, cutting, and pivoting sports underwent testing before their competitive season. During testing, athletes performed drop-jump tasks from which biomechanical measures were captured. Using data from these tasks, latent profile analysis (LPA) was conducted to identify distinct profiles based on preintervention biomechanical and neuromuscular measures. As a validation, we examined whether the profile membership was a significant predictor of the KAM. LPA using 6 preintervention biomechanical measures selected a priori resulted in 3 distinct profiles, including a low (profile 1), moderate (profile 2), and high (profile 3) risk for ACL injuries. Athletes with profiles 2 and 3 had a significantly higher KAM compared with those with profile 1 (P < .05). This is the first study to use LPA of biomechanical landing data to create ACL injury risk profiles. Three distinct risk groups were identified based on differences in the peak KAM. These findings demonstrate the existence of discernable groups of athletes that may benefit from injury prevention interventions. ClinicalTrials.gov NCT identifier: NCT01034527. © 2016 The Author(s).

  8. Tensor decomposition-based and principal-component-analysis-based unsupervised feature extraction applied to the gene expression and methylation profiles in the brains of social insects with multiple castes.

    PubMed

    Taguchi, Y-H

    2018-05-08

    Even though coexistence of multiple phenotypes sharing the same genomic background is interesting, it remains incompletely understood. Epigenomic profiles may represent key factors, with unknown contributions to the development of multiple phenotypes, and social-insect castes are a good model for elucidation of the underlying mechanisms. Nonetheless, previous studies have failed to identify genes associated with aberrant gene expression and methylation profiles because of the lack of suitable methodology that can address this problem properly. A recently proposed principal component analysis (PCA)-based and tensor decomposition (TD)-based unsupervised feature extraction (FE) can solve this problem because these two approaches can deal with gene expression and methylation profiles even when a small number of samples is available. PCA-based and TD-based unsupervised FE methods were applied to the analysis of gene expression and methylation profiles in the brains of two social insects, Polistes canadensis and Dinoponera quadriceps. Genes associated with differential expression and methylation between castes were identified, and analysis of enrichment of Gene Ontology terms confirmed reliability of the obtained sets of genes from the biological standpoint. Biologically relevant genes, shown to be associated with significant differential gene expression and methylation between castes, were identified here for the first time. The identification of these genes may help understand the mechanisms underlying epigenetic control of development of multiple phenotypes under the same genomic conditions.

  9. A Social Judgment Analysis of Information Source Preference Profiles: An Exploratory Study to Empirically Represent Media Selection Patterns.

    ERIC Educational Resources Information Center

    Stefl-Mabry, Joette

    2003-01-01

    Describes a study that empirically identified individual preferences profiles to understand information-seeking behavior among professional groups for six selected information sources. Highlights include Social Judgment Analysis; the development of the survey used, a copy of which is appended; hypotheses tested; results of multiple regression…

  10. Identifying Students with Learning Disabilities: Composite Profile Analysis Using the Cognitive Assessment System

    ERIC Educational Resources Information Center

    Huang, Leesa V.; Bardos, Achilles N.; D'Amato, Rik Carl

    2010-01-01

    The detection of cognitive patterns in children with learning disabilities (LD) has been a priority in the identification process. Subtest profile analysis from traditional cognitive assessment has drawn sharp criticism for inaccurate identification and weak connections to educational planning. Therefore, the purpose of this study is to use a new…

  11. Parent Prevention Communication Profiles and Adolescent Substance Use: A Latent Profile Analysis and Growth Curve Model

    PubMed Central

    Choi, Hye Jeong; Miller-Day, Michelle; Shin, YoungJu; Hecht, Michael L.; Pettigrew, Jonathan; Krieger, Janice L.; Lee, JeongKyu; Graham, John W.

    2017-01-01

    This current study identifies distinct parent prevention communication profiles and examines whether youth with different parental communication profiles have varying substance use trajectories over time. Eleven schools in two rural school districts in the Midwestern United States were selected, and 784 students were surveyed at three time points from the beginning of 7th grade to the end of 8th grade. A series of latent profile analyses were performed to identify discrete profiles/subgroups of substance-specific prevention communication (SSPC). The results revealed a 4-profile model of SSPC: Active-Open, Passive-Open, Active-Silent, and Passive-Silent. A growth curve model revealed different rates of lifetime substance use depending on the youth’s SSPC profile. These findings have implications for parenting interventions and tailoring messages for parents to fit specific SSPC profiles. PMID:29056872

  12. Multidimensional profiles of health locus of control in Hispanic Americans.

    PubMed

    Champagne, Brian R; Fox, Rina S; Mills, Sarah D; Sadler, Georgia Robins; Malcarne, Vanessa L

    2016-10-01

    Latent profile analysis identified health locus of control profiles among 436 Hispanic Americans who completed the Multidimensional Health Locus of Control scales. Results revealed four profiles: Internally Oriented-Weak, -Moderate, -Strong, and Externally Oriented. The profile groups were compared on sociocultural and demographic characteristics, health beliefs and behaviors, and physical and mental health outcomes. The Internally Oriented-Strong group had less cancer fatalism, religiosity, and equity health attributions, and more alcohol consumption than the other three groups; the Externally Oriented group had stronger equity health attributions and less alcohol consumption. Deriving multidimensional health locus of control profiles through latent profile analysis allows examination of the relationships of health locus of control subtypes to health variables. © The Author(s) 2015.

  13. Stability of Language and Literacy Profiles of Children With Language Impairment in the Public Schools.

    PubMed

    Tambyraja, Sherine R; Schmitt, Mary Beth; Farquharson, Kelly; Justice, Laura M

    2015-08-01

    The present study focused on the identification and stability of language and literacy profiles of primary school children receiving school-based language therapy over the course of one academic year. Participants included 272 early elementary school-age children (144 boys, 128 girls) who had been clinically identified as having a language impairment. A latent profile analysis was used to identify distinct profiles on the basis of a battery of language and literacy assessments in the fall and spring of the academic year. Four profiles were identified in both fall and spring that could be best described as representing high, average, and low overall abilities. Two average groups were identified that differentiated according to phonological awareness abilities. Children's profile membership was variable from fall to spring with nearly 60% of children shifting into a higher profile. The results of t tests comparing children who shifted into higher profiles from those who remained stable in profile membership revealed group differences regarding language severity, socio-economic status, and proportion of therapy sessions received in the classroom. These results provide further evidence regarding the heterogeneity of children with language impairment served in the public schools, indicating that differences may be best conceptualized along a continuum of severity.

  14. A risk-based approach to management of leachables utilizing statistical analysis of extractables.

    PubMed

    Stults, Cheryl L M; Mikl, Jaromir; Whelehan, Oliver; Morrical, Bradley; Duffield, William; Nagao, Lee M

    2015-04-01

    To incorporate quality by design concepts into the management of leachables, an emphasis is often put on understanding the extractable profile for the materials of construction for manufacturing disposables, container-closure, or delivery systems. Component manufacturing processes may also impact the extractable profile. An approach was developed to (1) identify critical components that may be sources of leachables, (2) enable an understanding of manufacturing process factors that affect extractable profiles, (3) determine if quantitative models can be developed that predict the effect of those key factors, and (4) evaluate the practical impact of the key factors on the product. A risk evaluation for an inhalation product identified injection molding as a key process. Designed experiments were performed to evaluate the impact of molding process parameters on the extractable profile from an ABS inhaler component. Statistical analysis of the resulting GC chromatographic profiles identified processing factors that were correlated with peak levels in the extractable profiles. The combination of statistically significant molding process parameters was different for different types of extractable compounds. ANOVA models were used to obtain optimal process settings and predict extractable levels for a selected number of compounds. The proposed paradigm may be applied to evaluate the impact of material composition and processing parameters on extractable profiles and utilized to manage product leachables early in the development process and throughout the product lifecycle.

  15. Defining the Human Macula Transcriptome and Candidate Retinal Disease Genes UsingEyeSAGE

    PubMed Central

    Rickman, Catherine Bowes; Ebright, Jessica N.; Zavodni, Zachary J.; Yu, Ling; Wang, Tianyuan; Daiger, Stephen P.; Wistow, Graeme; Boon, Kathy; Hauser, Michael A.

    2009-01-01

    Purpose To develop large-scale, high-throughput annotation of the human macula transcriptome and to identify and prioritize candidate genes for inherited retinal dystrophies, based on ocular-expression profiles using serial analysis of gene expression (SAGE). Methods Two human retina and two retinal pigment epithelium (RPE)/choroid SAGE libraries made from matched macula or midperipheral retina and adjacent RPE/choroid of morphologically normal 28- to 66-year-old donors and a human central retina longSAGE library made from 41- to 66-year-old donors were generated. Their transcription profiles were entered into a relational database, EyeSAGE, including microarray expression profiles of retina and publicly available normal human tissue SAGE libraries. EyeSAGE was used to identify retina- and RPE-specific and -associated genes, and candidate genes for retina and RPE disease loci. Differential and/or cell-type specific expression was validated by quantitative and single-cell RT-PCR. Results Cone photoreceptor-associated gene expression was elevated in the macula transcription profiles. Analysis of the longSAGE retina tags enhanced tag-to-gene mapping and revealed alternatively spliced genes. Analysis of candidate gene expression tables for the identified Bardet-Biedl syndrome disease gene (BBS5) in the BBS5 disease region table yielded BBS5 as the top candidate. Compelling candidates for inherited retina diseases were identified. Conclusions The EyeSAGE database, combining three different gene-profiling platforms including the authors’ multidonor-derived retina/RPE SAGE libraries and existing single-donor retina/RPE libraries, is a powerful resource for definition of the retina and RPE transcriptomes. It can be used to identify retina-specific genes, including alternatively spliced transcripts and to prioritize candidate genes within mapped retinal disease regions. PMID:16723438

  16. Defining the human macula transcriptome and candidate retinal disease genes using EyeSAGE.

    PubMed

    Bowes Rickman, Catherine; Ebright, Jessica N; Zavodni, Zachary J; Yu, Ling; Wang, Tianyuan; Daiger, Stephen P; Wistow, Graeme; Boon, Kathy; Hauser, Michael A

    2006-06-01

    To develop large-scale, high-throughput annotation of the human macula transcriptome and to identify and prioritize candidate genes for inherited retinal dystrophies, based on ocular-expression profiles using serial analysis of gene expression (SAGE). Two human retina and two retinal pigment epithelium (RPE)/choroid SAGE libraries made from matched macula or midperipheral retina and adjacent RPE/choroid of morphologically normal 28- to 66-year-old donors and a human central retina longSAGE library made from 41- to 66-year-old donors were generated. Their transcription profiles were entered into a relational database, EyeSAGE, including microarray expression profiles of retina and publicly available normal human tissue SAGE libraries. EyeSAGE was used to identify retina- and RPE-specific and -associated genes, and candidate genes for retina and RPE disease loci. Differential and/or cell-type specific expression was validated by quantitative and single-cell RT-PCR. Cone photoreceptor-associated gene expression was elevated in the macula transcription profiles. Analysis of the longSAGE retina tags enhanced tag-to-gene mapping and revealed alternatively spliced genes. Analysis of candidate gene expression tables for the identified Bardet-Biedl syndrome disease gene (BBS5) in the BBS5 disease region table yielded BBS5 as the top candidate. Compelling candidates for inherited retina diseases were identified. The EyeSAGE database, combining three different gene-profiling platforms including the authors' multidonor-derived retina/RPE SAGE libraries and existing single-donor retina/RPE libraries, is a powerful resource for definition of the retina and RPE transcriptomes. It can be used to identify retina-specific genes, including alternatively spliced transcripts and to prioritize candidate genes within mapped retinal disease regions.

  17. Towards a typology of business process management professionals: identifying patterns of competences through latent semantic analysis

    NASA Astrophysics Data System (ADS)

    Müller, Oliver; Schmiedel, Theresa; Gorbacheva, Elena; vom Brocke, Jan

    2016-01-01

    While researchers have analysed the organisational competences that are required for successful Business Process Management (BPM) initiatives, individual BPM competences have not yet been studied in detail. In this study, latent semantic analysis is used to examine a collection of 1507 BPM-related job advertisements in order to develop a typology of BPM professionals. This empirical analysis reveals distinct ideal types and profiles of BPM professionals on several levels of abstraction. A closer look at these ideal types and profiles confirms that BPM is a boundary-spanning field that requires interdisciplinary sets of competence that range from technical competences to business and systems competences. Based on the study's findings, it is posited that individual and organisational alignment with the identified ideal types and profiles is likely to result in high employability and organisational BPM success.

  18. Analysis of Motivational Profiles of Satisfaction and Importance of Physical Education in High School Adolescents

    PubMed Central

    Granero-Gallegos, Antonio; Baena-Extremera, Antonio; Pérez-Quero, Francisco J.; Ortiz-Camacho, Maria M.; Bracho-Amador, Clara

    2012-01-01

    The purpose of this study was to analyze the motivational profiles of satisfaction with and importance of physical education in high school students and its relation with gender and the practice of sport. The sample comprised 2002 students aged from 12 to 19 who completed the Sport Motivation Scale (Núñez et al., 2006), the Sport Satisfaction Instrument (Baena-Extremera et al., 2012) and the Importance of Physical Education Scale (Moreno et al., 2009). Descriptive analyzes, correlations between the scales, a cluster analysis for profiles, and a MANOVA were conducted to examine differences by gender. Three clusters (profiles) were identified. The first profile identified was "moderate" motivation (n = 463) and was associated with boys who practice physical activity for less than 3 hours per week. The second profile identified was "low" motivation (n = 545) and was associated mainly with girls who practice physical activity for less than 3 hours per week. And lastly the third profile identified was "high" motivation (n = 910), which was found to be greater in boys who practiced physical exercise for more than 3 hours a week. Key points High school students’ motivation was mainly intrinsic, scoring very low on a motivation and high on satisfaction/fun; equally, these students were task-oriented. There appears to be a positive relationship between intrinsic motivation and task-orientation in high school students. The subject of PE is considered very highly by the students, and hence it obtains high values on satisfaction/fun and is positively associated with the importance given to PE. PMID:24150070

  19. Characterization of the transcriptome profiles related to globin gene switching during in vitro erythroid maturation

    PubMed Central

    2012-01-01

    Background The fetal and adult globin genes in the human β-globin cluster on chromosome 11 are sequentially expressed to achieve normal hemoglobin switching during human development. The pharmacological induction of fetal γ-globin (HBG) to replace abnormal adult sickle βS-globin is a successful strategy to treat sickle cell disease; however the molecular mechanism of γ-gene silencing after birth is not fully understood. Therefore, we performed global gene expression profiling using primary erythroid progenitors grown from human peripheral blood mononuclear cells to characterize gene expression patterns during the γ-globin to β-globin (γ/β) switch observed throughout in vitro erythroid differentiation. Results We confirmed erythroid maturation in our culture system using cell morphologic features defined by Giemsa staining and the γ/β-globin switch by reverse transcription-quantitative PCR (RT-qPCR) analysis. We observed maximal γ-globin expression at day 7 with a switch to a predominance of β-globin expression by day 28 and the γ/β-globin switch occurred around day 21. Expression patterns for transcription factors including GATA1, GATA2, KLF1 and NFE2 confirmed our system produced the expected pattern of expression based on the known function of these factors in globin gene regulation. Subsequent gene expression profiling was performed with RNA isolated from progenitors harvested at day 7, 14, 21, and 28 in culture. Three major gene profiles were generated by Principal Component Analysis (PCA). For profile-1 genes, where expression decreased from day 7 to day 28, we identified 2,102 genes down-regulated > 1.5-fold. Ingenuity pathway analysis (IPA) for profile-1 genes demonstrated involvement of the Cdc42, phospholipase C, NF-Kβ, Interleukin-4, and p38 mitogen activated protein kinase (MAPK) signaling pathways. Transcription factors known to be involved in γ-and β-globin regulation were identified. The same approach was used to generate profile-2 genes where expression was up-regulated over 28 days in culture. IPA for the 2,437 genes with > 1.5-fold induction identified the mitotic roles of polo-like kinase, aryl hydrocarbon receptor, cell cycle control, and ATM (Ataxia Telangiectasia Mutated Protein) signaling pathways; transcription factors identified included KLF1, GATA1 and NFE2 among others. Finally, profile-3 was generated from 1,579 genes with maximal expression at day 21, around the time of the γ/β-globin switch. IPA identified associations with cell cycle control, ATM, and aryl hydrocarbon receptor signaling pathways. Conclusions The transcriptome analysis completed with erythroid progenitors grown in vitro identified groups of genes with distinct expression profiles, which function in metabolic pathways associated with cell survival, hematopoiesis, blood cells activation, and inflammatory responses. This study represents the first report of a transcriptome analysis in human primary erythroid progenitors to identify transcription factors involved in hemoglobin switching. Our results also demonstrate that the in vitro liquid culture system is an excellent model to define mechanisms of global gene expression and the DNA-binding protein and signaling pathways involved in globin gene regulation. PMID:22537182

  20. The Association of Latino Children's Kindergarten School Readiness Profiles with Grade 2-5 Literacy Achievement Trajectories

    ERIC Educational Resources Information Center

    Quirk, Matthew; Grimm, Ryan; Furlong, Michael J.; Nylund-Gibson, Karen; Swami, Sruthi

    2016-01-01

    This study utilized latent class analysis (LCA) to identify 5 discernible profiles of Latino children's (N = 1,253) social-emotional, physical, and cognitive school readiness at the time of kindergarten entry. In addition, a growth mixture modeling (GMM) approach was used to identify 3 unique literacy achievement trajectories, across Grades 2-5,…

  1. A Comprehensive Approach to Sequence-oriented IsomiR annotation (CASMIR): demonstration with IsomiR profiling in colorectal neoplasia.

    PubMed

    Wu, Chung Wah; Evans, Jared M; Huang, Shengbing; Mahoney, Douglas W; Dukek, Brian A; Taylor, William R; Yab, Tracy C; Smyrk, Thomas C; Jen, Jin; Kisiel, John B; Ahlquist, David A

    2018-05-25

    MicroRNA (miRNA) profiling is an important step in studying biological associations and identifying marker candidates. miRNA exists in isoforms, called isomiRs, which may exhibit distinct properties. With conventional profiling methods, limitations in assay and analysis platforms may compromise isomiR interrogation. We introduce a comprehensive approach to sequence-oriented isomiR annotation (CASMIR) to allow unbiased identification of global isomiRs from small RNA sequencing data. In this approach, small RNA reads are maintained as independent sequences instead of being summarized under miRNA names. IsomiR features are identified through step-wise local alignment against canonical forms and precursor sequences. Through customizing the reference database, CASMIR is applicable to isomiR annotation across species. To demonstrate its application, we investigated isomiR profiles in normal and neoplastic human colorectal epithelia. We also ran miRDeep2, a popular miRNA analysis algorithm to validate isomiRs annotated by CASMIR. With CASMIR, specific and biologically relevant isomiR patterns could be identified. We note that specific isomiRs are often more abundant than their canonical forms. We identify isomiRs that are commonly up-regulated in both colorectal cancer and advanced adenoma, and illustrate advantages in targeting isomiRs as potential biomarkers over canonical forms. Studying miRNAs at the isomiR level could reveal new insight into miRNA biology and inform assay design for specific isomiRs. CASMIR facilitates comprehensive annotation of isomiR features in small RNA sequencing data for isomiR profiling and differential expression analysis.

  2. CBCL Pediatric Bipolar Disorder Profile and ADHD: Comorbidity and Quantitative Trait Loci Analysis

    ERIC Educational Resources Information Center

    McGough, James J.; Loo, Sandra K.; McCracken, James T.; Dang, Jeffery; Clark, Shaunna; Nelson, Stanley F.; Smalley, Susan L.

    2008-01-01

    The pediatric bipolar disorder profile of the Child Behavior checklist is used to differentiate patterns of comorbidity and to search for quantitative trait loci in multiple affected ADHD sibling pairs. The CBCL-PBD profiling identified 8 percent of individuals with severe psychopathology and increased rates of oppositional defiant, conduct and…

  3. The Child Behavior Checklist-Dysregulation Profile Predicts Substance Use, Suicidality, and Functional Impairment: A Longitudinal Analysis

    ERIC Educational Resources Information Center

    Holtmann, Martin; Buchmann, Arlette F.; Esser, Guenter; Schmidt, Martin H.; Banaschewski, Tobias; Laucht, Manfred

    2011-01-01

    Background: Recent studies have identified a Child Behavior Checklist profile that characterizes children with severe affective and behavioral dysregulation (CBCL-dysregulation profile, CBCL-DP). In two recent longitudinal studies the CBCL-DP in childhood was associated with heightened rates of comorbid psychiatric disorders, among them bipolar…

  4. Singapore Primary Students' Pursuit of Multiple Achievement Goals: A Latent Profile Analysis

    ERIC Educational Resources Information Center

    Ning, Hoi Kwan

    2018-01-01

    Based on measures of approach and avoidance mastery and performance goals delineated in the 2 × 2 achievement goal framework, this study utilized a person-centered approach to examine Singapore primary students' (N = 819) multiple goals pursuit in the general school context. Latent profile analysis identified six types of students with distinct…

  5. Neuropsychological phenotypes among men with and without HIV disease in the multicenter AIDS cohort study.

    PubMed

    Molsberry, Samantha A; Cheng, Yu; Kingsley, Lawrence; Jacobson, Lisa; Levine, Andrew J; Martin, Eileen; Miller, Eric N; Munro, Cynthia A; Ragin, Ann; Sacktor, Ned; Becker, James T

    2018-05-11

    Mild forms of HIV-associated neurocognitive disorder (HAND) remain prevalent in the combination anti-retroviral therapy (cART) era. This study's objective was to identify neuropsychological subgroups within the Multicenter AIDS Cohort Study (MACS) based on the participant-based latent structure of cognitive function and to identify factors associated with subgroups. The MACS is a four-site longitudinal study of the natural and treated history of HIV disease among gay and bisexual men. Using neuropsychological domain scores we used a cluster variable selection algorithm to identify the optimal subset of domains with cluster information. Latent profile analysis was applied using scores from identified domains. Exploratory and post-hoc analyses were conducted to identify factors associated with cluster membership and the drivers of the observed associations. Cluster variable selection identified all domains as containing cluster information except for Working Memory. A three-profile solution produced the best fit for the data. Profile 1 performed below average on all domains, Profile 2 performed average on executive functioning, motor, and speed and below average on learning and memory, Profile 3 performed at or above average across all domains. Several demographic, cognitive, and social factors were associated with profile membership; these associations were driven by differences between Profile 1 and the other profiles. There is an identifiable pattern of neuropsychological performance among MACS members determined by all domains except Working Memory. Neither HIV nor HIV-related biomarkers were related with cluster membership, consistent with other findings that cognitive performance patterns do not map directly onto HIV serostatus.

  6. Rapid Identification of Laboratory Contamination with Mycobacterium tuberculosis Using Variable Number Tandem Repeat Analysis

    PubMed Central

    Gascoyne-Binzi, Deborah M.; Barlow, Rachael E. L.; Frothingham, Richard; Robinson, Grant; Collyns, Timothy A.; Gelletlie, Ruth; Hawkey, Peter M.

    2001-01-01

    Compared with solid media, broth-based mycobacterial culture systems have increased sensitivity but also have higher false-positive rates due to cross-contamination. Systematic strain typing is rarely undertaken because the techniques are technically demanding and the data are difficult to organize. Variable number tandem repeat (VNTR) analysis by PCR is rapid and reproducible. The digital profile is easily manipulated in a database. We undertook a retrospective study of Mycobacterium tuberculosis isolates collected over an 18-month period following the introduction of the BACTEC MGIT 960 system. VNTR allele profiles were determined with early positive broth cultures and entered into a database with the specimen processing date and other specimen data. We found 36 distinct VNTR profiles in cultures from 144 patients. Three common VNTR profiles accounted for 45% of true-positive cases. By combining VNTR results with specimen data, we identified nine cross-contamination incidents, six of which were previously unsuspected. These nine incidents resulted in 34 false-positive cultures for 29 patients. False-positive cultures were identified for three patients who had previously been culture positive for tuberculosis and were receiving treatment. Identification of cross-contamination incidents requires careful documentation of specimen data and good communication between clinical and laboratory staff. Automated broth culture systems should be supplemented with molecular analysis to identify cross-contamination events. VNTR analysis is reproducible and provides timely results when applied to early positive broth cultures. This method should ensure that patients are not placed on unnecessary tuberculosis therapy or that cases are not falsely identified as treatment failures. In addition, areas where existing procedures may be improved can be identified. PMID:11136751

  7. Clinical Profiles of Children with Disruptive Behaviors Based on the Severity of Their Conduct Problems, Callous-Unemotional Traits and Emotional Difficulties.

    PubMed

    Andrade, Brendan F; Sorge, Geoff B; Na, Jennifer Jiwon; Wharton-Shukster, Erika

    2015-08-01

    This study identified clinical profiles of referred children based on the severity of callous-unemotional (CU) traits, emotional difficulties, and conduct problems. Parents of 166 children (132 males) aged 6-12 years referred to a hospital clinic because of disruptive behavior completed measures to assess these key indicators, and person-centered analysis was used to identify profiles. Four distinct profiles were identified that include: (1) Children low in severity on the three domains, (2) Children high in severity on the three domains, (3) Children high in severity in conduct problems and CU traits with minimal emotional difficulties, and (4) Children high in severity in conduct problems and emotional difficulties with minimal CU traits. Profiles differed in degree of aggression and behavioral impairment. Findings show that clinic-referred children with disruptive behaviors can be grouped based on these important indicators into profiles that have important implications for assessment and treatment selection.

  8. Appreciating Complexity in Adolescent Self-Harm Risk Factors: Psychological Profiling in a Longitudinal Community Sample.

    PubMed

    Stanford, Sarah; Jones, Michael P; Hudson, Jennifer L

    2018-05-01

    Past research identifies a number of risk factors for adolescent self-harm, but often fails to account for overlap between these factors. This study investigated the underlying, broader concepts by identifying different psychological profiles among adolescents. We then compared new self-harm rates over a six-month period across different psychological profiles. Australian high school students (n = 326, 68.1% female) completed a questionnaire including a broad range of psychological and socioenvironmental risk and protective factors. Non-hierarchical cluster analysis produced six groups with different psychological profiles at baseline and rate of new self-harm at follow-up. The lowest rate was 1.4% in a group that appeared psychologically healthy; the highest rate was 37.5% in a group that displayed numerous psychological difficulties. Four groups with average self-harm had varied psychological profiles including low impulsivity, anxiety, impulsivity, and poor use of positive coping strategies. Identifying multiple profiles with distinct psychological characteristics can improve detection, guide prevention, and tailor treatment.

  9. 6C.04: INTEGRATED SNP ANALYSIS AND METABOLOMIC PROFILES OF METABOLIC SYNDROME.

    PubMed

    Marrachelli, V; Monleon, D; Morales, J M; Rentero, P; Martínez, F; Chaves, F J; Martin-Escudero, J C; Redon, J

    2015-06-01

    Metabolic syndrome (MS) has become a health and financial burden worldwide. Susceptibility of genetically determined metabotype of MS has not yet been investigated. We aimed to identify a distinctive metabolic profile of blood serum which might correlates to the early detection of the development of MS associated to genetic polymorphism. We applied high resolution NMR spectroscopy to profile blood serum from patients without MS (n = 945) or with (n = 291). Principal component analysis (PCA) and projection to latent structures for discriminant analysis (PLS-DA) were applied to NMR spectral datasets. Results were cross-validated using the Venetian Blinds approach. Additionally, five SNPs previously associated with MS were genotyped with SNPlex and tested for associations between the metabolic profiles and the genetic variants. Statistical analysis was performed using in-house MATLAB scripts and the PLS Toolbox statistical multivariate analysis library. Our analysis provided a PLS-DA Metabolic Syndrome discrimination model based on NMR metabolic profile (AUC = 0.86) with 84% of sensitivity and 72% specificity. The model identified 11 metabolites differentially regulated in patients with MS. Among others, fatty acids, glucose, alanine, hydroxyisovalerate, acetone, trimethylamine, 2-phenylpropionate, isobutyrate and valine, significantly contributed to the model. The combined analysis of metabolomics and SNP data revealed an association between the metabolic profile of MS and genes polymorphism involved in the adiposity regulation and fatty acids metabolism: rs2272903_TT (TFAP2B), rs3803_TT (GATA2), rs174589_CC (FADS2) and rs174577_AA (FADS2). In addition, individuals with the rs2272903-TT genotype seem to develop MS earlier than general population. Our study provides new insights on the metabolic alterations associated with a MS high-risk genotype. These results could help in future development of risk assessment and predictive models for subclinical cardiovascular disease.

  10. Study to determine the IFR operational profile and problems of the general aviation single pilot

    NASA Technical Reports Server (NTRS)

    Weislogel, G. S.

    1983-01-01

    General aviation single pilot operating under instrument flight rules (GA SPIFR) was studied. The objectives of the study were to (1) develop a GA SPIFR operational profile, (2) identify problems experienced by the GA SPIFR pilot, and (3) identify research tasks which have the potential for eliminating or reducing the severity of the problems. To obtain the information necessary to accomplish these objectives, a mail questionnaire survey of instrument rated pilots was conducted. The general aviation IFR single pilot operational profile and selected data analysis examples are presented.

  11. "Heroes" and "villains" of world history across cultures.

    PubMed

    Hanke, Katja; Liu, James H; Sibley, Chris G; Paez, Dario; Gaines, Stanley O; Moloney, Gail; Leong, Chan-Hoong; Wagner, Wolfgang; Licata, Laurent; Klein, Olivier; Garber, Ilya; Böhm, Gisela; Hilton, Denis J; Valchev, Velichko; Khan, Sammyh S; Cabecinhas, Rosa

    2015-01-01

    Emergent properties of global political culture were examined using data from the World History Survey (WHS) involving 6,902 university students in 37 countries evaluating 40 figures from world history. Multidimensional scaling and factor analysis techniques found only limited forms of universality in evaluations across Western, Catholic/Orthodox, Muslim, and Asian country clusters. The highest consensus across cultures involved scientific innovators, with Einstein having the most positive evaluation overall. Peaceful humanitarians like Mother Theresa and Gandhi followed. There was much less cross-cultural consistency in the evaluation of negative figures, led by Hitler, Osama bin Laden, and Saddam Hussein. After more traditional empirical methods (e.g., factor analysis) failed to identify meaningful cross-cultural patterns, Latent Profile Analysis (LPA) was used to identify four global representational profiles: Secular and Religious Idealists were overwhelmingly prevalent in Christian countries, and Political Realists were common in Muslim and Asian countries. We discuss possible consequences and interpretations of these different representational profiles.

  12. Extracting body image symptom dimensions among eating disorder patients: the Profile Analysis via Multidimensional Scaling (PAMS) approach.

    PubMed

    Olatunji, Bunmi O; Kim, Se-Kang; Wall, David

    2015-09-01

    The present study employs Profile Analysis via Multidimensional Scaling (PAMS), a procedure for extracting dimensions, in order to identify core eating disorder symptoms in a clinical sample. A large sample of patients with eating disorders (N=5193) presenting for treatment completed the Eating Disorders Inventory-2 (EDI-2; Garner, 1991), and PAMS was then employed to estimate individual profile weights that reflect the degree to which an individual's observed symptom profile approximates the pattern of the dimensions. The findings revealed three symptom dimensions: Body Thinness, Body Perfectionism, and Body Awareness. Subsequent analysis using individual level data illustrate that the PAMS profiles properly operate as prototypical profiles that encapsulate all individuals' response patterns. The implications of these dimensional findings for the assessment and diagnosis of eating disorders are discussed. Copyright © 2015 Elsevier Ltd. All rights reserved.

  13. A clustering approach to identify severe bronchiolitis profiles in children

    PubMed Central

    Dumas, Orianne; Mansbach, Jonathan M; Jartti, Tuomas; Hasegawa, Kohei; Sullivan, Ashley F; Piedra, Pedro A; Camargo, Carlos A

    2016-01-01

    Objective Although bronchiolitis is generally considered a single disease, recent studies suggest heterogeneity. We aimed to identify severe bronchiolitis profiles using a clustering approach. Methods We analyzed data from two prospective, multi-center cohorts of children younger than 2 years hospitalized with bronchiolitis, one in the U.S. (2007–2010 winter seasons, n=2,207) and one in Finland (2008–2010 winter seasons, n=408). Severe bronchiolitis profiles were determined by latent class analysis, classifying children based on clinical factors and viral etiology. Results In the U.S. study, four profiles were identified. Profile A (12%) was characterized by history of wheezing and eczema, wheezing at the ED presentation and rhinovirus infection. Profile B (36%) included children with wheezing at the ED presentation, but, in contrast to profile A, most did not have history of wheezing or eczema; this profile had the largest probability of RSV-infection. Profile C (34%) was the most severely ill group, with longer hospital stay and moderate-to-severe retractions. Profile D (17%) had the least severe illness, including non-wheezing children with shorter length-of-stay. Two of these profiles (A and D) were replicated in the Finnish cohort; a third group (“BC”) included Finnish children with characteristics of profiles B and/or C in the U.S. population. Conclusion Several distinct clinical profiles (phenotypes) were identified by a clustering approach in two multicenter studies of children hospitalized for bronchiolitis. The observed heterogeneity has important implications for future research on the etiology, management and long-term outcomes of bronchiolitis, such as future risk of childhood asthma. PMID:27339060

  14. Identifying the Career-Interest Profiles of Junior-High-School Students Through Latent Profile Analysis.

    PubMed

    Sung, Yao-Ting; Cheng, Yu-Wen; Hsueh, Jen-Hu

    2017-04-03

    Exploring the career-interest profiles of students has both practical and theoretical significance; however, a minimal amount of research has been conducted to address this issue. The present study combined latent profile analysis and differentiation values to investigate the career-interest profiles of 13,853 junior-high-school students. The results indicate that while the students' interests could be stratified into 25 profiles, 44.6% of students could be classified the as having low-differentiation profiles (such as like or dislike all types of vocational activities) and 24.9% of students could be classified the as having the artistic-social (like both artistic and social types of activities) profile. In addition, the proportions of females and males differed significantly among the profiles, but different grades did not. The proportion of males was higher for all three low-differentiation groups than of female proportions. Implications for career practices and future research are proposed.

  15. Development of a Typology of Dual-Earner Couples Caring for Children and Aging Parents

    ERIC Educational Resources Information Center

    Cullen, Jennifer C.; Hammer, Leslie B.; Neal, Margaret B.; Sinclair, Robert R.

    2009-01-01

    Using a national sample of 267 couples, the authors identify distinct profiles of dual-earner couples in the sandwiched generation (i.e., those caring for children and aging parents) using cluster analysis and then assess the relationship between these profiles and work-family conflict. The profiles are defined by characteristics of couples' child…

  16. What Is Successful Writing? An Investigation into the Multiple Ways Writers Can Write Successful Essays

    ERIC Educational Resources Information Center

    Crossley, Scott A.; Roscoe, Rod; McNamara, Danielle S.

    2014-01-01

    This study identifies multiple profiles of successful essays via a cluster analysis approach using linguistic features reported by a variety of natural language processing tools. The findings from the study indicate that there are four profiles of successful writers for the samples analyzed. These four profiles are linguistically distinct from one…

  17. Multivariate proteomic profiling identifies novel accessory proteins of coated vesicles

    PubMed Central

    Antrobus, Robin; Hirst, Jennifer; Bhumbra, Gary S.; Kozik, Patrycja; Jackson, Lauren P.; Sahlender, Daniela A.

    2012-01-01

    Despite recent advances in mass spectrometry, proteomic characterization of transport vesicles remains challenging. Here, we describe a multivariate proteomics approach to analyzing clathrin-coated vesicles (CCVs) from HeLa cells. siRNA knockdown of coat components and different fractionation protocols were used to obtain modified coated vesicle-enriched fractions, which were compared by stable isotope labeling of amino acids in cell culture (SILAC)-based quantitative mass spectrometry. 10 datasets were combined through principal component analysis into a “profiling” cluster analysis. Overall, 136 CCV-associated proteins were predicted, including 36 new proteins. The method identified >93% of established CCV coat proteins and assigned >91% correctly to intracellular or endocytic CCVs. Furthermore, the profiling analysis extends to less well characterized types of coated vesicles, and we identify and characterize the first AP-4 accessory protein, which we have named tepsin. Finally, our data explain how sequestration of TACC3 in cytosolic clathrin cages causes the severe mitotic defects observed in auxilin-depleted cells. The profiling approach can be adapted to address related cell and systems biological questions. PMID:22472443

  18. Bully/Victim Profiles’ Differential Risk for Worsening Peer Acceptance: The Role of Friendship

    PubMed Central

    Kochel, Karen P.; Ladd, Gary W.; Bagwell, Catherine L.; Yabko, Brandon A.

    2015-01-01

    Study aims were to: (1) evaluate the association between bully/victim profiles, derived via latent profile analysis (LPA), and changes in peer acceptance from the fall to spring of 7th grade, and (2) investigate the likelihood of friendlessness, and the protective function of mutual friendship, among identified profiles. Participants were 2,587 7th graders; peer nomination and rating-scale data were collected in the fall and spring. Four profiles, including bullies, victims, bully-victims, and uninvolved adolescents, were identified at each time point. Findings showed that for victims, more so than for bullies and uninvolved profiles, acceptance scores worsened over time. Results further revealed that bully-victim and victim profiles included a greater proportion of friendless youth relative to the bully profile, which, in turn, contained a greater proportion of friendless adolescents than the uninvolved profile. Findings also provided evidence for the buffering role of friendship among all bully/victim profiles and among bully-victims especially. PMID:26309346

  19. Profiles of Reactivity in Cocaine-Exposed Children

    PubMed Central

    Schuetze, Pamela; Molnar, Danielle S.; Eiden, Rina D.

    2012-01-01

    This study explored the possibility that specific, theoretically consistent profiles of reactivity could be identified in a sample of cocaine-exposed infants and whether these profiles were associated with a range of infant and/or maternal characteristics. Cluster analysis was used to identify distinct groups of infants based on physiological, behavioral and maternal reported measures of reactivity. Five replicable clusters were identified which corresponded to 1) Dysregulated/High Maternal Report Reactors, 2) Low Behavioral Reactors, 3) High Reactors, 4) Optimal Reactors and 5) Dysregulated/Low Maternal Report Reactors. These clusters were associated with differences in prenatal cocaine exposure status, birthweight, maternal depressive symptoms, and maternal negative affect during mother-infant interactions. These results support the presence of distinct reactivity profiles among high risk infants recruited on the basis of prenatal cocaine exposure and demographically similar control group infants not exposed to cocaine. PMID:23204615

  20. Differentiation of mixed biological traces in sexual assaults using DNA fragment analysis

    PubMed Central

    Apostolov, Аleksandar

    2014-01-01

    During the investigation of sexual abuse, it is not rare that mixed genetic material from two or more persons is detected. In such cases, successful profiling can be achieved using DNA fragment analysis, resulting in individual genetic profiles of offenders and their victims. This has led to an increase in the percentage of identified perpetrators of sexual offenses. The classic and modified genetic models used, allowed us to refine and implement appropriate extraction, polymerase chain reaction and electrophoretic procedures with individual assessment and approach to conducting research. Testing mixed biological traces using DNA fragment analysis appears to be the only opportunity for identifying perpetrators in gang rapes. PMID:26019514

  1. Molecular identification and cluster analysis of homofermentative thermophilic lactobacilli isolated from dairy products.

    PubMed

    Andrighetto, C; De Dea, P; Lombardi, A; Neviani, E; Rossetti, L; Giraffa, G

    1998-10-01

    Twenty-five strains of thermophilic lactobacilli isolated from yoghurt and from semi-hard and hard cheeses (in parallel with nine type or reference strains) were identified and grouped according to their genetic relatedness. Strains were identified by sugar fermentation patterns using the "API 50 CHL" galleries, by species-specific DNA probes in dot-blot hybridization experiments, by amplification and restriction analysis of the 16S rRNA gene (ARDRA) and by polymerase chain reaction (PCR) using species-specific oligonucleotide primers. Strains were classified as Lactobacillus delbrueckii subsp. lactis and subsp. bulgaricus, L. helveticus, and L. acidophilus. Strains which were atypical by sugar fermentation patterns were also identified. Most of the strains could not be grouped using carbohydrate fermentation profiles. PCR fingerprinting was used to identify DNA profiles for the 25 lactobacilli. Experimentally obtained PCR profiles enabled discrimination of all strains, which were grouped according to the similarities in their combined patterns. In general, the clustering of the strains corresponded well with species delineation obtained by molecular identification. The dendrogram of genetic relatedness enabled the unambiguous identification of most of the strains which were shown to be atypical by the sugar fermentation profile, except for a discrepancy in one L. delbrueckii subsp. lactis strain and one atypical Lactobacillus sp. strain.

  2. Attachment in psychosis: A latent profile analysis of attachment styles and association with symptoms in a large psychosis cohort.

    PubMed

    Bucci, Sandra; Emsley, Richard; Berry, Katherine

    2017-01-01

    Attachment has been identified as one of various possible mechanisms involved in understanding models of psychosis, but measures that reliably and validly assess attachment styles in psychosis are limited. The aim of this study was to identify attachment patterns in psychosis and examine demographic and clinical correlates across attachment groups. Latent profile analysis on attachment data from 588 participants who met criteria for non-affective psychosis was used to classify people into attachment classes. Four latent classes of attachment were identified: secure, insecure-anxious, insecure-avoidant and disorganised. Secure attachment was the most common attachment style, suggesting that a significant number of clients with psychosis are inherently resilient. Disorganised attachment was associated with a higher proportion of sexual and physical abuse and more severe positive symptoms compared to other attachment classes. This is not only the largest study to examine attachment styles, their demographic and clinical profile, and the clinical profile of disorganised attachment more specifically, in psychosis, but also the first study to use a validated self-report measure of attachment in psychosis to identify four classes of attachment style. Findings advance developmental models of attachment and psychosis; participants with disorganised attachment report more frequent trauma history and more severe psychotic symptoms. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  3. Profiles of family needs of children and youth with cerebral palsy.

    PubMed

    Almasri, N; Palisano, R J; Dunst, C; Chiarello, L A; O'Neil, M E; Polansky, M

    2012-11-01

    To identify profiles of family needs of families of children and youth with cerebral palsy (CP), and determine whether profile membership is related to child, family and service characteristics. Participants were mostly mothers (80%) of 579 children and youth with CP. A family member completed modified version of the Family Needs Survey and questionnaires about their child, family and services. Research assistants determined the Gross Motor Function Classification System levels. K-means cluster analysis identified profiles of needs. Cluster membership was analysed to examine differences in clusters based on selected characteristics. Four profiles of needs were identified: Low needs, Needs related to community and financial resources, Needs related to child health condition and High needs. Profile membership was differentiated based on child/youth gross motor function, adaptive behaviour, family relationships, family income, access and effort to co-ordinate services. Despite heterogeneity among individuals with CP and their families, four profiles of family needs were identified. In total, 51% of families had low needs suggesting that they are effectively managing their children's health conditions while 11% of families had high needs that may require high levels of services and supports. Service providers are encouraged to partner with families, provide anticipatory guidance and co-ordinate services. © 2011 Blackwell Publishing Ltd.

  4. Profiles of drug addicts in relation to personality variables and disorders.

    PubMed

    Carou, María; Romero, Estrella; Luengo, Mª Ángeles

    2016-10-07

    In recent decades, research has identified a set of impulsive/disinhibited personality variables closely associated with drug addiction. As well as this, disorders linked with these variables, such as ADHD and personality disorders, are being closely studied in the field of drug addiction. Although much knowledge has been accumulated about the relation of these variables and disorders taken separately, less is known about how these constructs allow identify-specific profiles within the drug dependent population to be identified. This work, on the basis of data collected on a sample of drug addicts in treatment, analyzes how impulsiveness, sensation seeking, self-control, ADHD and personality disorders contribute to identifying specific profiles of addicts. Cluster analysis allowed two profiles to be outlined according to these personality and psychopathology characteristics. Self-control, impulsiveness, impulsive and antisocial personality disorders, as well as scores in ADHD, emerge as the variables that contribute more to profile differentiation. One of these profiles (56.1% of participants) with a high disinhibition pattern, is associated with severe indicators of consumption and criminal career patterns. These results allow us to emphasize the role of personality and impulsiveness-related disorders in the identification of distinctive profiles within the addict population, and suggest the need to generate treatment strategies adapted to personal/psychopathology configurations of drug addicts.

  5. Profiles of internalizing and externalizing symptoms associated with bullying victimization.

    PubMed

    Eastman, Meridith; Foshee, Vangie; Ennett, Susan; Sotres-Alvarez, Daniela; Reyes, H Luz McNaughton; Faris, Robert; North, Kari

    2018-06-01

    This study identified profiles of internalizing (anxiety and depression) and externalizing (delinquency and violence against peers) symptoms among bullying victims and examined associations between bullying victimization characteristics and profile membership. The sample consisted of 1196 bullying victims in grades 8-10 (M age  = 14.4, SD = 1.01) who participated in The Context Study in three North Carolina counties in Fall 2003. Five profiles were identified using latent profile analysis: an asymptomatic profile and four profiles capturing combinations of internalizing and externalizing symptoms. Associations between bullying characteristics and membership in symptom profiles were tested using multinomial logistic regression. More frequent victimization increased odds of membership in the two high internalizing profiles compared to the asymptomatic profile. Across all multinomial logistic regression models, when the high internalizing, high externalizing profile was the reference category, adolescents who received any type of bullying (direct, indirect, or dual) were more likely to be in this category than any others. Copyright © 2018 The Foundation for Professionals in Services for Adolescents. Published by Elsevier Ltd. All rights reserved.

  6. National Profiles of Classroom Quality and Family Involvement: A Multilevel Examination of Proximal Influences on Head Start Children's School Readiness

    ERIC Educational Resources Information Center

    Bulotsky-Shearer, Rebecca J.; Wen, Xiaoli; Faria, Ann-Marie; Hahs-Vaughn, Debbie L.; Korfmacher, Jon

    2012-01-01

    Guided by a developmental and ecological model, the study employed latent profile analysis to identify a multilevel typology of family involvement and Head Start classroom quality. Using the nationally representative Head Start Family and Child Experiences Survey (FACES 1997; N = 1870), six multilevel latent profiles were estimated, characterized…

  7. Using Latent Class Analysis to Identify Profiles of Elder Abuse Perpetrators.

    PubMed

    DeLiema, Marguerite; Yonashiro-Cho, Jeanine; Gassoumis, Zach D; Yon, Yongjie; Conrad, Ken J

    2018-06-14

    Research suggests that abuser risk factors differ across elder mistreatment types, but abuse interventions are not individualized. To move away from assumptions of perpetrator homogeneity and to inform intervention approaches, this study classifies abusers into subtypes according to their behavior profiles. Data are from the Older Adult Mistreatment Assessment administered to victims by Adult Protective Service (APS) in Illinois. Latent class analysis was used to categorize abusers (N = 336) using victim and caseworker reports on abusers' harmful and supportive behaviors and characteristics. Multinomial logistic regression was then used to determine which abuser profiles are associated with 4 types of mistreatment-neglect, physical, emotional, and financial-and other sociodemographic characteristics. Abusers fall into 4 profiles descriptively labeled "Caregiver," "Temperamental," "Dependent Caregiver," and "Dangerous." Dangerous abusers have the highest levels of aggression, financial dependency, substance abuse, and irresponsibility. Caregivers are lowest in harmful characteristics and highest in providing emotional and instrumental support to victims. The 4 profiles significantly differ in the average age and gender of the abuser, the relationship to victims, and types of mistreatment committed. This is the first quantitative study to identify and characterize abuser subtypes. Tailored interventions are needed to reduce problem behaviors and enhance strengths specific to each abuser profile.

  8. Passion and intrinsic motivation in digital gaming.

    PubMed

    Wang, Chee Keng John; Khoo, Angeline; Liu, Woon Chia; Divaharan, Shanti

    2008-02-01

    Digital gaming is fast becoming a favorite activity all over the world. Yet very few studies have examined the underlying motivational processes involved in digital gaming. One motivational force that receives little attention in psychology is passion, which could help us understand the motivation of gamers. The purpose of the present study was to identify subgroups of young people with distinctive passion profiles on self-determined regulations, flow dispositions, affect, and engagement time in gaming. One hundred fifty-five students from two secondary schools in Singapore participated in the survey. There were 134 males and 8 females (13 unspecified). The participants completed a questionnaire to measure harmonious passion (HP), obsessive passion (OP), perceived locus of causality, disposition flow, positive and negative affects, and engagement time in gaming. Cluster analysis found three clusters with distinct passion profiles. The first cluster had an average HP/OP profile, the second cluster had a low HP/OP profile, and the third cluster had a high HP/OP profile. The three clusters displayed different levels of cognitive, affective, and behavioral outcomes. Cluster analysis, as this study shows, is useful in identifying groups of gamers with different passion profiles. It has helped us gain a deeper understanding of motivation in digital gaming.

  9. What Are Adolescents Showing the World About Their Health Risk Behaviors on MySpace?

    PubMed Central

    Moreno, Megan A.; Parks, Malcolm; Richardson, Laura P.

    2007-01-01

    Context MySpace is a popular social networking Web site where users create individual Web profiles. Little data are available about what types of health risk behaviors adolescents display on MySpace profiles. There are potential risks and intervention opportunities associated with posting such information on a public Web site. Objective To examine publicly available 16- and 17-year-old MySpace Web profiles and determine the prevalence of personal risk behavior descriptions and identifiable information. Design Cross-sectional observational study using content analysis of Web profiles. Setting www.MySpace.com Patients In order to target frequently visited adolescent Web profiles, we sequentially selected 142 publicly available Web profiles of 16 and 17 year olds from the class of 2008 MySpace group. Interventions None. Main outcome measures Prevalence of displayed health risk behaviors pertaining to substance use or sexual behavior, prevalence of personally identifying information, date of last log-in to Web profile. Results Of Web profiles, 47% contained risk behavior information: Twenty-one percent described sexual activity; 25% described alcohol use; 9% described cigarette use; and 6% described drug use. 97.2% Contained personally identifying information: Seventy-four percent included an identifiable picture; 75% included subjects' first names or surnames; and 78% included subjects' hometowns. Eighty-six percent of users had visited their own profiles within 24 hours. Conclusions Most 16- and 17-year-old MySpace profiles include identifiable information, are frequently accessed by owners, and half include personal risk behavior information. Further study is needed to assess the risks associated with displaying personal information and to evaluate the use of social networking sites for health behavior interventions targeting at-risk teens. PMID:18311359

  10. Victimization and Human Immunodeficiency Virus-Related Risk Among Transgender Women in India: A Latent Profile Analysis.

    PubMed

    Willie, Tiara C; Chakrapani, Venkatesan; White Hughto, Jaclyn M; Kershaw, Trace S

    2017-12-01

    Globally, transgender women (TGW) experience multiple forms of victimization such as violence and discrimination that can place them at risk for poor sexual health. To date, research overlooks the heterogeneity in experiences of victimization among TGW. Furthermore, few studies have examined the association between victimization and sexual risk among TGW in India, despite the high burden of HIV and victimization in this community. Latent profile analysis was performed to identify patterns of victimization in a convenience sample of 299 TGW recruited from nongovernmental organizations across four states in India. Analysis of covariance was performed to examine differences in sexual risk (i.e., alcohol use before sex; inconsistent condom use with a male regular partner, a male causal partner, and a male paying partner; and having multiple sexual partners) between latent profiles. Five distinct profiles of Indian TGW were identified based on the type and severity of victimization: (1) Low victimization, (2) High verbal police victimization, (3) High verbal and physical police victimization, (4) Moderate victimization, and (5) High victimization. While controlling for age, education, income, HIV status, and marital status, results revealed that TGW in the moderate victimization and high victimization profiles had higher sexual risk than TGW in the low victimization and high verbal police victimization profiles. In addition, TGW in high verbal and physical police victimization profile had higher sexual risk than TGW in low victimization profile. These findings underscore the importance of tailoring sexual risk reduction interventions to the specific needs of TGW based on patterns of victimization.

  11. A personality-based latent class typology of outpatients with major depressive disorder: association with symptomatology, prescription pattern and social function.

    PubMed

    Hori, Hiroaki; Teraishi, Toshiya; Nagashima, Anna; Koga, Norie; Ota, Miho; Hattori, Kotaro; Kim, Yoshiharu; Higuchi, Teruhiko; Kunugi, Hiroshi

    2017-08-01

    While major depressive disorder (MDD) is considered to be a heterogeneous disorder, the nature of the heterogeneity remains unclear. Studies have attempted to classify patients with MDD using latent variable techniques, yet the empirical approaches to symptom-based subtyping of MDD have not provided conclusive evidence. Here we aimed to identify homogeneous classes of MDD based on personality traits, using a latent profile analysis. We studied 238 outpatients with DSM-IV MDD recruited from our specialized depression outpatient clinic and assessed their dimensional personality traits with the Temperament and Character Inventory. Latent profile analysis was conducted with 7 dimensions of the Temperament and Character Inventory as indicators. Relationships of the identified classes with symptomatology, prescription pattern, and social function were then examined. The latent profile analysis indicated that a 3-class solution best fit the data. Of the sample, 46.2% was classified into a "neurotic" group characterized by high harm avoidance and low self-directedness; 30.3% into an "adaptive" group characterized by high self-directedness and cooperativeness; and 23.5% into a "socially-detached" group characterized by low reward dependence and cooperativeness and high self-transcendence. The 2 maladaptive groups, namely neurotic and socially-detached groups, demonstrated unique patterns of symptom expression, different classes of psychotropic medication use, and lower social functioning. Generalizability of the findings was limited since our patients were recruited from the specialized depression outpatient clinic. Our personality-based latent profile analysis identified clinically meaningful 3 MDD groups that were markedly different in their personality profiles associated with distinct symptomatology and functioning. Copyright © 2017 Elsevier B.V. All rights reserved.

  12. A chronological expression profile of gene activity during embryonic mouse brain development.

    PubMed

    Goggolidou, P; Soneji, S; Powles-Glover, N; Williams, D; Sethi, S; Baban, D; Simon, M M; Ragoussis, I; Norris, D P

    2013-12-01

    The brain is a functionally complex organ, the patterning and development of which are key to adult health. To help elucidate the genetic networks underlying mammalian brain patterning, we conducted detailed transcriptional profiling during embryonic development of the mouse brain. A total of 2,400 genes were identified as showing differential expression between three developmental stages. Analysis of the data identified nine gene clusters to demonstrate analogous expression profiles. A significant group of novel genes of as yet undiscovered biological function were detected as being potentially relevant to brain development and function, in addition to genes that have previously identified roles in the brain. Furthermore, analysis for genes that display asymmetric expression between the left and right brain hemispheres during development revealed 35 genes as putatively asymmetric from a combined data set. Our data constitute a valuable new resource for neuroscience and neurodevelopment, exposing possible functional associations between genes, including novel loci, and encouraging their further investigation in human neurological and behavioural disorders.

  13. Comparative analysis of gene expression profiles of hip articular cartilage between non-traumatic necrosis and osteoarthritis.

    PubMed

    Wang, Wenyu; Liu, Yang; Hao, Jingcan; Zheng, Shuyu; Wen, Yan; Xiao, Xiao; He, Awen; Fan, Qianrui; Zhang, Feng; Liu, Ruiyu

    2016-10-10

    Hip cartilage destruction is consistently observed in the non-traumatic osteonecrosis of femoral head (NOFH) and accelerates its bone necrosis. The molecular mechanism underlying the cartilage damage of NOFH remains elusive. In this study, we conducted a systematically comparative study of gene expression profiles between NOFH and osteoarthritis (OA). Hip articular cartilage specimens were collected from 12 NOFH patients and 12 controls with traumatic femoral neck fracture for microarray (n=4) and quantitative real-time PCR validation experiments (n=8). Gene expression profiling of articular cartilage was performed using Agilent Human 4×44K Microarray chip. The accuracy of microarray experiment was further validated by qRT-PCR. Gene expression results of OA hip cartilage were derived from previously published study. Significance Analysis of Microarrays (SAM) software was applied for identifying differently expressed genes. Gene ontology (GO) and pathway enrichment analysis were conducted by Gene Set Enrichment Analysis software and DAVID tool, respectively. Totally, 27 differently expressed genes were identified for NOFH. Comparing the gene expression profiles of NOFH cartilage and OA cartilage detected 8 common differently expressed genes, including COL5A1, OGN, ANGPTL4, CRIP1, NFIL3, METRNL, ID2 and STEAP1. GO comparative analysis identified 10 common significant GO terms, mainly implicated in apoptosis and development process. Pathway comparative analysis observed that ECM-receptor interaction pathway and focal adhesion pathway were enriched in the differently expressed genes of both NOFH and hip OA. In conclusion, we identified a set of differently expressed genes, GO and pathways for NOFH articular destruction, some of which were also involved in the hip OA. Our study results may help to reveal the pathogenetic similarities and differences of cartilage damage of NOFH and hip OA. Copyright © 2016 Elsevier B.V. All rights reserved.

  14. Cumulative Socioeconomic Status Risk, Allostatic Load, and Adjustment: A Prospective Latent Profile Analysis With Contextual and Genetic Protective Factors

    PubMed Central

    Brody, Gene H.; Yu, Tianyi; Chen, Yi-fu; Kogan, Steven M.; Evans, Gary W.; Beach, Steven R. H.; Windle, Michael; Simons, Ronald L.; Gerrard, Meg; Gibbons, Frederick X.; Philibert, Robert A.

    2012-01-01

    The health disparities literature identified a common pattern among middle-aged African Americans that includes high rates of chronic disease along with low rates of psychiatric disorders despite exposure to high levels of cumulative SES risk. The current study was designed to test hypotheses about the developmental precursors to this pattern. Hypotheses were tested with a representative sample of 443 African American youths living in the rural South. Cumulative SES risk and protective processes were assessed at 11-13 years; psychological adjustment was assessed at ages 14-18 years; genotyping at the 5-HTTLPR was conducted at age 16 years; and allostatic load (AL) was assessed at age 19 years. A Latent Profile Analysis identified 5 profiles that evinced distinct patterns of SES risk, AL, and psychological adjustment, with 2 relatively large profiles designated as focal profiles: a physical health vulnerability profile characterized by high SES risk/high AL/low adjustment problems, and a resilient profile characterized by high SES risk/low AL/low adjustment problems. The physical health vulnerability profile mirrored the pattern found in the adult health disparities literature. Multinomial logistic regression analyses indicated that carrying an s allele at the 5-HTTLPR and receiving less peer support distinguished the physical health vulnerability profile from the resilient profile. Protective parenting and planful self-regulation distinguished both focal profiles from the other 3 profiles. The results suggest the public health importance of preventive interventions that enhance coping and reduce the effects of stress across childhood and adolescence. PMID:22709130

  15. Cumulative socioeconomic status risk, allostatic load, and adjustment: a prospective latent profile analysis with contextual and genetic protective factors.

    PubMed

    Brody, Gene H; Yu, Tianyi; Chen, Yi-fu; Kogan, Steven M; Evans, Gary W; Beach, Steven R H; Windle, Michael; Simons, Ronald L; Gerrard, Meg; Gibbons, Frederick X; Philibert, Robert A

    2013-05-01

    The health disparities literature has identified a common pattern among middle-aged African Americans that includes high rates of chronic disease along with low rates of psychiatric disorders despite exposure to high levels of cumulative socioeconomic status (SES) risk. The current study was designed to test hypotheses about the developmental precursors to this pattern. Hypotheses were tested with a representative sample of 443 African American youths living in the rural South. Cumulative SES risk and protective processes were assessed at ages 11-13 years; psychological adjustment was assessed at ages 14-18 years; genotyping at the 5-HTTLPR was conducted at age 16 years; and allostatic load (AL) was assessed at age 19 years. A latent profile analysis identified 5 profiles that evinced distinct patterns of SES risk, AL, and psychological adjustment, with 2 relatively large profiles designated as focal profiles: a physical health vulnerability profile characterized by high SES risk/high AL/low adjustment problems, and a resilient profile characterized by high SES risk/low AL/low adjustment problems. The physical health vulnerability profile mirrored the pattern found in the adult health disparities literature. Multinomial logistic regression analyses indicated that carrying an s allele at the 5-HTTLPR and receiving less peer support distinguished the physical health vulnerability profile from the resilient profile. Protective parenting and planful self-regulation distinguished both focal profiles from the other 3 profiles. The results suggest the public health importance of preventive interventions that enhance coping and reduce the effects of stress across childhood and adolescence.

  16. Serum Metabolic Profiling of Oocyst-Induced Toxoplasma gondii Acute and Chronic Infections in Mice Using Mass-Spectrometry

    PubMed Central

    Zhou, Chun-Xue; Cong, Wei; Chen, Xiao-Qing; He, Shen-Yi; Elsheikha, Hany M.; Zhu, Xing-Quan

    2018-01-01

    Toxoplasma gondii is an obligate intracellular parasite causing severe diseases in immunocompromised individuals and congenitally infected neonates, such as encephalitis and chorioretinitis. This study aimed to determine whether serum metabolic profiling can (i) identify metabolites associated with oocyst-induced T. gondii infection and (ii) detect systemic metabolic differences between T. gondii-infected mice and controls. We performed the first global metabolomics analysis of mice serum challenged with 100 sporulated T. gondii Pru oocysts (Genotype II). Sera from acutely infected mice (11 days post-infection, dpi), chronically infected mice (33 dpi) and control mice were collected and analyzed using LC-MS/MS platform. Following False Discovery Rate filtering, we identified 3871 and 2825 ions in ESI+ or ESI− mode, respectively. Principal Component Analysis (PCA) and Partial Least Squares Discriminant Analysis (PLS-DA) identified metabolomic profiles that clearly differentiated T. gondii-infected and -uninfected serum samples. Acute infection significantly influenced the serum metabolome. Our results identified common and uniquely perturbed metabolites and pathways. Acutely infected mice showed perturbations in metabolites associated with glycerophospholipid metabolism, biosynthesis of amino acid, and tyrosine metabolism. These findings demonstrated that acute T. gondii infection induces a global perturbation of mice serum metabolome, providing new insights into the mechanisms underlying systemic metabolic changes during early stage of T. gondii infection. PMID:29354104

  17. Label-Free LC-MS/MS Proteomic Analysis of Cerebrospinal Fluid Identifies Protein/Pathway Alterations and Candidate Biomarkers for Amyotrophic Lateral Sclerosis.

    PubMed

    Collins, Mahlon A; An, Jiyan; Hood, Brian L; Conrads, Thomas P; Bowser, Robert P

    2015-11-06

    Analysis of the cerebrospinal fluid (CSF) proteome has proven valuable to the study of neurodegenerative disorders. To identify new protein/pathway alterations and candidate biomarkers for amyotrophic lateral sclerosis (ALS), we performed comparative proteomic profiling of CSF from sporadic ALS (sALS), healthy control (HC), and other neurological disease (OND) subjects using label-free liquid chromatography-tandem mass spectrometry (LC-MS/MS). A total of 1712 CSF proteins were detected and relatively quantified by spectral counting. Levels of several proteins with diverse biological functions were significantly altered in sALS samples. Enrichment analysis was used to link these alterations to biological pathways, which were predominantly related to inflammation, neuronal activity, and extracellular matrix regulation. We then used our CSF proteomic profiles to create a support vector machines classifier capable of discriminating training set ALS from non-ALS (HC and OND) samples. Four classifier proteins, WD repeat-containing protein 63, amyloid-like protein 1, SPARC-like protein 1, and cell adhesion molecule 3, were identified by feature selection and externally validated. The resultant classifier distinguished ALS from non-ALS samples with 83% sensitivity and 100% specificity in an independent test set. Collectively, our results illustrate the utility of CSF proteomic profiling for identifying ALS protein/pathway alterations and candidate disease biomarkers.

  18. A method to identify differential expression profiles of time-course gene data with Fourier transformation.

    PubMed

    Kim, Jaehee; Ogden, Robert Todd; Kim, Haseong

    2013-10-18

    Time course gene expression experiments are an increasingly popular method for exploring biological processes. Temporal gene expression profiles provide an important characterization of gene function, as biological systems are both developmental and dynamic. With such data it is possible to study gene expression changes over time and thereby to detect differential genes. Much of the early work on analyzing time series expression data relied on methods developed originally for static data and thus there is a need for improved methodology. Since time series expression is a temporal process, its unique features such as autocorrelation between successive points should be incorporated into the analysis. This work aims to identify genes that show different gene expression profiles across time. We propose a statistical procedure to discover gene groups with similar profiles using a nonparametric representation that accounts for the autocorrelation in the data. In particular, we first represent each profile in terms of a Fourier basis, and then we screen out genes that are not differentially expressed based on the Fourier coefficients. Finally, we cluster the remaining gene profiles using a model-based approach in the Fourier domain. We evaluate the screening results in terms of sensitivity, specificity, FDR and FNR, compare with the Gaussian process regression screening in a simulation study and illustrate the results by application to yeast cell-cycle microarray expression data with alpha-factor synchronization.The key elements of the proposed methodology: (i) representation of gene profiles in the Fourier domain; (ii) automatic screening of genes based on the Fourier coefficients and taking into account autocorrelation in the data, while controlling the false discovery rate (FDR); (iii) model-based clustering of the remaining gene profiles. Using this method, we identified a set of cell-cycle-regulated time-course yeast genes. The proposed method is general and can be potentially used to identify genes which have the same patterns or biological processes, and help facing the present and forthcoming challenges of data analysis in functional genomics.

  19. Pre-clinical cognitive phenotypes for Alzheimer disease: a latent profile approach.

    PubMed

    Hayden, Kathleen M; Kuchibhatla, Maragatha; Romero, Heather R; Plassman, Brenda L; Burke, James R; Browndyke, Jeffrey N; Welsh-Bohmer, Kathleen A

    2014-11-01

    Cognitive profiles for pre-clinical Alzheimer disease (AD) can be used to identify groups of individuals at risk for disease and better characterize pre-clinical disease. Profiles or patterns of performance as pre-clinical phenotypes may be more useful than individual test scores or measures of global decline. To evaluate patterns of cognitive performance in cognitively normal individuals to derive latent profiles associated with later onset of disease using a combination of factor analysis and latent profile analysis. The National Alzheimer Coordinating Centers collect data, including a battery of neuropsychological tests, from participants at 29 National Institute on Aging-funded Alzheimer Disease Centers across the United States. Prior factor analyses of this battery demonstrated a four-factor structure comprising memory, attention, language, and executive function. Factor scores from these analyses were used in a latent profile approach to characterize cognition among a group of cognitively normal participants (N = 3,911). Associations between latent profiles and disease outcomes an average of 3 years later were evaluated with multinomial regression models. Similar analyses were used to determine predictors of profile membership. Four groups were identified; each with distinct characteristics and significantly associated with later disease outcomes. Two groups were significantly associated with development of cognitive impairment. In post hoc analyses, both the Trail Making Test Part B, and a contrast score (Delayed Recall - Trails B), significantly predicted group membership and later cognitive impairment. Latent profile analysis is a useful method to evaluate patterns of cognition in large samples for the identification of preclinical AD phenotypes; comparable results, however, can be achieved with very sensitive tests and contrast scores. Copyright © 2014 American Association for Geriatric Psychiatry. Published by Elsevier Inc. All rights reserved.

  20. The Different Facets of Work Stress: A Latent Profile Analysis of Nurses' Work Demands.

    PubMed

    Jenull, Brigitte B; Wiedermann, Wolfgang

    2015-10-01

    Work-related stress has been identified as a relevant problem leading to negative effects on health and quality of life. Using data from 844 nurses, latent profile analyses (LPA) were applied to identify distinct patterns of work stress. Several sociodemographic variables, including nurses' working and living conditions, as well as nurses' reactions to workload, were considered to predict respondents' profile membership. LPA revealed three distinct profiles that can be distinguished by a low, moderate, and higher stress level. Being financially secure is positively related to the low stress profile, whereas working in an urban area and having low job satisfaction increases the chance of belonging to the higher stress profile. Our results can be used as a basis to develop interventions to create a healthy nursing home environment by supporting the balance between family and work, providing access to job resources and optimizing recovery opportunities. © The Author(s) 2013.

  1. A social network-informed latent class analysis of patterns of substance use, sexual behavior, and mental health: Social Network Study III, Winnipeg, Manitoba, Canada.

    PubMed

    Hopfer, Suellen; Tan, Xianming; Wylie, John L

    2014-05-01

    We assessed whether a meaningful set of latent risk profiles could be identified in an inner-city population through individual and network characteristics of substance use, sexual behaviors, and mental health status. Data came from 600 participants in Social Network Study III, conducted in 2009 in Winnipeg, Manitoba, Canada. We used latent class analysis (LCA) to identify risk profiles and, with covariates, to identify predictors of class. A 4-class model of risk profiles fit the data best: (1) solitary users reported polydrug use at the individual level, but low probabilities of substance use or concurrent sexual partners with network members; (2) social-all-substance users reported polydrug use at the individual and network levels; (3) social-noninjection drug users reported less likelihood of injection drug and solvent use; (4) low-risk users reported low probabilities across substances. Unstable housing, preadolescent substance use, age, and hepatitis C status predicted risk profiles. Incorporation of social network variables into LCA can distinguish important subgroups with varying patterns of risk behaviors that can lead to sexually transmitted and bloodborne infections.

  2. Analysis of the Human Prostate-Specific Proteome Defined by Transcriptomics and Antibody-Based Profiling Identifies TMEM79 and ACOXL as Two Putative, Diagnostic Markers in Prostate Cancer

    PubMed Central

    O'Hurley, Gillian; Busch, Christer; Fagerberg, Linn; Hallström, Björn M.; Stadler, Charlotte; Tolf, Anna; Lundberg, Emma; Schwenk, Jochen M.; Jirström, Karin; Bjartell, Anders; Gallagher, William M.; Uhlén, Mathias; Pontén, Fredrik

    2015-01-01

    To better understand prostate function and disease, it is important to define and explore the molecular constituents that signify the prostate gland. The aim of this study was to define the prostate specific transcriptome and proteome, in comparison to 26 other human tissues. Deep sequencing of mRNA (RNA-seq) and immunohistochemistry-based protein profiling were combined to identify prostate specific gene expression patterns and to explore tissue biomarkers for potential clinical use in prostate cancer diagnostics. We identified 203 genes with elevated expression in the prostate, 22 of which showed more than five-fold higher expression levels compared to all other tissue types. In addition to previously well-known proteins we identified two poorly characterized proteins, TMEM79 and ACOXL, with potential to differentiate between benign and cancerous prostatic glands in tissue biopsies. In conclusion, we have applied a genome-wide analysis to identify the prostate specific proteome using transcriptomics and antibody-based protein profiling to identify genes with elevated expression in the prostate. Our data provides a starting point for further functional studies to explore the molecular repertoire of normal and diseased prostate including potential prostate cancer markers such as TMEM79 and ACOXL. PMID:26237329

  3. School profiles of at-risk student concentration: Differential growth in oral reading fluency

    PubMed Central

    Logan, Jessica A.R.; Petscher, Yaacov

    2010-01-01

    The present study provides a data-driven approach to identifying groups of schools based on the concentration of at-risk students the school serves. The percentage of English language learners, minority students, and students eligible for free or reduced priced lunch were used as indicators in a latent profile analysis of 569 schools. The goal of the present study was to determine whether school-level average student reading performance varied as a function of the groups identified in the latent profile analysis. To do so, groups extracted by the latent profile analysis were used as school-level predictors of growth in oral reading fluency, which was modeled at the within-student level of a three-level hierarchical growth curve model. Oral reading fluency was measured at four points during the year in a large cross-sectional sample of first-, second-, and third-grade students. Results indicated that schools were able to be classified into four distinct groups based on their concentrations and types of at-risk students. Further, in all three grades, there were significant differences between the four identified groups observed in average reading fluency scores at the beginning of the year, the end of the year, and growth during the year indicating that groups based on school-concentration of at-risk students were significantly related to average student achievement in reading ability. PMID:20159224

  4. An approach to functionally relevant clustering of the protein universe: Active site profile-based clustering of protein structures and sequences.

    PubMed

    Knutson, Stacy T; Westwood, Brian M; Leuthaeuser, Janelle B; Turner, Brandon E; Nguyendac, Don; Shea, Gabrielle; Kumar, Kiran; Hayden, Julia D; Harper, Angela F; Brown, Shoshana D; Morris, John H; Ferrin, Thomas E; Babbitt, Patricia C; Fetrow, Jacquelyn S

    2017-04-01

    Protein function identification remains a significant problem. Solving this problem at the molecular functional level would allow mechanistic determinant identification-amino acids that distinguish details between functional families within a superfamily. Active site profiling was developed to identify mechanistic determinants. DASP and DASP2 were developed as tools to search sequence databases using active site profiling. Here, TuLIP (Two-Level Iterative clustering Process) is introduced as an iterative, divisive clustering process that utilizes active site profiling to separate structurally characterized superfamily members into functionally relevant clusters. Underlying TuLIP is the observation that functionally relevant families (curated by Structure-Function Linkage Database, SFLD) self-identify in DASP2 searches; clusters containing multiple functional families do not. Each TuLIP iteration produces candidate clusters, each evaluated to determine if it self-identifies using DASP2. If so, it is deemed a functionally relevant group. Divisive clustering continues until each structure is either a functionally relevant group member or a singlet. TuLIP is validated on enolase and glutathione transferase structures, superfamilies well-curated by SFLD. Correlation is strong; small numbers of structures prevent statistically significant analysis. TuLIP-identified enolase clusters are used in DASP2 GenBank searches to identify sequences sharing functional site features. Analysis shows a true positive rate of 96%, false negative rate of 4%, and maximum false positive rate of 4%. F-measure and performance analysis on the enolase search results and comparison to GEMMA and SCI-PHY demonstrate that TuLIP avoids the over-division problem of these methods. Mechanistic determinants for enolase families are evaluated and shown to correlate well with literature results. © 2017 The Authors Protein Science published by Wiley Periodicals, Inc. on behalf of The Protein Society.

  5. Friendship Group Composition and Juvenile Institutional Misconduct.

    PubMed

    Reid, Shannon E

    2017-02-01

    The present study examines both the patterns of friendship networks and how these network characteristics relate to the risk factors of institutional misconduct for incarcerated youth. Using friendship networks collected from males incarcerated with California's Division of Juvenile Justice (DJJ), latent profile analysis was utilized to create homogeneous groups of friendship patterns based on alter attributes and network structure. The incarcerated youth provided 144 egocentric networks reporting 558 social network relationships. Latent profile analysis identified three network profiles: expected group (67%), new breed group (20%), and model citizen group (13%). The three network profiles were integrated into a multiple group analysis framework to examine the relative influence of individual-level risk factors on their rate of institutional misconduct. The analysis finds variation in predictors of institutional misconduct across profile types. These findings suggest that the close friendships of incarcerated youth are patterned across the individual characteristics of the youth's friends and that the friendship network can act as a moderator for individual risk factors for institutional misconduct.

  6. Study to determine the IFR operational profile and problems to the general aviation pilot

    NASA Technical Reports Server (NTRS)

    Weislogel, S.

    1983-01-01

    A study of the general aviation single pilot operating under instrument flight rules (GA SPIFR) has been conducted for NASA Langley Research Center. The objectives of the study were to (1) develop a GA SPIFR operational profile, (2) identify problems experienced by the GA SPIFR pilot, and (3) identify research tasks which have the potential for eliminating or reducing the severity of the problems. To obtain the information necessary to accomplish these objectives, a mail questionnaire survey of instrument rated pilots was conducted. Complete questionnaire data is reported in NASA CR-165805, "Statistical Summary: Study to Determine the IFR Operational Profile and Problems of the General Aviation Single Pilot'-Based upon the results of the GA SPIFR survey, this final report presents the general aviation IFR single pilot operational profile, illustrates selected data analysis, examples, identifies the problems which he is experiencing, and recommends further research.

  7. Multidimensional Characterization of Sexual Minority Adolescents’ Sexual Safety Strategies

    PubMed Central

    Masters, N. Tatiana; Beadnell, Blair; Morrison, Diane M.; Hoppe, Marilyn J.; Wells, Elizabeth A.

    2013-01-01

    Young adults have high rates of sexually transmitted infections (STIs). Sexual minority youths’ risk for STIs, including HIV, is as high as or higher than sexual majority peers’. Sexual safety, while often treated as a single behavior such as condom use, can be best conceptualized as the result of multiple factors. We used latent class analysis to identify profiles based on ever-used sexual safety strategies and lifetime number of partners among 425 self-identified LGBTQ youth aged 14-19. Data collection took place anonymously online. We identified four specific subgroup profiles for males and three for females, with each subgroup representing a different level and type of sexual safety. Profiles differed from each other in terms of age and outness for males, and in outness, personal homonegativity, and amount of education received about sexual/romantic relationships for females. Youths’ sexual safety profiles have practice implications for sexuality educators, health care professionals, and parents. PMID:24011111

  8. Profiles of Childhood Trauma in Patients with Alcohol Dependence and Their Associations with Addiction-Related Problems.

    PubMed

    Lotzin, Annett; Haupt, Lena; von Schönfels, Julia; Wingenfeld, Katja; Schäfer, Ingo

    2016-03-01

    The high occurrence of childhood trauma in individuals with alcohol dependence is well-recognized. Nevertheless, researchers have rarely studied which types of childhood trauma often co-occur and how these combinations of different types and severities of childhood trauma are related to the patients' current addiction-related problems. We aimed to identify childhood trauma profiles in patients with alcohol dependence and examined relations of these trauma profiles with the patients' current addiction-related problems. In 347 alcohol-dependent patients, 5 types of childhood trauma (sexual abuse, physical abuse, emotional abuse, emotional neglect, and physical neglect) were measured using the Childhood Trauma Questionnaire. Childhood trauma profiles were identified using cluster analysis. The patients' current severity of addiction-related problems was assessed using the European Addiction Severity Index. We identified 6 profiles that comprised different types and severities of childhood trauma. The patients' trauma profiles predicted the severity of addiction-related problems in the domains of psychiatric symptoms, family relationships, social relationships, and drug use. Childhood trauma profiles may provide more useful information about the patient's risk of current addiction-related problems than the common distinction between traumatized versus nontraumatized patients. Copyright © 2016 by the Research Society on Alcoholism.

  9. Transcriptome profiling to identify ATRA-responsive genes in human iPSC-derived endoderm for high-throughput point of departure analysis (SOT Annual Meeting)

    EPA Science Inventory

    Toxicological tipping points occur at chemical concentrations that overwhelm a cell’s adaptive response leading to permanent effects. We focused on retinoid signaling in differentiating endoderm to identify developmental pathways for tipping point analysis. Human induced pluripot...

  10. Analysis of waterborne paints by gas chromatography-mass spectrometry with a temperature-programmable pyrolyzer.

    PubMed

    Nakamura, S; Takino, M; Daishima, S

    2001-04-06

    Gas chromatography-mass spectrometry (GC-MS) with a temperature-programmable pyrolyzer was used for the analysis of waterborne paints. Evolved gas analysis (EGA) profiles of the waterborne paints were obtained by this temperature-programmed pyrolysis directly coupled with MS via a deactivated metal capillary tube. The EGA profile suggested the optimal thermal desorption conditions for solvents and additives and the subsequent optimal pyrolysis temperature for the remaining polymeric material. Polymers were identified from pyrograms with the assistance of a new polymer library. The solvents were identified from the electron ionization mass spectra with the corresponding chemical ionization mass spectra. The additive was identified as zinc pyrithione by comparison with authentic standard. Zinc pyrithione cannot be analyzed by GC-MS as it is. However, the thermal decomposition products of zinc pyrithione could be detected. The information on the decomposition temperature and products was useful for the identification of the original compound.

  11. Metabolites Associated With Malnutrition in the Intensive Care Unit Are Also Associated With 28-Day Mortality.

    PubMed

    Mogensen, Kris M; Lasky-Su, Jessica; Rogers, Angela J; Baron, Rebecca M; Fredenburgh, Laura E; Rawn, James; Robinson, Malcolm K; Massarro, Anthony; Choi, Augustine M K; Christopher, Kenneth B

    2017-02-01

    We hypothesized that metabolic profiles would differ in critically ill patients with malnutrition relative to those without. We performed a prospective cohort study on 85 adult patients with systemic inflammatory response syndrome or sepsis admitted to a 20-bed medical intensive care unit (ICU) in Boston. We generated metabolomic profiles using gas and liquid chromatography and mass spectroscopy. We followed this by logistic regression and partial least squares discriminant analysis to identify individual metabolites that were significant. We then interrogated the entire metabolomics profile using metabolite set enrichment analysis and network model construction of chemical-protein target interactions to identify groups of metabolites and pathways that were differentiates in patients with and without malnutrition. Of the cohort, 38% were malnourished at admission to the ICU. Metabolomic profiles differed in critically ill patients with malnutrition relative to those without. Ten metabolites were significantly associated with malnutrition ( P < .05). A parsimonious model of 5 metabolites effectively differentiated patients with malnutrition (AUC = 0.76), including pyroglutamine and hypoxanthine. Using pathway enrichment analysis, we identified a critical role of glutathione and purine metabolism in predicting nutrition. Nutrition status was associated with 28-day mortality, even after adjustment for known phenotypic variables associated with ICU mortality. Importantly, 7 metabolites associated with nutrition status were also associated with 28-day mortality. Malnutrition is associated with differential metabolic profiles early in critical illness. Common to all of our metabolome analyses, glutathione and purine metabolism, which play principal roles in cellular redox regulation and accelerated tissue adenosine triphosphate degradation, respectively, were significantly altered with malnutrition.

  12. Evaluation of facial attractiveness in black people according to the subjective facial analysis criteria.

    PubMed

    Melo, Andréa Reis de; Conti, Ana Cláudia de Castro Ferreira; Almeida-Pedrin, Renata Rodrigues; Didier, Victor; Valarelli, Danilo Pinelli; Capelozza Filho, Leopoldino

    2017-02-01

    The objective of this study was to evaluate the facial attractiveness in 30 black individuals, according to the Subjective Facial Analysis criteria. Frontal and profile view photographs of 30 black individuals were evaluated for facial attractiveness and classified as esthetically unpleasant, acceptable, or pleasant by 50 evaluators: the 30 individuals from the sample, 10 orthodontists, and 10 laymen. Besides assessing the facial attractiveness, the evaluators had to identify the structures responsible for the classification as unpleasant and pleasant. Intraexaminer agreement was assessed by using Spearman's correlation, correlation within each category using Kendall concordance coefficient, and correlation between the 3 categories using chi-square test and proportions. Most of the frontal (53. 5%) and profile view (54. 9%) photographs were classified as esthetically acceptable. The structures most identified as esthetically unpleasant were the mouth, lips, and face, in the frontal view; and nose and chin in the profile view. The structures most identified as esthetically pleasant were harmony, face, and mouth, in the frontal view; and harmony and nose in the profile view. The ratings by the examiners in the sample and laymen groups showed statistically significant correlation in both views. The orthodontists agreed with the laymen on the evaluation of the frontal view and disagreed on profile view, especially regarding whether the images were esthetically unpleasant or acceptable. Based on these results, the evaluation of facial attractiveness according to the Subjective Facial Analysis criteria proved to be applicable and to have a subjective influence; therefore, it is suggested that the patient's opinion regarding the facial esthetics should be considered in orthodontic treatmentplanning.

  13. “Heroes” and “Villains” of World History across Cultures

    PubMed Central

    Hanke, Katja; Liu, James H.; Sibley, Chris G.; Paez, Dario; Gaines, Stanley O.; Moloney, Gail; Leong, Chan-Hoong; Wagner, Wolfgang; Licata, Laurent; Klein, Olivier; Garber, Ilya; Böhm, Gisela; Hilton, Denis J.; Valchev, Velichko; Khan, Sammyh S.; Cabecinhas, Rosa

    2015-01-01

    Emergent properties of global political culture were examined using data from the World History Survey (WHS) involving 6,902 university students in 37 countries evaluating 40 figures from world history. Multidimensional scaling and factor analysis techniques found only limited forms of universality in evaluations across Western, Catholic/Orthodox, Muslim, and Asian country clusters. The highest consensus across cultures involved scientific innovators, with Einstein having the most positive evaluation overall. Peaceful humanitarians like Mother Theresa and Gandhi followed. There was much less cross-cultural consistency in the evaluation of negative figures, led by Hitler, Osama bin Laden, and Saddam Hussein. After more traditional empirical methods (e.g., factor analysis) failed to identify meaningful cross-cultural patterns, Latent Profile Analysis (LPA) was used to identify four global representational profiles: Secular and Religious Idealists were overwhelmingly prevalent in Christian countries, and Political Realists were common in Muslim and Asian countries. We discuss possible consequences and interpretations of these different representational profiles. PMID:25651504

  14. Polarization Behavior Across Profile Modes For B0329+54: What Consistent Non-RVM Polarization Tells About the Emission Processes

    NASA Astrophysics Data System (ADS)

    Brinkman-Traverse, Casey; Rankin, Joanna M.; Mitra, Dipanjan

    2017-01-01

    In this paper, we analyze the quirky polarization behavior across different profile modes for the pulsar B0329+54. We have multi-frequency observations in both the normal and abnormal profile modes, and have identified a non-RVM polarization kink in the core component of the emission. Mitra et al initially identified this kink in the normal profile mode of the pulsar in 2007, and a mirror analysis has been done here for abnormal profile modes at three different frequencies. This kink is intensity dependent, showing up only in the abberated/retarded high intensity pulses, and is frequency independent. This parallel between profile modes shows that the same geometric phenomenon—a height dependent amplifier—is responsible for the non-RVM polarization behavior in each. The question then arises: what can be the source of the profile change, which does not change the polarization characteristics of the pulsar. This pulsar gives us a unique opportunity to study the process of pulsar emission by showing what cannot be responsible for switches in profile mode, and thus profile shape.

  15. Progression Rate Associated Peripheral Blood Biomarkers of Parkinson's Disease.

    PubMed

    Fan, Yanxia; Xiao, Shuping

    2018-06-23

    Parkinson disease (PD) is one of the most frequent neurodegenerative disorders. The aim of this study was to identify blood biomarkers capable to discriminate PD patients with different progression rates. Differentially expressed genes (DEGs) were acquired by comparing the expression profiles of PD patients with rapid and slow progression rates, using an expression dataset from Gene Expression Omnibus (GEO) under accession code of GSE80599. Altered biological processes and pathways were revealed by functional annotation. Potential biomarkers of PD were identified by protein-protein interaction (PPI) network analysis. Critical transcription factors (TFs) and miRNAs regulating DEGs were predicted by TF analysis and miRNA analysis. A total of 225 DEGs were identified between PD patients with rapid and slow progression profiles. These genes were significantly enriched in biological processes and pathways related to fatty acid metabolism. Among these DEGs, ZFAND4, SRMS, UBL4B, PVALB, DIRAS1, PDP2, LRCH1, and MYL4 were potential progression rate associated biomarkers of PD. Additionally, these DEGs may be regulated by miRNAs of the miR-30 family and TFs STAT1 and GRHL3. Our results may contribute to our understanding of the molecular mechanisms underlying different PD progression profiles.

  16. Gene expression profiles in rainbow trout, Onchorynchus mykiss, exposed to a simple chemical mixture.

    PubMed

    Hook, Sharon E; Skillman, Ann D; Gopalan, Banu; Small, Jack A; Schultz, Irvin R

    2008-03-01

    Among proposed uses for microarrays in environmental toxiciology is the identification of key contributors to toxicity within a mixture. However, it remains uncertain whether the transcriptomic profiles resulting from exposure to a mixture have patterns of altered gene expression that contain identifiable contributions from each toxicant component. We exposed isogenic rainbow trout Onchorynchus mykiss, to sublethal levels of ethynylestradiol, 2,2,4,4-tetrabromodiphenyl ether, and chromium VI or to a mixture of all three toxicants Fluorescently labeled complementary DNA (cDNA) were generated and hybridized against a commercially available Salmonid array spotted with 16,000 cDNAs. Data were analyzed using analysis of variance (p<0.05) with a Benjamani-Hochberg multiple test correction (Genespring [Agilent] software package) to identify up and downregulated genes. Gene clustering patterns that can be used as "expression signatures" were determined using hierarchical cluster analysis. The gene ontology terms associated with significantly altered genes were also used to identify functional groups that were associated with toxicant exposure. Cross-ontological analytics approach was used to assign functional annotations to genes with "unknown" function. Our analysis indicates that transcriptomic profiles resulting from the mixture exposure resemble those of the individual contaminant exposures, but are not a simple additive list. However, patterns of altered genes representative of each component of the mixture are clearly discernible, and the functional classes of genes altered represent the individual components of the mixture. These findings indicate that the use of microarrays to identify transcriptomic profiles may aid in the identification of key stressors within a chemical mixture, ultimately improving environmental assessment.

  17. Nano-LC-ESI MS/MS analysis of proteins in dried sea dragon Solenognathus hardwickii and bioinformatic analysis of its protein expression profiling.

    PubMed

    Zhang, Dong-Mei; Feng, Li-Xing; Li, Lu; Liu, Miao; Jiang, Bao-Hong; Yang, Min; Li, Guo-Qiang; Wu, Wan-Ying; Guo, De-An; Liu, Xuan

    2016-09-01

    The sea dragon Solenognathus hardwickii has long been used as a traditional Chinese medicine for the treatment of various diseases, such as male impotency. To gain a comprehensive insight into the protein components of the sea dragon, shotgun proteomic analysis of its protein expression profiling was conducted in the present study. Proteins were extracted from dried sea dragon using a trichloroacetic acid/acetone precipitation method and then separated by SDS-PAGE. The protein bands were cut from the gel and digested by trypsin to generate peptide mixture. The peptide fragments were then analyzed using nano liquid chromatography tandem mass spectrometry (nano-LC-ESI MS/MS). 810 proteins and 1 577 peptides were identified in the dried sea dragon. The identified proteins exhibited molecular weight values ranging from 1 900 to 3 516 900 Da and pI values from 3.8 to 12.18. Bioinformatic analysis was conducted using the DAVID Bioinformatics Resources 6.7 Gene Ontology (GO) analysis tool to explore possible functions of the identified proteins. Ascribed functions of the proteins mainly included intracellular non-membrane-bound organelle, non-membrane-bounded organelle, cytoskeleton, structural molecule activity, calcium ion binding and etc. Furthermore, possible signal networks of the identified proteins were predicted using STRING (Search Tool for the Retrieval of Interacting Genes) database. Ribosomal protein synthesis was found to play an important role in the signal network. The results of this study, to best of our knowledge, were the first to provide a reference proteome profile for the sea dragon, and would aid in the understanding of the expression and functions of the identified proteins. Copyright © 2016 China Pharmaceutical University. Published by Elsevier B.V. All rights reserved.

  18. Analysis of alkylamides in Echinacea plant materials and dietary supplements by ultrafast liquid chromatography with diode array and mass spectrometric detection.

    PubMed

    Mudge, Elizabeth; Lopes-Lutz, Daise; Brown, Paula; Schieber, Andreas

    2011-08-10

    Alkylamides are a class of compounds present in plants of the genus Echinacea (Asteraceae), which have been shown to have high bioavailability and immunomodulatory effects. Fast analysis to identify these components in a variety of products is essential to profile products used in clinical trials and for quality control of these products. A method based on ultrafast liquid chromatography (UFLC) coupled with diode array detection and electrospray ionization mass spectrometry was developed for the analysis of alkylamides from the roots of Echinacea angustifolia (DC.) Hell., Echinacea purpurea (L.) Moench, and commercial dietary supplements. A total of 24 alkylamides were identified by LC-MS. The analysis time for these components is 15 min. Compared to the alkylamide profiles determined in the Echinacea root materials, the commercial products showed a more complex profile due to the blending of root and aerial parts of E. purpurea. This versatile method allows for the identification of alkylamides in a variety of Echinacea products and presents the most extensive characterization of alkylamides in E. angustifolia roots so far.

  19. Chemotaxonomic Study of Citrus, Poncirus and Fortunella Genotypes Based on Peel Oil Volatile Compounds - Deciphering the Genetic Origin of Mangshanyegan (Citrus nobilis Lauriro)

    PubMed Central

    Liu, Cuihua; Jiang, Dong; Cheng, Yunjiang; Deng, Xiuxin; Chen, Feng; Fang, Liu; Ma, Zhaocheng; Xu, Juan

    2013-01-01

    Volatile profiles yielded from gas chromatography-mass spectrometry (GC-MS) analysis provide abundant information not only for metabolism-related research, but also for chemotaxonomy. To study the chemotaxonomy of Mangshanyegan, its volatile profiles of fruit and leaf and those of 29 other genotypes of Citrus, Poncirus, and Fortunella were subjected to phylogenetic analyses. Results showed that 145 identified (including 64 tentatively identified) and 15 unidentified volatile compounds were detected from their peel oils. The phylogenetic analysis of peel oils based on hierarchical cluster analysis (HCA) demonstrated a good agreement with the Swingle taxonomy system, in which the three genera of Citrus, Poncirus, and Fortunella were almost completely separated. As to Citrus, HCA indicated that Citrophorum, Cephalocitrus, and Sinocitrus fell into three subgroups, respectively. Also, it revealed that Mangshanyegan contain volatile compounds similar to those from pummelo, though it is genetically believed to be a mandarin. These results were further supported by the principal component analysis of the peel oils and the HCA results of volatile profiles of leaves in the study. PMID:23516475

  20. Genome-wide transcriptional analysis of flagellar regeneration in Chlamydomonas reinhardtii identifies orthologs of ciliary disease genes

    NASA Technical Reports Server (NTRS)

    Stolc, Viktor; Samanta, Manoj Pratim; Tongprasit, Waraporn; Marshall, Wallace F.

    2005-01-01

    The important role that cilia and flagella play in human disease creates an urgent need to identify genes involved in ciliary assembly and function. The strong and specific induction of flagellar-coding genes during flagellar regeneration in Chlamydomonas reinhardtii suggests that transcriptional profiling of such cells would reveal new flagella-related genes. We have conducted a genome-wide analysis of RNA transcript levels during flagellar regeneration in Chlamydomonas by using maskless photolithography method-produced DNA oligonucleotide microarrays with unique probe sequences for all exons of the 19,803 predicted genes. This analysis represents previously uncharacterized whole-genome transcriptional activity profiling study in this important model organism. Analysis of strongly induced genes reveals a large set of known flagellar components and also identifies a number of important disease-related proteins as being involved with cilia and flagella, including the zebrafish polycystic kidney genes Qilin, Reptin, and Pontin, as well as the testis-expressed tubby-like protein TULP2.

  1. Systemic bioinformatics analysis of skeletal muscle gene expression profiles of sepsis

    PubMed Central

    Yang, Fang; Wang, Yumei

    2018-01-01

    Sepsis is a type of systemic inflammatory response syndrome with high morbidity and mortality. Skeletal muscle dysfunction is one of the major complications of sepsis that may also influence the outcome of sepsis. The aim of the present study was to explore and identify potential mechanisms and therapeutic targets of sepsis. Systemic bioinformatics analysis of skeletal muscle gene expression profiles from the Gene Expression Omnibus was performed. Differentially expressed genes (DEGs) in samples from patients with sepsis and control samples were screened out using the limma package. Differential co-expression and coregulation (DCE and DCR, respectively) analysis was performed based on the Differential Co-expression Analysis package to identify differences in gene co-expression and coregulation patterns between the control and sepsis groups. Gene Ontology terms and Kyoto Encyclopedia of Genes and Genomes pathways of DEGs were identified using the Database for Annotation, Visualization and Integrated Discovery, and inflammatory, cancer and skeletal muscle development-associated biological processes and pathways were identified. DCE and DCR analysis revealed several potential therapeutic targets for sepsis, including genes and transcription factors. The results of the present study may provide a basis for the development of novel therapeutic targets and treatment methods for sepsis. PMID:29805480

  2. Gene co-expression network analysis in Rhodobacter capsulatus and application to comparative expression analysis of Rhodobacter sphaeroides

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

    Pena-Castillo, Lourdes; Mercer, Ryan; Gurinovich, Anastasia

    2014-08-28

    The genus Rhodobacter contains purple nonsulfur bacteria found mostly in freshwater environments. Representative strains of two Rhodobacter species, R. capsulatus and R. sphaeroides, have had their genomes fully sequenced and both have been the subject of transcriptional profiling studies. Gene co-expression networks can be used to identify modules of genes with similar expression profiles. Functional analysis of gene modules can then associate co-expressed genes with biological pathways, and network statistics can determine the degree of module preservation in related networks. In this paper, we constructed an R. capsulatus gene co-expression network, performed functional analysis of identified gene modules, and investigatedmore » preservation of these modules in R. capsulatus proteomics data and in R. sphaeroides transcriptomics data. Results: The analysis identified 40 gene co-expression modules in R. capsulatus. Investigation of the module gene contents and expression profiles revealed patterns that were validated based on previous studies supporting the biological relevance of these modules. We identified two R. capsulatus gene modules preserved in the protein abundance data. We also identified several gene modules preserved between both Rhodobacter species, which indicate that these cellular processes are conserved between the species and are candidates for functional information transfer between species. Many gene modules were non-preserved, providing insight into processes that differentiate the two species. In addition, using Local Network Similarity (LNS), a recently proposed metric for expression divergence, we assessed the expression conservation of between-species pairs of orthologs, and within-species gene-protein expression profiles. Conclusions: Our analyses provide new sources of information for functional annotation in R. capsulatus because uncharacterized genes in modules are now connected with groups of genes that constitute a joint functional annotation. We identified R. capsulatus modules enriched with genes for ribosomal proteins, porphyrin and bacteriochlorophyll anabolism, and biosynthesis of secondary metabolites to be preserved in R. sphaeroides whereas modules related to RcGTA production and signalling showed lack of preservation in R. sphaeroides. In addition, we demonstrated that network statistics may also be applied within-species to identify congruence between mRNA expression and protein abundance data for which simple correlation measurements have previously had mixed results.« less

  3. A hierarchical approach employing metabolic and gene expression profiles to identify the pathways that confer cytotoxicity in HepG2 cells

    PubMed Central

    Li, Zheng; Srivastava, Shireesh; Yang, Xuerui; Mittal, Sheenu; Norton, Paul; Resau, James; Haab, Brian; Chan, Christina

    2007-01-01

    Background Free fatty acids (FFA) and tumor necrosis factor alpha (TNF-α) have been implicated in the pathogenesis of many obesity-related metabolic disorders. When human hepatoblastoma cells (HepG2) were exposed to different types of FFA and TNF-α, saturated fatty acid was found to be cytotoxic and its toxicity was exacerbated by TNF-α. In order to identify the processes associated with the toxicity of saturated FFA and TNF-α, the metabolic and gene expression profiles were measured to characterize the cellular states. A computational model was developed to integrate these disparate data to reveal the underlying pathways and mechanisms involved in saturated fatty acid toxicity. Results A hierarchical framework consisting of three stages was developed to identify the processes and genes that regulate the toxicity. First, discriminant analysis identified that fatty acid oxidation and intracellular triglyceride accumulation were the most relevant in differentiating the cytotoxic phenotype. Second, gene set enrichment analysis (GSEA) was applied to the cDNA microarray data to identify the transcriptionally altered pathways and processes. Finally, the genes and gene sets that regulate the metabolic responses identified in step 1 were identified by integrating the expression of the enriched gene sets and the metabolic profiles with a multi-block partial least squares (MBPLS) regression model. Conclusion The hierarchical approach suggested potential mechanisms involved in mediating the cytotoxic and cytoprotective pathways, as well as identified novel targets, such as NADH dehydrogenases, aldehyde dehydrogenases 1A1 (ALDH1A1) and endothelial membrane protein 3 (EMP3) as modulator of the toxic phenotypes. These predictions, as well as, some specific targets that were suggested by the analysis were experimentally validated. PMID:17498300

  4. Risk profiles for weight gain among postmenopausal women: A classification and regression tree analysis approach

    USDA-ARS?s Scientific Manuscript database

    Risk factors for obesity and weight gain are typically evaluated individually while "adjusting for" the influence of other confounding factors, and few studies, if any, have created risk profiles by clustering risk factors. We identified subgroups of postmenopausal women homogeneous in their cluster...

  5. Achievement Goal Orientations and Subjective Well-Being: A Person-Centred Analysis

    ERIC Educational Resources Information Center

    Tuominen-Soini, Heta; Salmela-Aro, Katariina; Niemivirta, Markku

    2008-01-01

    This study examined whether students with different achievement goal orientation profiles differ in terms of subjective well-being (i.e., self-esteem, depressive symptoms, school-related burnout, and educational goal appraisals). Six groups of students with unique motivational profiles were identified. Observed differences in subjective well-being…

  6. Profiles of Canadian Postsecondary Education Dropouts

    ERIC Educational Resources Information Center

    Ma, Xin; Frempong, George

    2013-01-01

    Using longitudinal data of 18-to 20-year-old youths from the Youth in Transition Survey (YITS), the present analysis identified and profiled Canadian postsecondary education dropouts based on the theoretical framework of Tinto (1993). Pertaining to characteristics of pre-postsecondary education conditions, dropouts tended to be male, set low…

  7. Psychosocial and Cognitive Functioning of Children with Specific Profiles of Maltreatment

    ERIC Educational Resources Information Center

    Pears, Katherine C.; Kim, Hyoun K.; Fisher, Philip A.

    2008-01-01

    Objective: Up to 90% of child welfare system cases involve multiple types of maltreatment; however, studies have rarely incorporated multiple dimensions of maltreatment. The present study employed a latent profile analysis to identify naturally occurring subgroups of children who had experienced maltreatment. Methods: Reports of maltreatment…

  8. EPA Positive Matrix Factorization (PMF) 5.0 Fundamentals and User Guide

    EPA Science Inventory

    PMF is a multivariate factor analysis tool that decomposes a matrix of speciated sample data into two matrices: factor contributions (G) and factor profiles (F). These factor profiles need to be interpreted by the user to identify the source types that may be contributing to the ...

  9. Dimensions, Patterns, and Personality Correlates of Drug Abuse in an Offender Population.

    ERIC Educational Resources Information Center

    Holland, Terrill R.

    1978-01-01

    Drug abuse scores from prisoners resulted in two factors describing lifetime use of cannabis versus opiates. Analysis of Minnesota Multiphasic Personality Inventory (MMPI) profiles versus drug abuse patterns indicated moderate, unidimensional relationship between variables. MMPI profiles of opiate users were similar to those identified in research…

  10. Risk Profiles of Children Entering Residential Care: A Cluster Analysis

    ERIC Educational Resources Information Center

    Hagaman, Jessica L.; Trout, Alexandra L.; Chmelka, M. Beth; Thompson, Ronald W.; Reid, Robert

    2010-01-01

    Children in residential care are a heterogeneous population, presenting various combinations of risks. Existing studies on these children suggest high variability across multiple domains (e.g., academics, behavior). Given this heterogeneity, it is important to begin to identify the combinations and patterns of multiple risks, or risk profiles,…

  11. WAIS-III index score profiles in the Canadian standardization sample.

    PubMed

    Lange, Rael T

    2007-01-01

    Representative index score profiles were examined in the Canadian standardization sample of the Wechsler Adult Intelligence Scale-Third Edition (WAIS-III). The identification of profile patterns was based on the methodology proposed by Lange, Iverson, Senior, and Chelune (2002) that aims to maximize the influence of profile shape and minimize the influence of profile magnitude on the cluster solution. A two-step cluster analysis procedure was used (i.e., hierarchical and k-means analyses). Cluster analysis of the four index scores (i.e., Verbal Comprehension [VCI], Perceptual Organization [POI], Working Memory [WMI], Processing Speed [PSI]) identified six profiles in this sample. Profiles were differentiated by pattern of performance and were primarily characterized as (a) high VCI/POI, low WMI/PSI, (b) low VCI/POI, high WMI/PSI, (c) high PSI, (d) low PSI, (e) high VCI/WMI, low POI/PSI, and (f) low VCI, high POI. These profiles are potentially useful for determining whether a patient's WAIS-III performance is unusual in a normal population.

  12. Circulating microRNAs as biomarkers of disease and typification of the atherothrombotic status in antiphospholipid syndrome

    PubMed Central

    Pérez-Sánchez, Carlos; Arias-de la Rosa, Iván; Aguirre, María Ángeles; Luque-Tévar, María; Ruiz-Limón, Patricia; Barbarroja, Nuria; Jiménez-Gómez, Yolanda; Ábalos-Aguilera, María Carmen; Collantes-Estévez, Eduardo; Segui, Pedro; Velasco, Francisco; Herranz, María Teresa; Lozano-Herrero, Jesús; Hernandez-Vidal, María Julia; Martínez, Constantino; González-Conejero, Rocío; Radin, Massimo; Sciascia, Savino; Cecchi, Irene; Cuadrado, María José; López-Pedrera, Chary

    2018-01-01

    We aimed to identify the plasma miRNA profile of antiphospholipid syndrome (APS) patients and to investigate the potential role of specific circulating miRNAs as non-invasive disease biomarkers. Ninety APS patients and 42 healthy donors were recruited. Profiling of miRNAs by PCR-array in plasma of APS patients identified a set of miRNAs differentially expressed and collectively involved in clinical features. Logistic regression and ROC analysis identified a signature of 10 miRNA ratios as biomarkers of disease. In addition, miRNA signature was related to fetal loss, atherosclerosis, and type of thrombosis, and correlated with parameters linked to inflammation, thrombosis, and autoimmunity. Hard clustering analysis differentiated 3 clusters representing different thrombotic risk profile groups. Significant differences between groups for several miRNA ratios were found. Moreover, miRNA signature remained stable over time, demonstrated by their analysis three months after the first sample collection. Parallel analysis in two additional cohorts of patients, including thrombosis without autoimmune disease, and systemic lupus erythematosus without antiphospholipid antibodies, each displayed specific miRNA profiles that were distinct from those of APS patients. In vitro, antiphospholipid antibodies of IgG isotype promoted deregulation in selected miRNAs and their potential atherothrombotic protein targets in monocytes and endothelial cells. Taken together, differentially expressed circulating miRNAs in APS patients, modulated at least partially by antiphospholipid antibodies of IgG isotype, might have the potential to serve as novel biomarkers of disease features and to typify patients’ atherothrombotic status, thus constituting a useful tool in the management of the disease. PMID:29545345

  13. Mindfulness and Psychological Health Outcomes: A Latent Profile Analysis among Military Personnel and College Students.

    PubMed

    Bravo, Adrian J; Pearson, Matthew R; Kelley, Michelle L

    2018-02-01

    Previous research on trait mindfulness facets using person-centered analyses (e.g., latent profile analysis [LPA]) has identified four distinct mindfulness profiles among college students: a high mindfulness group (high on all facets of the Five-Factor Mindfulness Questionnaire [FFMQ]), a judgmentally observing group (highest on observing, but low on non-judging of inner experience and acting with awareness), a non-judgmentally aware group (high on non-judging of inner experience and acting with awareness, but very low on observing), and a low mindfulness group (low on all facets of the FFMQ). In the present study, we used LPA to identify distinct mindfulness profiles in a community based sample of U.S. military personnel (majority veterans; n = 407) and non-military college students ( n = 310) and compare these profiles on symptoms of psychological health outcomes (e.g., suicidality, PTSD, anxiety, rumination) and percentage of participants exceeding clinically significant cut-offs for depressive symptoms, substance use, and alcohol use. In the subsample of college students, we replicated previous research and found four distinct mindfulness profiles; however, in the military subsample we found three distinct mindfulness profiles (a combined low mindfulness/judgmentally observing class). In both subsamples, we found that the most adaptive profile was the "high mindfulness" profile (i.e., demonstrated the lowest scores on all psychological symptoms and the lowest probability of exceeding clinical cut-offs). Based on these findings, we purport that the comprehensive examination of an individual's mindfulness profile could help clinicians tailor interventions/treatments that capitalize on individual's specific strengths and work to address their specific deficits.

  14. Symptom-Hemodynamic Mismatch and Heart Failure Event Risk

    PubMed Central

    Lee, Christopher S.; Hiatt, Shirin O.; Denfeld, Quin E.; Mudd, James O.; Chien, Christopher; Gelow, Jill M.

    2014-01-01

    Background Heart failure (HF) is a heterogeneous condition of both symptoms and hemodynamics. Objective The goal of this study was to identify distinct profiles among integrated data on physical and psychological symptoms and hemodynamics, and quantify differences in 180-day event-risk among observed profiles. Methods A secondary analysis of data collected during two prospective cohort studies by a single group of investigators was performed. Latent class mixture modeling was used to identify distinct symptom-hemodynamic profiles. Cox proportional hazards modeling was used to quantify difference in event-risk (HF emergency visit, hospitalization or death) among profiles. Results The mean age (n=291) was 57±13 years, 38% were female, and 61% had class III/IV HF. Three distinct symptom-hemodynamic profiles were identified. 17.9% of patients had concordant symptoms and hemodynamics (i.e. moderate physical and psychological symptoms matched the comparatively hemodynamic profile), 17.9% had severe symptoms and average hemodynamics, and 64.2% had poor hemodynamics and mild symptoms. Compared to those in the concordant profile, both profiles of symptom-hemodynamic mismatch were associated with a markedly increased event-risk (severe symptoms hazards ratio = 3.38, p=0.033; poor hemodynamics hazards ratio = 3.48, p=0.016). Conclusions A minority of adults with HF have concordant symptoms and hemodynamics. Either profile of symptom-hemodynamic mismatch in HF is associated with a greater risk of healthcare utilization for HF or death. PMID:24988323

  15. Identifying seasonal mobility profiles from anonymized and aggregated mobile phone data. Application in food security.

    PubMed

    Zufiria, Pedro J; Pastor-Escuredo, David; Úbeda-Medina, Luis; Hernandez-Medina, Miguel A; Barriales-Valbuena, Iker; Morales, Alfredo J; Jacques, Damien C; Nkwambi, Wilfred; Diop, M Bamba; Quinn, John; Hidalgo-Sanchís, Paula; Luengo-Oroz, Miguel

    2018-01-01

    We propose a framework for the systematic analysis of mobile phone data to identify relevant mobility profiles in a population. The proposed framework allows finding distinct human mobility profiles based on the digital trace of mobile phone users characterized by a Matrix of Individual Trajectories (IT-Matrix). This matrix gathers a consistent and regularized description of individual trajectories that enables multi-scale representations along time and space, which can be used to extract aggregated indicators such as a dynamic multi-scale population count. Unsupervised clustering of individual trajectories generates mobility profiles (clusters of similar individual trajectories) which characterize relevant group behaviors preserving optimal aggregation levels for detailed and privacy-secured mobility characterization. The application of the proposed framework is illustrated by analyzing fully anonymized data on human mobility from mobile phones in Senegal at the arrondissement level over a calendar year. The analysis of monthly mobility patterns at the livelihood zone resolution resulted in the discovery and characterization of seasonal mobility profiles related with economic activities, agricultural calendars and rainfalls. The use of these mobility profiles could support the timely identification of mobility changes in vulnerable populations in response to external shocks (such as natural disasters, civil conflicts or sudden increases of food prices) to monitor food security.

  16. Distinct developmental profiles in typical speech acquisition

    PubMed Central

    Campbell, Thomas F.; Shriberg, Lawrence D.; Green, Jordan R.; Abdi, Hervé; Rusiewicz, Heather Leavy; Venkatesh, Lakshmi; Moore, Christopher A.

    2012-01-01

    Three- to five-year-old children produce speech that is characterized by a high level of variability within and across individuals. This variability, which is manifest in speech movements, acoustics, and overt behaviors, can be input to subgroup discovery methods to identify cohesive subgroups of speakers or to reveal distinct developmental pathways or profiles. This investigation characterized three distinct groups of typically developing children and provided normative benchmarks for speech development. These speech development profiles, identified among 63 typically developing preschool-aged speakers (ages 36–59 mo), were derived from the children's performance on multiple measures. These profiles were obtained by submitting to a k-means cluster analysis of 72 measures that composed three levels of speech analysis: behavioral (e.g., task accuracy, percentage of consonants correct), acoustic (e.g., syllable duration, syllable stress), and kinematic (e.g., variability of movements of the upper lip, lower lip, and jaw). Two of the discovered group profiles were distinguished by measures of variability but not by phonemic accuracy; the third group of children was characterized by their relatively low phonemic accuracy but not by an increase in measures of variability. Analyses revealed that of the original 72 measures, 8 key measures were sufficient to best distinguish the 3 profile groups. PMID:22357794

  17. Transcriptomic and phenotypic profiling in developing zebrafish exposed to thyroid hormone receptor agonists

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

    Haggard, Derik E.; Noyes, Pamela D.; Waters, Katrina M.

    There is a need to develop novel, high-throughput screening and prioritization methods to identify chemicals with adverse estrogen, androgen, and thyroid activity to protect human health and the environment and is of interest to the Endocrine Disruptor Screening Program. The current aim is to explore the utility of zebrafish as a testing paradigm to classify endocrine activity using phenotypically anchored transcriptome profiling. Transcriptome analysis was conducted on embryos exposed to 25 estrogen-, androgen-, or thyroid-active chemicals at a concentration that elicited adverse malformations or mortality at 120 hours post-fertilization in 80% of the animals exposed. Analysis of the top 1000more » significant differentially expressed transcripts across all treatments identified a unique transcriptional and phenotypic profile for thyroid hormone receptor agonists, which can be used as a biomarker screen for potential thyroid hormone agonists.« less

  18. Effect of masticatory stimulation on the quantity and quality of saliva and the salivary metabolomic profile.

    PubMed

    Okuma, Nobuyuki; Saita, Makiko; Hoshi, Noriyuki; Soga, Tomoyoshi; Tomita, Masaru; Sugimoto, Masahiro; Kimoto, Katsuhiko

    2017-01-01

    This study characterized the changes in quality and quantity of saliva, and changes in the salivary metabolomic profile, to understand the effects of masticatory stimulation. Stimulated and unstimulated saliva samples were collected from 55 subjects and salivary hydrophilic metabolites were comprehensively quantified using capillary electrophoresis-time-of-flight mass spectrometry. In total, 137 metabolites were identified and quantified. The concentrations of 44 metabolites in stimulated saliva were significantly higher than those in unstimulated saliva. Pathway analysis identified the upregulation of the urea cycle and synthesis and degradation pathways of glycine, serine, cysteine and threonine in stimulated saliva. A principal component analysis revealed that the effect of masticatory stimulation on salivary metabolomic profiles was less dependent on sample population sex, age, and smoking. The concentrations of only 1 metabolite in unstimulated saliva, and of 3 metabolites stimulated saliva, showed significant correlation with salivary secretion volume, indicating that the salivary metabolomic profile and salivary secretion volume were independent factors. Masticatory stimulation affected not only salivary secretion volume, but also metabolite concentration patterns. A low correlation between the secretion volume and these patterns supports the conclusion that the salivary metabolomic profile may be a new indicator to characterize masticatory stimulation.

  19. Goal motives and multiple-goal striving in sport and academia: A person-centered investigation of goal motives and inter-goal relations.

    PubMed

    Healy, Laura C; Ntoumanis, Nikos; Duda, Joan L

    2016-12-01

    This investigation extended the goal striving literature by examining motives for two goals being pursued simultaneously. Grounded in self-determination theory, we examined how student-athletes' motives for their sporting and academic goals were associated with inter-goal facilitation and interference. Cross-sectional survey. UK university student-athletes (n=204) identified their most important sporting and academic goals. They then rated their extrinsic, introjected, identified and intrinsic motives for these goals and completed questionnaires assessing inter-goal facilitation and interference. Using a person-centered approach via latent profile analysis, we identified three distinct profiles of goal motives. Auxiliary analyses showed that the profile with high identified motives for both goals reported greater inter-goal facilitation. Extending the previous literature, the findings demonstrate the benefits of autonomous motives when simultaneously pursing goals in sport and academia. Copyright © 2016. Published by Elsevier Ltd.

  20. Novel molecular subtypes of serous and endometrioid ovarian cancer linked to clinical outcome.

    PubMed

    Tothill, Richard W; Tinker, Anna V; George, Joshy; Brown, Robert; Fox, Stephen B; Lade, Stephen; Johnson, Daryl S; Trivett, Melanie K; Etemadmoghadam, Dariush; Locandro, Bianca; Traficante, Nadia; Fereday, Sian; Hung, Jillian A; Chiew, Yoke-Eng; Haviv, Izhak; Gertig, Dorota; DeFazio, Anna; Bowtell, David D L

    2008-08-15

    The study aim to identify novel molecular subtypes of ovarian cancer by gene expression profiling with linkage to clinical and pathologic features. Microarray gene expression profiling was done on 285 serous and endometrioid tumors of the ovary, peritoneum, and fallopian tube. K-means clustering was applied to identify robust molecular subtypes. Statistical analysis identified differentially expressed genes, pathways, and gene ontologies. Laser capture microdissection, pathology review, and immunohistochemistry validated the array-based findings. Patient survival within k-means groups was evaluated using Cox proportional hazards models. Class prediction validated k-means groups in an independent dataset. A semisupervised survival analysis of the array data was used to compare against unsupervised clustering results. Optimal clustering of array data identified six molecular subtypes. Two subtypes represented predominantly serous low malignant potential and low-grade endometrioid subtypes, respectively. The remaining four subtypes represented higher grade and advanced stage cancers of serous and endometrioid morphology. A novel subtype of high-grade serous cancers reflected a mesenchymal cell type, characterized by overexpression of N-cadherin and P-cadherin and low expression of differentiation markers, including CA125 and MUC1. A poor prognosis subtype was defined by a reactive stroma gene expression signature, correlating with extensive desmoplasia in such samples. A similar poor prognosis signature could be found using a semisupervised analysis. Each subtype displayed distinct levels and patterns of immune cell infiltration. Class prediction identified similar subtypes in an independent ovarian dataset with similar prognostic trends. Gene expression profiling identified molecular subtypes of ovarian cancer of biological and clinical importance.

  1. Identification of genes showing differential expression profile associated with growth rate in skeletal muscle tissue of Landrace weanling pig.

    PubMed

    Komatsu, Yuuta; Sukegawa, Shin; Yamashita, Mai; Katsuda, Naoki; Tong, Bin; Ohta, Takeshi; Kose, Hiroyuki; Yamada, Takahisa

    2016-06-01

    Suppression subtractive hybridization was used to identify genes showing differential expression profile associated with growth rate in skeletal muscle tissue of Landrace weanling pig. Two subtracted cDNA populations were generated from musculus longissimus muscle tissues of selected pigs with extreme expected breeding values at the age of 100 kg. Three upregulated genes (EEF1A2, TSG101 and TTN) and six downregulated genes (ATP5B, ATP5C1, COQ3, HADHA, MYH1 and MYH7) in pig with genetic propensity for higher growth rate were identified by sequence analysis of 12 differentially expressed clones selected by differential screening following the generation of the subtracted cDNA population. Real-time PCR analysis confirmed difference in expression profiles of the identified genes in musculus longissimus muscle tissues between the two Landrace weanling pig groups with divergent genetic propensity for growth rate. Further, differential expression of the identified genes except for the TTN was validated by Western blot analysis. Additionally, the eight genes other than the ATP5C1 colocalized with the same chromosomal positions as QTLs that have been previously identified for growth rate traits. Finally, the changes of expression predicted from gene function suggested association of upregulation of expression of the EEF1A2, TSG101 and TTN genes and downregulation of the ATP5B, ATP5C1, COQ3, HADHA, MYH1 and MYH7 gene expression with increased growth rate. The identified genes will provide an important insight in understanding the molecular mechanism underlying growth rate in Landrace pig breed.

  2. Comparative prion disease gene expression profiling using the prion disease mimetic, cuprizone

    PubMed Central

    Moody, Laura R; Herbst, Allen J; Yoo, Han Sang; Vanderloo, Joshua P

    2009-01-01

    Identification of genes expressed in response to prion infection may elucidate biomarkers for disease, identify factors involved in agent replication, mechanisms of neuropathology and therapeutic targets. Although several groups have sought to identify gene expression changes specific to prion disease, expression profiles rife with cell population changes have consistently been identified. Cuprizone, a neurotoxicant, qualitatively mimics the cell population changes observed in prion disease, resulting in both spongiform change and astrocytosis. The use of cuprizone-treated animals as an experimental control during comparative expression profiling allows for the identification of transcripts whose expression increases during prion disease and remains unchanged during cuprizone-triggered neuropathology. In this study, expression profiles from the brains of mice preclinically and clinically infected with Rocky Mountain Laboratory (RML) mouse-adapted scrapie agent and age-matched controls were profiled using Affymetrix gene arrays. In total, 164 genes were differentially regulated during prion infection. Eighty-three of these transcripts have been previously undescribed as differentially regulated during prion disease. A 0.4% cuprizone diet was utilized as a control for comparative expression profiling. Cuprizone treatment induced spongiosis and astrocyte proliferation as indicated by glial fibrillary acidic protein (Gfap) transcriptional activation and immunohistochemistry. Gene expression profiles from brain tissue obtained from cuprizone-treated mice identified 307 differentially regulated transcript changes. After comparative analysis, 17 transcripts unaffected by cuprizone treatment but increasing in expression from preclinical to clinical prion infection were identified. Here we describe the novel use of the prion disease mimetic, cuprizone, to control for cell population changes in the brain during prion infection. PMID:19535908

  3. Alcohol References on Undergraduate Males’ Facebook Profiles

    PubMed Central

    Egan, Katie G.; Moreno, Megan A.

    2011-01-01

    Perceived peer alcohol use is a predictor of consumption in college males; frequent references to alcohol on Facebook may encourage alcohol consumption. Content analysis of college males’ Facebook profiles identified references to alcohol. The average age of 225 identified profiles was 19.9 years. Alcohol references were present on 85.3% of the profiles; the prevalence of alcohol was similar across each undergraduate grade. The average number of alcohol references per profile was 8.5 but increased with undergraduate year (p = .003; confidence interval = 1.5, 7.5). Students who were of legal drinking age referenced alcohol 4.5 times more than underage students, and an increase in number of Facebook friends was associated with an increase in displayed alcohol references (p < .001; confidence interval = 0.009, 0.02). Facebook is widely used in the college population; widespread alcohol displays on Facebook may influence social norms and cause increases in male college students’ alcohol use. PMID:21406490

  4. Principal component analysis of TOF-SIMS spectra, images and depth profiles: an industrial perspective

    NASA Astrophysics Data System (ADS)

    Pacholski, Michaeleen L.

    2004-06-01

    Principal component analysis (PCA) has been successfully applied to time-of-flight secondary ion mass spectrometry (TOF-SIMS) spectra, images and depth profiles. Although SIMS spectral data sets can be small (in comparison to datasets typically discussed in literature from other analytical techniques such as gas or liquid chromatography), each spectrum has thousands of ions resulting in what can be a difficult comparison of samples. Analysis of industrially-derived samples means the identity of most surface species are unknown a priori and samples must be analyzed rapidly to satisfy customer demands. PCA enables rapid assessment of spectral differences (or lack there of) between samples and identification of chemically different areas on sample surfaces for images. Depth profile analysis helps define interfaces and identify low-level components in the system.

  5. Towards improved migraine management: Determining potential trigger factors in individual patients.

    PubMed

    Peris, Francesc; Donoghue, Stephen; Torres, Ferran; Mian, Alec; Wöber, Christian

    2017-04-01

    Background Certain chronic diseases such as migraine result in episodic, debilitating attacks for which neither cause nor timing is well understood. Historically, possible triggers were identified through analysis of aggregated data from populations of patients. However, triggers common in populations may not be wholly responsible for an individual's attacks. To explore this hypothesis we developed a method to identify individual 'potential trigger' profiles and analysed the degree of inter-individual variation. Methods We applied N = 1 statistical analysis to a 326-migraine-patient database from a study in which patients used paper-based diaries for 90 days to track 33 factors (potential triggers or premonitory symptoms) associated with their migraine attacks. For each patient, univariate associations between factors and migraine events were analysed using Cox proportional hazards models. Results We generated individual factor-attack association profiles for 87% of the patients. The average number of factors associated with attacks was four per patient: Factor profiles were highly individual and were unique in 85% of patients with at least one identified association. Conclusion Accurate identification of individual factor-attack profiles is a prerequisite for testing which are true triggers and for development of trigger avoidance or desensitisation strategies. Our methodology represents a necessary development toward this goal.

  6. Identifying prebariatric subtypes based on temperament traits, emotion dysregulation, and disinhibited eating: A latent profile analysis.

    PubMed

    Schäfer, Lisa; Hübner, Claudia; Carus, Thomas; Herbig, Beate; Seyfried, Florian; Kaiser, Stefan; Schütz, Tatjana; Dietrich, Arne; Hilbert, Anja

    2017-10-01

    The efficacy of bariatric surgery has been proven; however, a subset of patients fails to achieve expected long-term weight loss postoperatively. As differences in surgery outcome may be influenced by heterogeneous psychological profiles in prebariatric patients, previous subtyping models differentiated patients based on temperament traits. The objective of this study was to expand these models by additionally considering emotion dysregulation and disinhibited eating behaviors for subtyping, as these factors were associated with maladaptive eating behaviors and poor postbariatric weight loss outcome. Within a prospective multicenter registry, N = 370 prebariatric patients were examined using interview and self-report questionnaires. A latent profile analysis was performed to identify subtypes based on temperament traits, emotion dysregulation, and disinhibited eating behaviors. Five prebariatric subtypes were identified with specific profiles regarding self-control, emotion dysregulation, and disinhibited eating behaviors. Subtypes were associated with different levels of eating disorder psychopathology, depression, and quality of life. The expanded model increased variance explanation compared to temperament-based models. By adding emotion dysregulation and disinhibited eating behaviors to previous subtyping models, specific prebariatric subtypes emerged with distinct psychological deficit patterns. Future investigations should test the predictive value of these subtypes for postbariatric weight loss and health-related outcomes. © 2017 Wiley Periodicals, Inc.

  7. Sensory subtypes in children with autism spectrum disorder: latent profile transition analysis using a national survey of sensory features.

    PubMed

    Ausderau, Karla K; Furlong, Melissa; Sideris, John; Bulluck, John; Little, Lauren M; Watson, Linda R; Boyd, Brian A; Belger, Aysenil; Dickie, Virginia A; Baranek, Grace T

    2014-08-01

    Sensory features are highly prevalent and heterogeneous among children with ASD. There is a need to identify homogenous groups of children with ASD based on sensory features (i.e., sensory subtypes) to inform research and treatment. Sensory subtypes and their stability over 1 year were identified through latent profile transition analysis (LPTA) among a national sample of children with ASD. Data were collected from caregivers of children with ASD ages 2-12 years at two time points (Time 1 N = 1294; Time 2 N = 884). Four sensory subtypes (Mild; Sensitive-Distressed; Attenuated-Preoccupied; Extreme-Mixed) were identified, which were supported by fit indices from the LPTA as well as current theoretical models that inform clinical practice. The Mild and Extreme-Mixed subtypes reflected quantitatively different sensory profiles, while the Sensitive-Distressed and Attenuated-Preoccupied subtypes reflected qualitatively different profiles. Further, subtypes reflected differential child (i.e., gender, developmental age, chronological age, autism severity) and family (i.e., income, mother's education) characteristics. Ninety-one percent of participants remained stable in their subtypes over 1 year. Characterizing the nature of homogenous sensory subtypes may facilitate assessment and intervention, as well as potentially inform biological mechanisms. © 2014 The Authors. Journal of Child Psychology and Psychiatry. © 2014 Association for Child and Adolescent Mental Health.

  8. microRNA expression profiling in fetal single ventricle malformation identified by deep sequencing.

    PubMed

    Yu, Zhang-Bin; Han, Shu-Ping; Bai, Yun-Fei; Zhu, Chun; Pan, Ya; Guo, Xi-Rong

    2012-01-01

    microRNAs (miRNAs) have emerged as key regulators in many biological processes, particularly cardiac growth and development, although the specific miRNA expression profile associated with this process remains to be elucidated. This study aimed to characterize the cellular microRNA profile involved in the development of congenital heart malformation, through the investigation of single ventricle (SV) defects. Comprehensive miRNA profiling in human fetal SV cardiac tissue was performed by deep sequencing. Differential expression of 48 miRNAs was revealed by sequencing by oligonucleotide ligation and detection (SOLiD) analysis. Of these, 38 were down-regulated and 10 were up-regulated in differentiated SV cardiac tissue, compared to control cardiac tissue. This was confirmed by real-time quantitative reverse transcription-polymerase chain reaction (qRT-PCR) analysis. Predicted target genes of the 48 differentially expressed miRNAs were analyzed by gene ontology and categorized according to cellular process, regulation of biological process and metabolic process. Pathway-Express analysis identified the WNT and mTOR signaling pathways as the most significant processes putatively affected by the differential expression of these miRNAs. The candidate genes involved in cardiac development were identified as potential targets for these differentially expressed microRNAs and the collaborative network of microRNAs and cardiac development related-mRNAs was constructed. These data provide the basis for future investigation of the mechanism of the occurrence and development of fetal SV malformations.

  9. Urinary Metabolomic Profiling to Identify Potential Biomarkers for the Diagnosis of Behcet's Disease by Gas Chromatography/Time-of-Flight-Mass Spectrometry.

    PubMed

    Ahn, Joong Kyong; Kim, Jungyeon; Hwang, Jiwon; Song, Juhwan; Kim, Kyoung Heon; Cha, Hoon-Suk

    2017-11-02

    Diagnosing Behcet's disease (BD) is challenging because of the lack of a diagnostic biomarker. The purposes of this study were to investigate distinctive metabolic changes in urine samples of BD patients and to identify urinary metabolic biomarkers for diagnosis of BD using gas chromatography/time-of-flight-mass spectrometry (GC/TOF-MS). Metabolomic profiling of urine samples from 44 BD patients and 41 healthy controls (HC) were assessed using GC/TOF-MS, in conjunction with multivariate statistical analysis. A total of 110 urinary metabolites were identified. The urine metabolite profiles obtained from GC/TOF-MS analysis could distinguish BD patients from the HC group in the discovery set. The parameter values of the orthogonal partial least squared-discrimination analysis (OPLS-DA) model were R ² X of 0.231, R ² Y of 0.804, and Q ² of 0.598. A biomarker panel composed of guanine, pyrrole-2-carboxylate, 3-hydroxypyridine, mannose, l-citrulline, galactonate, isothreonate, sedoheptuloses, hypoxanthine, and gluconic acid lactone were selected and adequately validated as putative biomarkers of BD (sensitivity 96.7%, specificity 93.3%, area under the curve 0.974). OPLS-DA showed clear discrimination of BD and HC groups by a biomarker panel of ten metabolites in the independent set (accuracy 88%). We demonstrated characteristic urinary metabolic profiles and potential urinary metabolite biomarkers that have clinical value in the diagnosis of BD using GC/TOF-MS.

  10. Newly discovered ergot alkaloids in Sorghum ergot Claviceps africana occurring for the first time in Israel.

    PubMed

    Shimshoni, J A; Cuneah, O; Sulyok, M; Krska, R; Sionov, E; Barel, S; Meller Harel, Y

    2017-03-15

    Sorghum ergot is a disease caused commonly by C. africana. In 2015, ergot was identified for the first time in sorghum fields in Israel, leading to measures of eradication and quarantine. The aims of the study were to identify the ergot species by molecular and ergot alkaloid profile analysis, to determine the ergot alkaloid profile in pure honeydew and in infected sorghum silages and to estimate the safety of sorghum silages as a feed source. C. africana was rapidly and reliably identified by microscopical and molecular analysis. Dihydroergosine was identified as the major ergot alkaloid. Dihydrolysergol and dihydroergotamine were identified for the first time as significant ergot alkaloid components within the C. africana sclerotia, thereby providing for the first time a proof for the natural occurrence of dihydroergotamine. The sorghum silages were found to be safe for feed consumption, since the ergot alkaloids and the regulated mycotoxins were below their regulated limits. Copyright © 2016 Elsevier Ltd. All rights reserved.

  11. Affinity proteomics within rare diseases: a BIO-NMD study for blood biomarkers of muscular dystrophies

    PubMed Central

    Ayoglu, Burcu; Chaouch, Amina; Lochmüller, Hanns; Politano, Luisa; Bertini, Enrico; Spitali, Pietro; Hiller, Monika; Niks, Eric H; Gualandi, Francesca; Pontén, Fredrik; Bushby, Kate; Aartsma-Rus, Annemieke; Schwartz, Elena; Le Priol, Yannick; Straub, Volker; Uhlén, Mathias; Cirak, Sebahattin; ‘t Hoen, Peter A C; Muntoni, Francesco; Ferlini, Alessandra; Schwenk, Jochen M; Nilsson, Peter; Al-Khalili Szigyarto, Cristina

    2014-01-01

    Despite the recent progress in the broad-scaled analysis of proteins in body fluids, there is still a lack in protein profiling approaches for biomarkers of rare diseases. Scarcity of samples is the main obstacle hindering attempts to apply discovery driven protein profiling in rare diseases. We addressed this challenge by combining samples collected within the BIO-NMD consortium from four geographically dispersed clinical sites to identify protein markers associated with muscular dystrophy using an antibody bead array platform with 384 antibodies. Based on concordance in statistical significance and confirmatory results obtained from analysis of both serum and plasma, we identified eleven proteins associated with muscular dystrophy, among which four proteins were elevated in blood from muscular dystrophy patients: carbonic anhydrase III (CA3) and myosin light chain 3 (MYL3), both specifically expressed in slow-twitch muscle fibers and mitochondrial malate dehydrogenase 2 (MDH2) and electron transfer flavoprotein A (ETFA). Using age-matched sub-cohorts, 9 protein profiles correlating with disease progression and severity were identified, which hold promise for the development of new clinical tools for management of dystrophinopathies. PMID:24920607

  12. Evaluation of Protein Profiles From Treated Xenograft Tumor Models Identifies an Antibody Panel for Formalin-fixed and Paraffin-embedded (FFPE) Tissue Analysis by Reverse Phase Protein Arrays (RPPA)*

    PubMed Central

    Bader, Sabine; Zajac, Magdalena; Friess, Thomas; Ruge, Elisabeth; Rieder, Natascha; Gierke, Berthold; Heubach, Yvonne; Thomas, Marlene; Pawlak, Michael

    2015-01-01

    Reverse phase protein arrays (RPPA) are an established tool for measuring the expression and activation status of multiple proteins in parallel using only very small amounts of tissue. Several studies have demonstrated the value of this technique for signaling pathway analysis using proteins extracted from fresh frozen (FF) tissue in line with validated antibodies for this tissue type; however, formalin fixation and paraffin embedding (FFPE) is the standard method for tissue preservation in the clinical setting. Hence, we performed RPPA to measure profiles for a set of 300 protein markers using matched FF and FFPE tissue specimens to identify which markers performed similarly using the RPPA technique in fixed and unfixed tissues. Protein lysates were prepared from matched FF and FFPE tissue specimens of individual tumors taken from three different xenograft models of human cancer. Materials from both untreated mice and mice treated with either anti-HER3 or bispecific anti-IGF-1R/EGFR monoclonal antibodies were analyzed. Correlations between signals from FF and FFPE tissue samples were investigated. Overall, 60 markers were identified that produced comparable profiles between FF and FFPE tissues, demonstrating significant correlation between the two sample types. The top 25 markers also showed significance after correction for multiple testing. The panel of markers covered several clinically relevant tumor signaling pathways and both phosphorylated and nonphosphorylated proteins were represented. Biologically relevant changes in marker expression were noted when RPPA profiles from treated and untreated xenografts were compared. These data demonstrate that, using appropriately selected antibodies, RPPA analysis from FFPE tissue is well feasible and generates biologically meaningful information. The identified panel of markers that generate similar profiles in matched fixed and unfixed tissue samples may be clinically useful for pharmacodynamic studies of drug effect using FFPE tissues. PMID:26106084

  13. Development and validation of a gene profile predicting benefit of postmastectomy radiotherapy in patients with high-risk breast cancer: a study of gene expression in the DBCG82bc cohort.

    PubMed

    Tramm, Trine; Mohammed, Hayat; Myhre, Simen; Kyndi, Marianne; Alsner, Jan; Børresen-Dale, Anne-Lise; Sørlie, Therese; Frigessi, Arnoldo; Overgaard, Jens

    2014-10-15

    To identify genes predicting benefit of radiotherapy in patients with high-risk breast cancer treated with systemic therapy and randomized to receive or not receive postmastectomy radiotherapy (PMRT). The study was based on the Danish Breast Cancer Cooperative Group (DBCG82bc) cohort. Gene-expression analysis was performed in a training set of frozen tumor tissue from 191 patients. Genes were identified through the Lasso method with the endpoint being locoregional recurrence (LRR). A weighted gene-expression index (DBCG-RT profile) was calculated and transferred to quantitative real-time PCR (qRT-PCR) in corresponding formalin-fixed, paraffin-embedded (FFPE) samples, before validation in FFPE from 112 additional patients. Seven genes were identified, and the derived DBCG-RT profile divided the 191 patients into "high LRR risk" and "low LRR risk" groups. PMRT significantly reduced risk of LRR in "high LRR risk" patients, whereas "low LRR risk" patients showed no additional reduction in LRR rate. Technical transfer of the DBCG-RT profile to FFPE/qRT-PCR was successful, and the predictive impact was successfully validated in another 112 patients. A DBCG-RT gene profile was identified and validated, identifying patients with very low risk of LRR and no benefit from PMRT. The profile may provide a method to individualize treatment with PMRT. ©2014 American Association for Cancer Research.

  14. Market niche analysis in the casino gaming industry.

    PubMed

    Dandurand, L

    1990-03-01

    This article discusses the nature of market niche analysis in the casino gaming industry. It presents four approaches for conducting market niche analysis. An an example of one approach, the Las Vegas Visitor Profile Study is used to identify a premium niche in the Las Vegas Slot Target Market. A detailed examination of the premium niche profile provides a description of the typical premium slot player. The description of the typical premium player leads to hypotheses regarding needs (the unique preference set) of the premium player. An analysis of the unique preference set suggests an appropriate enhanced marketing program.

  15. Primary School Teachers’ Assessment Profiles in Mathematics Education

    PubMed Central

    Veldhuis, Michiel; van den Heuvel-Panhuizen, Marja

    2014-01-01

    The aim of this study was to contribute to knowledge about classroom assessment by identifying profiles of teachers’ assessment of their students’ understanding of mathematics. For carrying out this study we used data of a nationwide teacher survey (N = 960) in the Netherlands. The data were collected by an online questionnaire. Through exploratory factor analyses the underlying structure of what is measured by this questionnaire was uncovered as consisting of five factors: Goal centeredness of assessment, Authentic nature of assessment, Perceived usefulness of assessment, Diversity of assessment problem format, and Allocated importance of assessing skills and knowledge. By using a latent class analysis four different assessment profiles of teachers were identified: Enthusiastic assessors, Mainstream assessors, Non-enthusiastic assessors, and Alternative assessors. The findings suggest that teachers with particular assessment profiles have qualitatively different assessment practices. The paper concludes with discussing theoretical implications of these assessment profiles and indications these profiles can offer both for designing material for professional development in classroom assessment and for evaluating changes in teachers’ classroom assessment practice. PMID:24466255

  16. Primary school teachers' assessment profiles in mathematics education.

    PubMed

    Veldhuis, Michiel; van den Heuvel-Panhuizen, Marja

    2014-01-01

    The aim of this study was to contribute to knowledge about classroom assessment by identifying profiles of teachers' assessment of their students' understanding of mathematics. For carrying out this study we used data of a nationwide teacher survey (N = 960) in the Netherlands. The data were collected by an online questionnaire. Through exploratory factor analyses the underlying structure of what is measured by this questionnaire was uncovered as consisting of five factors: Goal centeredness of assessment, Authentic nature of assessment, Perceived usefulness of assessment, Diversity of assessment problem format, and Allocated importance of assessing skills and knowledge. By using a latent class analysis four different assessment profiles of teachers were identified: Enthusiastic assessors, Mainstream assessors, Non-enthusiastic assessors, and Alternative assessors. The findings suggest that teachers with particular assessment profiles have qualitatively different assessment practices. The paper concludes with discussing theoretical implications of these assessment profiles and indications these profiles can offer both for designing material for professional development in classroom assessment and for evaluating changes in teachers' classroom assessment practice.

  17. Healthcare managers' leadership profiles in relation to perceptions of work stressors and stress.

    PubMed

    Lornudd, Caroline; Bergman, David; Sandahl, Christer; von Thiele Schwarz, Ulrica

    2016-05-03

    Purpose The purpose of this study is to investigate the relationship between leadership profiles and differences in managers' own levels of work stress symptoms and perceptions of work stressors causing stress. Design/methodology/approach Cross-sectional data were used. Healthcare managers ( n = 188) rated three dimensions of their leadership behavior and levels of work stressors and stress. Hierarchical cluster analysis was performed to identify leadership profiles based on leadership behaviors. Differences in stress-related outcomes between profiles were assessed using one-way analysis of variance. Findings Four distinct clusters of leadership profiles were found. They discriminated in perception of work stressors and stress: the profile distinguished by the lowest mean in all behavior dimensions, exhibited a pattern with significantly more negative ratings compared to the other profiles. Practical implications This paper proposes that leadership profile is an individual factor involved in the stress process, including work stressors and stress, which may inform targeted health promoting interventions for healthcare managers. Originality/value This is the first study to investigate the relationship between leadership profiles and work stressors and stress in healthcare managers.

  18. Which Emotional Profiles Exhibit the Best Learning Outcomes? A Person-Centered Analysis of Students' Academic Emotions

    ERIC Educational Resources Information Center

    Ganotice, Fraide A., Jr.; Datu, Jesus Alfonso D.; King, Ronnel B.

    2016-01-01

    Previous studies on academic emotions have mostly used variable-centered approaches. Although these studies have elucidated the relationships between academic emotions and key academic outcomes, they cannot identify naturally-occurring groups of students defined by distinct academic emotion profiles. In this study, we adopted a person-centered…

  19. Mexican-Origin Mothers' and Fathers' Involvement in Adolescents' Peer Relationships: A Pattern-Analytic Approach

    ERIC Educational Resources Information Center

    Updegraff, Kimberly A.; Perez-Brena, Norma J.; Baril, Megan E.; McHale, Susan M.; Umana-Taylor, Adriana J.

    2012-01-01

    Using latent profile analysis, the authors examined patterns of mother-father involvement in adolescents' peer relationships along three dimensions--support, guidance, and restrictions--in 240 Mexican-origin families. Three profiles were identified: (a) High Mother Involvement (mothers higher than fathers on all three dimensions), (b) High…

  20. An Analysis of the Relative Importance of Ely's Eight Implementation Conditions

    ERIC Educational Resources Information Center

    Surry, Daniel W.; Jackson, Katherine; Porter, Barry E.; Ensminger, David, C.

    2006-01-01

    This paper reports the results of a study to determine implementation profiles within a sample of 179 participants from a variety of education and business fields. Implementation profiling identifies the conditions that participants perceive are most important when implementing an innovation. Information about the relative importance of the eight…

  1. Anger Problem Profiles among Partner Violent Men: Differences in Clinical Presentation and Treatment Outcome

    ERIC Educational Resources Information Center

    Murphy, Christopher M.; Taft, Casey T.; Eckhardt, Christopher I.

    2007-01-01

    Cluster analysis of 139 partner violent men's self-reports on the State-Trait Anger Expression Inventory identified profiles reflecting pathological anger (PA), low anger control (LAC), and normal anger (NA). The PA group self-reported higher pretreatment partner abuse, interpersonal dysfunction, distress, and substance abuse and had lower…

  2. A Systematic Approach to Time-series Metabolite Profiling and RNA-seq Analysis of Chinese Hamster Ovary Cell Culture.

    PubMed

    Hsu, Han-Hsiu; Araki, Michihiro; Mochizuki, Masao; Hori, Yoshimi; Murata, Masahiro; Kahar, Prihardi; Yoshida, Takanobu; Hasunuma, Tomohisa; Kondo, Akihiko

    2017-03-02

    Chinese hamster ovary (CHO) cells are the primary host used for biopharmaceutical protein production. The engineering of CHO cells to produce higher amounts of biopharmaceuticals has been highly dependent on empirical approaches, but recent high-throughput "omics" methods are changing the situation in a rational manner. Omics data analyses using gene expression or metabolite profiling make it possible to identify key genes and metabolites in antibody production. Systematic omics approaches using different types of time-series data are expected to further enhance understanding of cellular behaviours and molecular networks for rational design of CHO cells. This study developed a systematic method for obtaining and analysing time-dependent intracellular and extracellular metabolite profiles, RNA-seq data (enzymatic mRNA levels) and cell counts from CHO cell cultures to capture an overall view of the CHO central metabolic pathway (CMP). We then calculated correlation coefficients among all the profiles and visualised the whole CMP by heatmap analysis and metabolic pathway mapping, to classify genes and metabolites together. This approach provides an efficient platform to identify key genes and metabolites in CHO cell culture.

  3. Modeling of 2D diffusion processes based on microscopy data: parameter estimation and practical identifiability analysis.

    PubMed

    Hock, Sabrina; Hasenauer, Jan; Theis, Fabian J

    2013-01-01

    Diffusion is a key component of many biological processes such as chemotaxis, developmental differentiation and tissue morphogenesis. Since recently, the spatial gradients caused by diffusion can be assessed in-vitro and in-vivo using microscopy based imaging techniques. The resulting time-series of two dimensional, high-resolutions images in combination with mechanistic models enable the quantitative analysis of the underlying mechanisms. However, such a model-based analysis is still challenging due to measurement noise and sparse observations, which result in uncertainties of the model parameters. We introduce a likelihood function for image-based measurements with log-normal distributed noise. Based upon this likelihood function we formulate the maximum likelihood estimation problem, which is solved using PDE-constrained optimization methods. To assess the uncertainty and practical identifiability of the parameters we introduce profile likelihoods for diffusion processes. As proof of concept, we model certain aspects of the guidance of dendritic cells towards lymphatic vessels, an example for haptotaxis. Using a realistic set of artificial measurement data, we estimate the five kinetic parameters of this model and compute profile likelihoods. Our novel approach for the estimation of model parameters from image data as well as the proposed identifiability analysis approach is widely applicable to diffusion processes. The profile likelihood based method provides more rigorous uncertainty bounds in contrast to local approximation methods.

  4. A method to identify differential expression profiles of time-course gene data with Fourier transformation

    PubMed Central

    2013-01-01

    Background Time course gene expression experiments are an increasingly popular method for exploring biological processes. Temporal gene expression profiles provide an important characterization of gene function, as biological systems are both developmental and dynamic. With such data it is possible to study gene expression changes over time and thereby to detect differential genes. Much of the early work on analyzing time series expression data relied on methods developed originally for static data and thus there is a need for improved methodology. Since time series expression is a temporal process, its unique features such as autocorrelation between successive points should be incorporated into the analysis. Results This work aims to identify genes that show different gene expression profiles across time. We propose a statistical procedure to discover gene groups with similar profiles using a nonparametric representation that accounts for the autocorrelation in the data. In particular, we first represent each profile in terms of a Fourier basis, and then we screen out genes that are not differentially expressed based on the Fourier coefficients. Finally, we cluster the remaining gene profiles using a model-based approach in the Fourier domain. We evaluate the screening results in terms of sensitivity, specificity, FDR and FNR, compare with the Gaussian process regression screening in a simulation study and illustrate the results by application to yeast cell-cycle microarray expression data with alpha-factor synchronization. The key elements of the proposed methodology: (i) representation of gene profiles in the Fourier domain; (ii) automatic screening of genes based on the Fourier coefficients and taking into account autocorrelation in the data, while controlling the false discovery rate (FDR); (iii) model-based clustering of the remaining gene profiles. Conclusions Using this method, we identified a set of cell-cycle-regulated time-course yeast genes. The proposed method is general and can be potentially used to identify genes which have the same patterns or biological processes, and help facing the present and forthcoming challenges of data analysis in functional genomics. PMID:24134721

  5. Serum Biochemical Phenotypes in the Domestic Dog

    PubMed Central

    Chang, Yu-Mei; Hadox, Erin; Szladovits, Balazs; Garden, Oliver A.

    2016-01-01

    The serum or plasma biochemical profile is essential in the diagnosis and monitoring of systemic disease in veterinary medicine, but current reference intervals typically take no account of breed-specific differences. Breed-specific hematological phenotypes have been documented in the domestic dog, but little has been published on serum biochemical phenotypes in this species. Serum biochemical profiles of dogs in which all measurements fell within the existing reference intervals were retrieved from a large veterinary database. Serum biochemical profiles from 3045 dogs were retrieved, of which 1495 had an accompanying normal glucose concentration. Sixty pure breeds plus a mixed breed control group were represented by at least 10 individuals. All analytes, except for sodium, chloride and glucose, showed variation with age. Total protein, globulin, potassium, chloride, creatinine, cholesterol, total bilirubin, ALT, CK, amylase, and lipase varied between sexes. Neutering status significantly impacted all analytes except albumin, sodium, calcium, urea, and glucose. Principal component analysis of serum biochemical data revealed 36 pure breeds with distinctive phenotypes. Furthermore, comparative analysis identified 23 breeds with significant differences from the mixed breed group in all biochemical analytes except urea and glucose. Eighteen breeds were identified by both principal component and comparative analysis. Tentative reference intervals were generated for breeds with a distinctive phenotype identified by comparative analysis and represented by at least 120 individuals. This is the first large-scale analysis of breed-specific serum biochemical phenotypes in the domestic dog and highlights potential genetic components of biochemical traits in this species. PMID:26919479

  6. Latent Profiles of Externalizing Psychopathology and Their Relation to Children's Aggression and Social Behavior.

    PubMed

    Andrade, Brendan F; Wade, Mark

    2016-01-01

    This study identified profiles of clinic-referred children with disruptive behavior and determined the association between identified profiles and children's aggression, peer problems, and prosocial skills. Parents and teachers of 208 children (163 boys) aged 6 to 12 years (Mage = 8.80, SD = 1.75) completed measures to assess children's callous-unemotional (CU) traits, inattentive-impulsive-overactive (IO) and oppositional-defiant (OD) behavior, aggression, and social behaviors. Latent class analysis was used to identify the profiles, and the pseudoclass draw method to test the equality of means for each of the aggression and social behavioral outcomes across the latent classes. Five profiles were identified: (1) Low (35.6% of children), with relatively low levels of CU traits and IO and OD behavior; (2) Low-Moderate (30.8%), with low-moderate levels of CU traits, low IO and moderate OD behavior; (3) Moderate (21.6%), with moderate levels of CU traits and IO and moderate-high OD behavior; (4) Moderate-High (7.2%), with moderate-high levels of CU traits, high IO and moderate-high OD behavior; and (5) High (4.8%), with high levels of CU traits, IO and OD behavior. Children categorized into profiles showed important differences in level of aggression and social behavior. The overlap between CU traits, IO, and OD behavior add to understanding of child psychopathology that influences behavior and clinical outcomes.

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

    PubMed

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

    2014-02-06

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

  8. Detecting and classifying method based on similarity matching of Android malware behavior with profile.

    PubMed

    Jang, Jae-Wook; Yun, Jaesung; Mohaisen, Aziz; Woo, Jiyoung; Kim, Huy Kang

    2016-01-01

    Mass-market mobile security threats have increased recently due to the growth of mobile technologies and the popularity of mobile devices. Accordingly, techniques have been introduced for identifying, classifying, and defending against mobile threats utilizing static, dynamic, on-device, and off-device techniques. Static techniques are easy to evade, while dynamic techniques are expensive. On-device techniques are evasion, while off-device techniques need being always online. To address some of those shortcomings, we introduce Andro-profiler, a hybrid behavior based analysis and classification system for mobile malware. Andro-profiler main goals are efficiency, scalability, and accuracy. For that, Andro-profiler classifies malware by exploiting the behavior profiling extracted from the integrated system logs including system calls. Andro-profiler executes a malicious application on an emulator in order to generate the integrated system logs, and creates human-readable behavior profiles by analyzing the integrated system logs. By comparing the behavior profile of malicious application with representative behavior profile for each malware family using a weighted similarity matching technique, Andro-profiler detects and classifies it into malware families. The experiment results demonstrate that Andro-profiler is scalable, performs well in detecting and classifying malware with accuracy greater than 98 %, outperforms the existing state-of-the-art work, and is capable of identifying 0-day mobile malware samples.

  9. Comparative expression profiling reveals gene functions in female meiosis and gametophyte development in Arabidopsis.

    PubMed

    Zhao, Lihua; He, Jiangman; Cai, Hanyang; Lin, Haiyan; Li, Yanqiang; Liu, Renyi; Yang, Zhenbiao; Qin, Yuan

    2014-11-01

    Megasporogenesis is essential for female fertility, and requires the accomplishment of meiosis and the formation of functional megaspores. The inaccessibility and low abundance of female meiocytes make it particularly difficult to elucidate the molecular basis underlying megasporogenesis. We used high-throughput tag-sequencing analysis to identify genes expressed in female meiocytes (FMs) by comparing gene expression profiles from wild-type ovules undergoing megasporogenesis with those from the spl mutant ovules, which lack megasporogenesis. A total of 862 genes were identified as FMs, with levels that are consistently reduced in spl ovules in two biological replicates. Fluorescence-assisted cell sorting followed by RNA-seq analysis of DMC1:GFP-labeled female meiocytes confirmed that 90% of the FMs are indeed detected in the female meiocyte protoplast profiling. We performed reverse genetic analysis of 120 candidate genes and identified four FM genes with a function in female meiosis progression in Arabidopsis. We further revealed that KLU, a putative cytochrome P450 monooxygenase, is involved in chromosome pairing during female meiosis, most likely by affecting the normal expression pattern of DMC1 in ovules during female meiosis. Our studies provide valuable information for functional genomic analyses of plant germline development as well as insights into meiosis. © 2014 The Authors The Plant Journal © 2014 John Wiley & Sons Ltd.

  10. Functional Abdominal Pain Patient Subtypes in Childhood Predict Functional Gastrointestinal Disorders with Chronic Pain and Psychiatric Comorbidities in Adolescence and Adulthood

    PubMed Central

    Walker, Lynn S.; Sherman, Amanda L.; Bruehl, Stephen; Garber, Judy; Smith, Craig A.

    2012-01-01

    Although pediatric functional abdominal pain (FAP) has been linked to abdominal pain later in life, childhood predictors of long-term outcomes have not been identified. This study evaluated whether distinct FAP profiles based on patterns of pain and adaptation in childhood could be identified and whether these profiles predicted differences in clinical outcomes and central sensitization (wind-up) on average 9 years later. In 843 pediatric FAP patients, cluster analysis was used to identify subgroups at initial FAP evaluation based on profiles of pain severity, gastrointestinal (GI) and non-GI symptoms, pain threat appraisal, pain coping efficacy, catastrophizing, negative affect, and activity impairment. Three profiles were identified: High Pain Dysfunctional, High Pain Adaptive, and Low Pain Adaptive. Logistic regression analyses controlling for age and sex showed that, compared to pediatric patients with the Low Pain Adaptive profile, those with the High Pain Dysfunctional profile were significantly more likely at long-term follow-up to meet criteria for pain-related functional gastrointestinal disorder (FGID) (OR: 3.45; CI: 1.95–6.11), FGID with comorbid non-abdominal chronic pain (OR: 2.6; CI:1.45–4.66), and FGID with comorbid anxiety or depressive psychiatric disorder (OR: 2.84; CI: 1.35–6.00). Pediatric patients with the High Pain Adaptive profile had baseline pain severity comparable to the High Pain Dysfunctional profile, but had outcomes as favorable as the Low Pain Adaptive profile. In laboratory pain testing at follow-up, High Pain Dysfunctional patients exhibited significantly greater thermal wind-up than Low Pain Adaptive patients, suggesting that a subgroup of FAP patients has outcomes consistent with widespread effects of heightened central sensitization. PMID:22721910

  11. Identifying patterns of motor performance, executive functioning, and verbal ability in preschool children: A latent profile analysis.

    PubMed

    Houwen, Suzanne; Kamphorst, Erica; van der Veer, Gerda; Cantell, Marja

    2018-04-30

    A relationship between motor performance and cognitive functioning is increasingly being recognized. Yet, little is known about the precise nature of the relationship between both domains, especially in early childhood. To identify distinct constellations of motor performance, executive functioning (EF), and verbal ability in preschool aged children; and to explore how individual and contextual variables are related to profile membership. The sample consisted of 119 3- to 4-year old children (62 boys; 52%). The home based assessments consisted of a standardized motor test (Movement Assessment Battery for Children - 2), five performance-based EF tasks measuring inhibition and working memory, and the Receptive Vocabulary subtest from the Wechsler Preschool and Primary Scale of Intelligence Third Edition. Parents filled out the Behavior Rating Inventory of Executive Function - Preschool version. Latent profile analysis (LPA) was used to delineate profiles of motor performance, EF, and verbal ability. Chi-square statistics and multinomial logistic regression analysis were used to examine whether profile membership was predicted by age, gender, risk of motor coordination difficulties, ADHD symptomatology, language problems, and socioeconomic status (SES). LPA yielded three profiles with qualitatively distinct response patterns of motor performance, EF, and verbal ability. Quantitatively, the profiles showed most pronounced differences with regard to parent ratings and performance-based tests of EF, as well as verbal ability. Risk of motor coordination difficulties and ADHD symptomatology were associated with profile membership, whereas age, gender, language problems, and SES were not. Our results indicate that there are distinct subpopulations of children who show differential relations with regard to motor performance, EF, and verbal ability. The fact that we found both quantitative as well as qualitative differences between the three patterns of profiles underscores the need for a person-centered approach with a focus on patterns of individual characteristics. Copyright © 2018 Elsevier Ltd. All rights reserved.

  12. The Galactic Isotropic γ-ray Background and Implications for Dark Matter

    NASA Astrophysics Data System (ADS)

    Campbell, Sheldon S.; Kwa, Anna; Kaplinghat, Manoj

    2018-06-01

    We present an analysis of the radial angular profile of the galacto-isotropic (GI) γ-ray flux-the statistically uniform flux in angular annuli centred on the Galactic centre. Two different approaches are used to measure the GI flux profile in 85 months of Fermi-LAT data: the BDS statistical method which identifies spatial correlations, and a new Poisson ordered-pixel method which identifies non-Poisson contributions. Both methods produce similar GI flux profiles. The GI flux profile is well-described by an existing model of bremsstrahlung, π0 production, inverse Compton scattering, and the isotropic background. Discrepancies with data in our full-sky model are not present in the GI component, and are therefore due to mis-modelling of the non-GI emission. Dark matter annihilation constraints based solely on the observed GI profile are close to the thermal WIMP cross section below 100 GeV, for fixed models of the dark matter density profile and astrophysical γ-ray foregrounds. Refined measurements of the GI profile are expected to improve these constraints by a factor of a few.

  13. Profiling depression in childhood and adolescence: the role of conduct problems.

    PubMed

    Riglin, Lucy; Thapar, Anita; Shelton, Katherine H; Langley, Kate; Frederickson, Norah; Rice, Frances

    2016-04-01

    Depression is typically more common in females and rates rise around puberty. However, studies of children and adolescents suggest that depression accompanied by conduct problems may represent a different subtype not characterised by a female preponderance, with differing risk factors and genetic architecture compared to pure-depression. This study aimed to identify aetiologically distinct profiles of depressive symptoms, distinguished by the presence or absence of co-occurring conduct problems. Latent profile analysis was conducted on a school sample of 1648 children (11-12 years) and replicated in a sample of 2006 twins (8-17 years). In both samples pure-depressive and conduct-depressive profiles were identified. The pure-depressive profile was associated with female gender, while the conduct-depressive profile was associated with lower cognitive ability but not with gender. Twin analyses indicated possible differences in genetic aetiology. There was evidence for aetiologically heterogeneous depression symptom profiles based on the presence or absence of co-occurring conduct problems. © 2015 The Authors. Journal of Child Psychology and Psychiatry published by John Wiley & Sons Ltd on behalf of Association for Child and Adolescent Mental Health.

  14. Contribution of Bacillus Isolates to the Flavor Profiles of Vanilla Beans Assessed through Aroma Analysis and Chemometrics.

    PubMed

    Gu, Fenglin; Chen, Yonggan; Fang, Yiming; Wu, Guiping; Tan, Lehe

    2015-10-09

    Colonizing Bacillus in vanilla (Vanilla planifolia Andrews) beans is involved in glucovanillin hydrolysis and vanillin formation during conventional curing. The flavor profiles of vanilla beans under Bacillus-assisted curing were analyzed through gas chromatography-mass spectrometry, electronic nose, and quantitative sensory analysis. The flavor profiles were analytically compared among the vanilla beans under Bacillus-assisted curing, conventional curing, and non-microorganism-assisted curing. Vanilla beans added with Bacillus vanillea XY18 and Bacillus subtilis XY20 contained higher vanillin (3.58%±0.05% and 3.48%±0.10%, respectively) than vanilla beans that underwent non-microorganism-assisted curing and conventional curing (3.09%±0.14% and 3.21%±0.15%, respectively). Forty-two volatiles were identified from endogenous vanilla metabolism. Five other compounds were identified from exogenous Bacillus metabolism. Electronic nose data confirmed that vanilla flavors produced through the different curing processes were easily distinguished. Quantitative sensory analysis confirmed that Bacillus-assisted curing increased vanillin production without generating any unpleasant sensory attribute. Partial least squares regression further provided a correlation model of different measurements. Overall, we comparatively analyzed the flavor profiles of vanilla beans under Bacillus-assisted curing, indirectly demonstrated the mechanism of vanilla flavor formation by microbes.

  15. Do recognizable lifetime eating disorder phenotypes naturally occur in a culturally asian population? A combined latent profile and taxometric approach.

    PubMed

    Thomas, Jennifer J; Eddy, Kamryn T; Ruscio, John; Ng, King Lam; Casale, Kristen E; Becker, Anne E; Lee, Sing

    2015-05-01

    We examined whether empirically derived eating disorder (ED) categories in Hong Kong Chinese patients (N = 454) would be consistent with recognizable lifetime ED phenotypes derived from latent structure models of European and American samples. We performed latent profile analysis (LPA) using indicator variables from data collected during routine assessment, and then applied taxometric analysis to determine whether latent classes were qualitatively versus quantitatively distinct. Latent profile analysis identified four classes: (i) binge/purge (47%); (ii) non-fat-phobic low-weight (34%); (iii) fat-phobic low-weight (12%); and (iv) overweight disordered eating (6%). Taxometric analysis identified qualitative (categorical) distinctions between the binge/purge and non-fat-phobic low-weight classes, and also between the fat-phobic and non-fat-phobic low-weight classes. Distinctions between the fat-phobic low-weight and binge/purge classes were indeterminate. Empirically derived categories in Hong Kong showed recognizable correspondence with recognizable lifetime ED phenotypes. Although taxometric findings support two distinct classes of low weight EDs, LPA findings also support heterogeneity among non-fat-phobic individuals. Copyright © 2015 John Wiley & Sons, Ltd and Eating Disorders Association.

  16. Circulating microRNAs as biomarkers of disease and typification of the atherothrombotic status in antiphospholipid syndrome.

    PubMed

    Pérez-Sánchez, Carlos; Arias-de la Rosa, Iván; Aguirre, María Ángeles; Luque-Tévar, María; Ruiz-Limón, Patricia; Barbarroja, Nuria; Jiménez-Gómez, Yolanda; Ábalos-Aguilera, María Carmen; Collantes-Estévez, Eduardo; Segui, Pedro; Velasco, Francisco; Herranz, María Teresa; Lozano-Herrero, Jesús; Hernandez-Vidal, María Julia; Martínez, Constantino; González-Conejero, Rocío; Radin, Massimo; Sciascia, Savino; Cecchi, Irene; Cuadrado, María José; López-Pedrera, Chary

    2018-05-01

    We aimed to identify the plasma miRNA profile of antiphospholipid syndrome (APS) patients and to investigate the potential role of specific circulating miRNAs as non-invasive disease biomarkers. Ninety APS patients and 42 healthy donors were recruited. Profiling of miRNAs by PCR-array in plasma of APS patients identified a set of miRNAs differentially expressed and collectively involved in clinical features. Logistic regression and ROC analysis identified a signature of 10 miRNA ratios as biomarkers of disease. In addition, miRNA signature was related to fetal loss, atherosclerosis, and type of thrombosis, and correlated with parameters linked to inflammation, thrombosis, and autoimmunity. Hard clustering analysis differentiated 3 clusters representing different thrombotic risk profile groups. Significant differences between groups for several miRNA ratios were found. Moreover, miRNA signature remained stable over time, demonstrated by their analysis three months after the first sample collection. Parallel analysis in two additional cohorts of patients, including thrombosis without autoimmune disease, and systemic lupus erythematosus without antiphospholipid antibodies, each displayed specific miRNA profiles that were distinct from those of APS patients. In vitro , antiphospholipid antibodies of IgG isotype promoted deregulation in selected miRNAs and their potential atherothrombotic protein targets in monocytes and endothelial cells. Taken together, differentially expressed circulating miRNAs in APS patients, modulated at least partially by antiphospholipid antibodies of IgG isotype, might have the potential to serve as novel biomarkers of disease features and to typify patients' atherothrombotic status, thus constituting a useful tool in the management of the disease. Copyright © 2018 Ferrata Storti Foundation.

  17. Maternal Food-Related Practices, Quality of Diet, and Well-Being: Profiles of Chilean Mother-Adolescent Dyads.

    PubMed

    Schnettler, Berta; Grunert, Klaus G; Lobos, Germán; Miranda-Zapata, Edgardo; Denegri, Marianela; Hueche, Clementina

    2018-04-03

    To identify mother-adolescent dyad profiles according to food-related parenting practices and to determine differences in diet quality, family meal frequency, life satisfaction, and sociodemographic characteristics. Cross-sectional study. Mothers and children were surveyed in their homes or at schools in Temuco, Chile. A total of 300 mothers (average age, 41.6 years) and their adolescent children (average age, 13.2 years; 48.7% female). Maternal feeding practices using the abbreviated Family Food Behavior Survey (AFFBS), life satisfaction, food-related and family life satisfaction, diet quality, and eating habits. Principal component factor analysis and confirmatory factor analysis were used to verify Family Food Behavior Survey components in mother and adolescent subsamples. Hierarchical cluster analysis was used to identify profiles. Three AFFBS components were detected: maternal control of child snacking behavior, maternal presence during eating, and child involvement in food consumption. Cluster analysis identified 3 mother-adolescent dyad profiles with different food-related parenting practices (P ≤ .001), mother (P ≤ .05) and child (P ≤ .001) diet quality, frequency of shared family meals (P ≤ .001), and mother (P ≤ .001) and child (P ≤ .05) life satisfaction levels. Results indicated that maternal well-being increased with an increased frequency of shared mealtime. Significantly, in contrast to the findings of previous studies, greater control over child eating habits was shown to affect adolescent well-being positively. These findings, among others, may contribute to the development of strategies for improving diet quality, overall well-being, and well-being in the food and family domains for all family members. Copyright © 2018 Society for Nutrition Education and Behavior. Published by Elsevier Inc. All rights reserved.

  18. Isomer-specific profiling of N-glycans derived from human serum for potential biomarker discovery in pancreatic cancer.

    PubMed

    Liu, Yufei; Wang, Chang; Wang, Ran; Wu, Yike; Zhang, Liang; Liu, Bi-Feng; Cheng, Liming; Liu, Xin

    2018-06-15

    Glycosylation is one of the most important post-translational modifications of protein. Recently, global profiling of human serum glycomics has become a noninvasive method for cancer-related biomarker discovery and many studies have focused on compositional glycan profiling. In contrast, structure-specific glycan profiling may provide more potential biomarkers with higher specificity than compositional profiling. In this work, N-glycans released from human serum were neutralized with methylamine and reduced by ammonia-borane complex prior to profiling using nanoLC-ESI-MS with porous graphitized carbon (PGC) and relative abundances of over 280 isomers were compared between pancreatic cancer (PC) cases (n = 32) and healthy controls (n = 32). Statistical analysis identified 25 specific-isomeric biomarkers with significant differences (p-value < 0.05). ROC and PCA analysis were performed to assess the potential biomarkers which were identified as being significantly altered in cancer. The AUCs of the significantly changed specific-isomers were ranging from 0.712 to 0.949. In addition, with the combination of all potential biomarkers, a higher AUC of 0.976 with sensitivity (93.5%) and specificity (90.6%) was obtained. Overall, the proposed strategy coupled to relative quantitative analysis of isomeric glycans make it possible to discover new biomarkers for the diagnosis of PC. Pancreatic cancer (PC) has a poor prognosis with a five-year survival rate <5%. Therefore, a strategy for accurate diagnosis of PC is indeed required. In this paper, a dual-derivatized strategy for structure-specific glycan profiling has been used and according to our best knowledge, this is the first application of this strategy for PC biomarker discovery, in which the separation, identification and relative quantification of isomeric glycans can be simultaneously obtained. In addition, by in-depth analysis of isomeric glycans, the full description of the stereo- and region- diversity of glycans can also be achieved, which might provide more potential information for PC biomarker discovery. Copyright © 2018 Elsevier B.V. All rights reserved.

  19. Genome-wide organization and expression profiling of the NAC transcription factor family in potato (Solanum tuberosum L.).

    PubMed

    Singh, Anil Kumar; Sharma, Vishal; Pal, Awadhesh Kumar; Acharya, Vishal; Ahuja, Paramvir Singh

    2013-08-01

    NAC [no apical meristem (NAM), Arabidopsis thaliana transcription activation factor [ATAF1/2] and cup-shaped cotyledon (CUC2)] proteins belong to one of the largest plant-specific transcription factor (TF) families and play important roles in plant development processes, response to biotic and abiotic cues and hormone signalling. Our genome-wide analysis identified 110 StNAC genes in potato encoding for 136 proteins, including 14 membrane-bound TFs. The physical map positions of StNAC genes on 12 potato chromosomes were non-random, and 40 genes were found to be distributed in 16 clusters. The StNAC proteins were phylogenetically clustered into 12 subgroups. Phylogenetic analysis of StNACs along with their Arabidopsis and rice counterparts divided these proteins into 18 subgroups. Our comparative analysis has also identified 36 putative TNAC proteins, which appear to be restricted to Solanaceae family. In silico expression analysis, using Illumina RNA-seq transcriptome data, revealed tissue-specific, biotic, abiotic stress and hormone-responsive expression profile of StNAC genes. Several StNAC genes, including StNAC072 and StNAC101that are orthologs of known stress-responsive Arabidopsis RESPONSIVE TO DEHYDRATION 26 (RD26) were identified as highly abiotic stress responsive. Quantitative real-time polymerase chain reaction analysis largely corroborated the expression profile of StNAC genes as revealed by the RNA-seq data. Taken together, this analysis indicates towards putative functions of several StNAC TFs, which will provide blue-print for their functional characterization and utilization in potato improvement.

  20. ChIP-chip versus ChIP-seq: Lessons for experimental design and data analysis

    PubMed Central

    2011-01-01

    Background Chromatin immunoprecipitation (ChIP) followed by microarray hybridization (ChIP-chip) or high-throughput sequencing (ChIP-seq) allows genome-wide discovery of protein-DNA interactions such as transcription factor bindings and histone modifications. Previous reports only compared a small number of profiles, and little has been done to compare histone modification profiles generated by the two technologies or to assess the impact of input DNA libraries in ChIP-seq analysis. Here, we performed a systematic analysis of a modENCODE dataset consisting of 31 pairs of ChIP-chip/ChIP-seq profiles of the coactivator CBP, RNA polymerase II (RNA PolII), and six histone modifications across four developmental stages of Drosophila melanogaster. Results Both technologies produce highly reproducible profiles within each platform, ChIP-seq generally produces profiles with a better signal-to-noise ratio, and allows detection of more peaks and narrower peaks. The set of peaks identified by the two technologies can be significantly different, but the extent to which they differ varies depending on the factor and the analysis algorithm. Importantly, we found that there is a significant variation among multiple sequencing profiles of input DNA libraries and that this variation most likely arises from both differences in experimental condition and sequencing depth. We further show that using an inappropriate input DNA profile can impact the average signal profiles around genomic features and peak calling results, highlighting the importance of having high quality input DNA data for normalization in ChIP-seq analysis. Conclusions Our findings highlight the biases present in each of the platforms, show the variability that can arise from both technology and analysis methods, and emphasize the importance of obtaining high quality and deeply sequenced input DNA libraries for ChIP-seq analysis. PMID:21356108

  1. Substantial equivalence analysis in fruits from three Theobroma species through chemical composition and protein profiling.

    PubMed

    Pérez-Mora, Walter; Jorrin-Novo, Jesús V; Melgarejo, Luz Marina

    2018-02-01

    Substantial equivalence studies were performed in three Theobroma spp., cacao, bicolor and grandiflorum through chemical composition analysis and protein profiling of fruit (pulp juice and seeds). Principal component analysis of sugar, organic acid, and phenol content in pulp juice revealed equivalence among the three species, with differences in some of the compounds that may result in different organoleptic properties. Proteins were extracted from seeds and pulp juice, resolved by two dimensional electrophoresis and major spots subjected to mass spectrometry analysis and identification. The protein profile, as revealed by principal component analysis, was variable among the three species in both seed and pulp, with qualitative and quantitative differences in some of protein species. The functional grouping of the identified proteins correlated with the biological role of each organ. Some of the identified proteins are of interest, being minimally discussed, including vicilin, a protease inhibitor, and a flavonol synthase/flavanone 3-hydroxylase. Theobroma grandiflorum and Theobroma bicolor are endemic Amazonian plants that are poorly traded at the local level. As close relatives of Theobroma cacao, they may provide a good alternative for human consumption and industrial purposes. In this regard, we performed equivalence studies by conducting a comparative biochemical and proteomics analysis of the fruit, pulp juice and seeds of these three species. The results indicated equivalent chemical compositions and variable protein profiles with some differences in the content of the specific compounds or protein species that may result in variable organoleptic properties between the species and can be exploited for traceability purposes. Copyright © 2017 Elsevier Ltd. All rights reserved.

  2. Exploring student learning profiles in algebra-based studio physics: A person-centered approach

    NASA Astrophysics Data System (ADS)

    Pond, Jarrad W. T.; Chini, Jacquelyn J.

    2017-06-01

    In this study, we explore the strategic self-regulatory and motivational characteristics of students in studio-mode physics courses at three universities with varying student populations and varying levels of success in their studio-mode courses. We survey students using questions compiled from several existing questionnaires designed to measure students' study strategies, attitudes toward and motivations for learning physics, organization of scientific knowledge, experiences outside the classroom, and demographics. Using a person-centered approach, we utilize cluster analysis methods to group students into learning profiles based on their individual responses to better understand the strategies and motives of algebra-based studio physics students. Previous studies have identified five distinct learning profiles across several student populations using similar methods. We present results from first-semester and second-semester studio-mode introductory physics courses across three universities. We identify these five distinct learning profiles found in previous studies to be present within our population of introductory physics students. In addition, we investigate interactions between these learning profiles and student demographics. We find significant interactions between a student's learning profile and their experience with high school physics, major, gender, grade expectation, and institution. Ultimately, we aim to use this method of analysis to take the characteristics of students into account in the investigation of successful strategies for using studio methods of physics instruction within and across institutions.

  3. Identifying Subgroups among Hardcore Smokers: a Latent Profile Approach

    PubMed Central

    Bommelé, Jeroen; Kleinjan, Marloes; Schoenmakers, Tim M.; Burk, William J.; van den Eijnden, Regina; van de Mheen, Dike

    2015-01-01

    Introduction Hardcore smokers are smokers who have little to no intention to quit. Previous research suggests that there are distinct subgroups among hardcore smokers and that these subgroups vary in the perceived pros and cons of smoking and quitting. Identifying these subgroups could help to develop individualized messages for the group of hardcore smokers. In this study we therefore used the perceived pros and cons of smoking and quitting to identify profiles among hardcore smokers. Methods A sample of 510 hardcore smokers completed an online survey on the perceived pros and cons of smoking and quitting. We used these perceived pros and cons in a latent profile analysis to identify possible subgroups among hardcore smokers. To validate the profiles identified among hardcore smokers, we analysed data from a sample of 338 non-hardcore smokers in a similar way. Results We found three profiles among hardcore smokers. ‘Receptive’ hardcore smokers (36%) perceived many cons of smoking and many pros of quitting. ‘Ambivalent’ hardcore smokers (59%) were rather undecided towards quitting. ‘Resistant’ hardcore smokers (5%) saw few cons of smoking and few pros of quitting. Among non-hardcore smokers, we found similar groups of ‘receptive’ smokers (30%) and ‘ambivalent’ smokers (54%). However, a third group consisted of ‘disengaged’ smokers (16%), who saw few pros and cons of both smoking and quitting. Discussion Among hardcore smokers, we found three distinct profiles based on perceived pros and cons of smoking. This indicates that hardcore smokers are not a homogenous group. Each profile might require a different tobacco control approach. Our findings may help to develop individualized tobacco control messages for the particularly hard-to-reach group of hardcore smokers. PMID:26207829

  4. Emotion Regulation Profiles, Temperament, and Adjustment Problems in Preadolescents

    PubMed Central

    Zalewski, Maureen; Lengua, Liliana J.; Trancik, Anika; Wilson, Anna C.; Bazinet, Alissa

    2014-01-01

    The longitudinal relations of emotion regulation profiles to temperament and adjustment in a community sample of preadolescents (N = 196, 8–11 years at Time 1) were investigated using person-oriented latent profile analysis (LPA). Temperament, emotion regulation, and adjustment were measured at 3 different time points, with each time point occurring 1 year apart. LPA identified 5 frustration and 4 anxiety regulation profiles based on children’s physiological, behavioral, and self-reported reactions to emotion-eliciting tasks. The relation of effortful control to conduct problems was mediated by frustration regulation profiles, as was the relation of effortful control to depression. Anxiety regulation profiles did not mediate relations between temperament and adjustment. PMID:21413935

  5. Exploitation of molecular profiling techniques for GM food safety assessment.

    PubMed

    Kuiper, Harry A; Kok, Esther J; Engel, Karl-Heinz

    2003-04-01

    Several strategies have been developed to identify unintended alterations in the composition of genetically modified (GM) food crops that may occur as a result of the genetic modification process. These include comparative chemical analysis of single compounds in GM food crops and their conventional non-GM counterparts, and profiling methods such as DNA/RNA microarray technologies, proteomics and metabolite profiling. The potential of profiling methods is obvious, but further exploration of specificity, sensitivity and validation is needed. Moreover, the successful application of profiling techniques to the safety evaluation of GM foods will require linked databases to be built that contain information on variations in profiles associated with differences in developmental stages and environmental conditions.

  6. Identification of key microRNAs and genes in preeclampsia by bioinformatics analysis

    PubMed Central

    Luo, Shouling; Cao, Nannan; Tang, Yao; Gu, Weirong

    2017-01-01

    Preeclampsia is a leading cause of perinatal maternal–foetal mortality and morbidity. The aim of this study is to identify the key microRNAs and genes in preeclampsia and uncover their potential functions. We downloaded the miRNA expression profile of GSE84260 and the gene expression profile of GSE73374 from the Gene Expression Omnibus database. Differentially expressed miRNAs and genes were identified and compared to miRNA-target information from MiRWalk 2.0, and a total of 65 differentially expressed miRNAs (DEMIs), including 32 up-regulated miRNAs and 33 down-regulated miRNAs, and 91 differentially expressed genes (DEGs), including 83 up-regulated genes and 8 down-regulated genes, were identified. The pathway enrichment analyses of the DEMIs showed that the up-regulated DEMIs were enriched in the Hippo signalling pathway and MAPK signalling pathway, and the down-regulated DEMIs were enriched in HTLV-I infection and miRNAs in cancers. The gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway (KEGG) enrichment analyses of the DEGs were performed using Multifaceted Analysis Tool for Human Transcriptome. The up-regulated DEGs were enriched in biological processes (BPs), including the response to cAMP, response to hydrogen peroxide and cell-cell adhesion mediated by integrin; no enrichment of down-regulated DEGs was identified. KEGG analysis showed that the up-regulated DEGs were enriched in the Hippo signalling pathway and pathways in cancer. A PPI network of the DEGs was constructed by using Cytoscape software, and FOS, STAT1, MMP14, ITGB1, VCAN, DUSP1, LDHA, MCL1, MET, and ZFP36 were identified as the hub genes. The current study illustrates a characteristic microRNA profile and gene profile in preeclampsia, which may contribute to the interpretation of the progression of preeclampsia and provide novel biomarkers and therapeutic targets for preeclampsia. PMID:28594854

  7. Phylogenetic Analysis of Enterohemorrhagic Escherichia coli O157, Germany, 1987–2008

    PubMed Central

    Jenke, Christian; Harmsen, Dag; Weniger, Thomas; Rothgänger, Jörg; Hyytiä-Trees, Eija; Bielaszewska, Martina; Karch, Helge

    2010-01-01

    Multilocus variable number tandem repeat analysis (MLVA) is a subtyping technique for characterizing human pathogenic bacteria such as enterohemorrhagic Escherichia coli (EHEC) O157. We determined the phylogeny of 202 epidemiologically unrelated EHEC O157:H7/H– clinical isolates through 8 MLVA loci obtained in Germany during 1987–2008. Biodiversity in the loci ranged from 0.66 to 0.90. Four of 8 loci showed null alleles and a frequency <44.1%. These loci were distributed among 48.5% of all strains. Overall, 141 MLVA profiles were identified. Phylogenetic analysis assigned 67.3% of the strains to 19 MLVA clusters. Specific MLVA profiles with an evolutionary persistence were identified, particularly within sorbitol-fermenting EHEC O157:H–.These pathogens belonged to the same MLVA cluster. Our findings indicate successful persistence of this clone. PMID:20350374

  8. Phylogenetic analysis of enterohemorrhagic Escherichia coli O157, Germany, 1987-2008.

    PubMed

    Jenke, Christian; Harmsen, Dag; Weniger, Thomas; Rothganger, Jorg; Hyytia-Trees, Eija; Bielaszewska, Martina; Karch, Helge; Mellmann, Alexander

    2010-04-01

    Multilocus variable number tandem repeat analysis (MLVA) is a subtyping technique for characterizing human pathogenic bacteria such as enterohemorrhagic Escherichia coli (EHEC) O157. We determined the phylogeny of 202 epidemiologically unrelated EHEC O157:H7/H- clinical isolates through 8 MLVA loci obtained in Germany during 1987-2008. Biodiversity in the loci ranged from 0.66 to 0.90. Four of 8 loci showed null alleles and a frequency < or =44.1%. These loci were distributed among 48.5% of all strains. Overall, 141 MLVA profiles were identified. Phylogenetic analysis assigned 67.3% of the strains to 19 MLVA clusters. Specific MLVA profiles with an evolutionary persistence were identified, particularly within sorbitol-fermenting EHEC O157:H-.These pathogens belonged to the same MLVA cluster. Our findings indicate successful persistence of this clone.

  9. Audiologist-patient communication profiles in hearing rehabilitation appointments.

    PubMed

    Meyer, Carly; Barr, Caitlin; Khan, Asaduzzaman; Hickson, Louise

    2017-08-01

    To profile the communication between audiologists and patients in initial appointments on a biomedical-psychosocial continuum; and explore the associations between these profiles and 1) characteristics of the appointment and 2) patients' decisions to pursue hearing aids. Sixty-three initial hearing assessment appointments were filmed and audiologist-patient communication was coded using the Roter Interaction Analysis System. A hierarchical cluster analysis was conducted to profile audiologist-patient communication, after which regression modelling and Chi-squared analyses were conducted. Two distinct audiologist-patient communication profiles were identified during both the history taking phase (46=biopsychosocial profile, 15=psychosocial profile) and diagnosis and management planning phase (45=expanded biomedical profile, 11=narrowly biomedical profile). Longer appointments were significantly more likely to be associated with an expanded biomedical interaction during the diagnosis and management planning phase. No significant associations were found between audiologist-patient communication profile and patients' decisions to pursue hearing aids. Initial audiology consultations appear to remain clinician-centred. Three quarters of appointments began with a biopsychosocial interaction; however, 80% ended with an expanded biomedical interaction. Findings suggest that audiologists could consider modifying their communication in initial appointments to more holistically address the needs of patients. Copyright © 2017 Elsevier B.V. All rights reserved.

  10. The resemblance and disparity of gene expression in dormant and non-dormant seeds and crown buds of leafy spurge (Euphorbia esula)

    USDA-ARS?s Scientific Manuscript database

    Overlaps in transcriptome profiles between different phases of bud and seed dormancy have not been determined. Thus, we compared various phases of dormancy between seeds and buds to identify common genes and molecular processes. Cluster analysis of expression profiles for 201 selected genes indicate...

  11. Urban Adolescents' Out-of-School Activity Profiles: Associations with Youth, Family, and School Transition Characteristics

    ERIC Educational Resources Information Center

    Pedersen, Sara

    2005-01-01

    This study applied individual growth trajectory analyses and person-oriented analysis to identify common profiles of out-of-school activity engagement trajectories among racially and ethnically diverse inner city teens (N = 1,430). On average, teens exhibited declining trajectories of participation in school-based and team sports activities and…

  12. Profiles of Teacher-Child Interaction Quality in Preschool Classrooms and Teachers' Professional Competence Features

    ERIC Educational Resources Information Center

    Hu, Bi Ying; Chen, Liang; Fan, Xitao

    2018-01-01

    This paper investigates early childhood education (ECE) teachers' self-reported and observed teacher-child interaction quality (TIQ) and the associated teachers' professional competence features using a latent profile analysis (LPA) approach to identify the variations in the quality of classroom experiences in Chinese preschools. A total of 164…

  13. Predicting Educational Outcomes and Psychological Well-Being in Adolescents Using Time Attitude Profiles

    ERIC Educational Resources Information Center

    Andretta, James R.; Worrell, Frank C.; Mello, Zena R.

    2014-01-01

    Using cluster analysis of Adolescent Time Attitude Scale (ATAS) scores in a sample of 300 adolescents ("M" age = 16 years; "SD" = 1.25; 60% male; 41% European American; 25.3% Asian American; 11% African American; 10.3% Latino), the authors identified five time attitude profiles based on positive and negative attitudes toward…

  14. An Empirical Taxonomy of Youths' Fears: Cluster Analysis of the American Fear Survey Schedule

    ERIC Educational Resources Information Center

    Burnham, Joy J.; Schaefer, Barbara A.; Giesen, Judy

    2006-01-01

    Fears profiles among children and adolescents were explored using the Fear Survey Schedule for Children-American version (FSSC-AM; J.J. Burnham, 1995, 2005). Eight cluster profiles were identified via multistage Euclidean grouping and supported by homogeneity coefficients and replication. Four clusters reflected overall level of fears (i.e., very…

  15. Subgroups of Adult Basic Education Learners with Different Profiles of Reading Skills

    ERIC Educational Resources Information Center

    MacArthur, Charles A.; Konold, Timothy R.; Glutting, Joseph J.; Alamprese, Judith A.

    2012-01-01

    The purpose of this study was to identify subgroups of adult basic education (ABE) learners with different profiles of skills in the core reading components of decoding, word recognition, spelling, fluency, and comprehension. The analysis uses factor scores of those 5 reading components from on a prior investigation of the reliability and…

  16. Single-cell genomic profiling of acute myeloid leukemia for clinical use: A pilot study

    PubMed Central

    Yan, Benedict; Hu, Yongli; Ban, Kenneth H.K.; Tiang, Zenia; Ng, Christopher; Lee, Joanne; Tan, Wilson; Chiu, Lily; Tan, Tin Wee; Seah, Elaine; Ng, Chin Hin; Chng, Wee-Joo; Foo, Roger

    2017-01-01

    Although bulk high-throughput genomic profiling studies have led to a significant increase in the understanding of cancer biology, there is increasing awareness that bulk profiling approaches do not completely elucidate tumor heterogeneity. Single-cell genomic profiling enables the distinction of tumor heterogeneity, and may improve clinical diagnosis through the identification and characterization of putative subclonal populations. In the present study, the challenges associated with a single-cell genomics profiling workflow for clinical diagnostics were investigated. Single-cell RNA-sequencing (RNA-seq) was performed on 20 cells from an acute myeloid leukemia bone marrow sample. Putative blasts were identified based on their gene expression profiles and principal component analysis was performed to identify outlier cells. Variant calling was performed on the single-cell RNA-seq data. The present pilot study demonstrates a proof of concept for clinical single-cell genomic profiling. The recognized limitations include significant stochastic RNA loss and the relatively low throughput of the current proposed platform. Although the results of the present study are promising, further technological advances and protocol optimization are necessary for single-cell genomic profiling to be clinically viable. PMID:28454300

  17. Application of global metabolomic profiling of synovial fluid for osteoarthritis biomarkers.

    PubMed

    Carlson, Alyssa K; Rawle, Rachel A; Adams, Erik; Greenwood, Mark C; Bothner, Brian; June, Ronald K

    2018-05-05

    Osteoarthritis affects over 250 million individuals worldwide. Currently, there are no options for early diagnosis of osteoarthritis, demonstrating the need for biomarker discovery. To find biomarkers of osteoarthritis in human synovial fluid, we used high performance liquid-chromatography mass spectrometry for global metabolomic profiling. Metabolites were extracted from human osteoarthritic (n = 5), rheumatoid arthritic (n = 3), and healthy (n = 5) synovial fluid, and a total of 1233 metabolites were detected. Principal components analysis clearly distinguished the metabolomic profiles of diseased from healthy synovial fluid. Synovial fluid from rheumatoid arthritis patients contained expected metabolites consistent with the inflammatory nature of the disease. Similarly, unsupervised clustering analysis found that each disease state was associated with distinct metabolomic profiles and clusters of co-regulated metabolites. For osteoarthritis, co-regulated metabolites that were upregulated compared to healthy synovial fluid mapped to known disease processes including chondroitin sulfate degradation, arginine and proline metabolism, and nitric oxide metabolism. We utilized receiver operating characteristic analysis to determine the diagnostic value of each metabolite and identified 35 metabolites as potential biomarkers of osteoarthritis, with an area under the receiver operating characteristic curve >0.9. These metabolites included phosphatidylcholine, lysophosphatidylcholine, ceramides, myristate derivatives, and carnitine derivatives. This pilot study provides strong justification for a larger cohort-based study of human osteoarthritic synovial fluid using global metabolomics. The significance of these data is the demonstration that metabolomic profiling of synovial fluid can identify relevant biomarkers of joint disease. Copyright © 2018 Elsevier Inc. All rights reserved.

  18. Transcriptional programming during cell wall maturation in the expanding Arabidopsis stem.

    PubMed

    Hall, Hardy; Ellis, Brian

    2013-01-25

    Plant cell walls are complex dynamic structures that play a vital role in coordinating the directional growth of plant tissues. The rapid elongation of the inflorescence stem in the model plant Arabidopsis thaliana is accompanied by radical changes in cell wall structure and chemistry, but analysis of the underlying mechanisms and identification of the genes that are involved has been hampered by difficulties in accurately sampling discrete developmental states along the developing stem. By creating stem growth kinematic profiles for individual expanding Arabidopsis stems we have been able to harvest and pool developmentally-matched tissue samples, and to use these for comparative analysis of global transcript profiles at four distinct phases of stem growth: the period of elongation rate increase, the point of maximum growth rate, the point of stem growth cessation and the fully matured stem. The resulting profiles identify numerous genes whose expression is affected as the stem tissues pass through these defined growth transitions, including both novel loci and genes identified in earlier studies. Of particular note is the preponderance of highly active genes associated with secondary cell wall deposition in the region of stem growth cessation, and of genes associated with defence and stress responses in the fully mature stem. The use of growth kinematic profiling to create tissue samples that are accurately positioned along the expansion growth continuum of Arabidopsis inflorescence stems establishes a new standard for transcript profiling analyses of such tissues. The resulting expression profiles identify a substantial number of genes whose expression is correlated for the first time with rapid cell wall extension and subsequent fortification, and thus provide an important new resource for plant biologists interested in gene discovery related to plant biomass accumulation.

  19. Effect of masticatory stimulation on the quantity and quality of saliva and the salivary metabolomic profile

    PubMed Central

    Hoshi, Noriyuki; Soga, Tomoyoshi; Tomita, Masaru; Sugimoto, Masahiro; Kimoto, Katsuhiko

    2017-01-01

    Background This study characterized the changes in quality and quantity of saliva, and changes in the salivary metabolomic profile, to understand the effects of masticatory stimulation. Methods Stimulated and unstimulated saliva samples were collected from 55 subjects and salivary hydrophilic metabolites were comprehensively quantified using capillary electrophoresis-time-of-flight mass spectrometry. Results In total, 137 metabolites were identified and quantified. The concentrations of 44 metabolites in stimulated saliva were significantly higher than those in unstimulated saliva. Pathway analysis identified the upregulation of the urea cycle and synthesis and degradation pathways of glycine, serine, cysteine and threonine in stimulated saliva. A principal component analysis revealed that the effect of masticatory stimulation on salivary metabolomic profiles was less dependent on sample population sex, age, and smoking. The concentrations of only 1 metabolite in unstimulated saliva, and of 3 metabolites stimulated saliva, showed significant correlation with salivary secretion volume, indicating that the salivary metabolomic profile and salivary secretion volume were independent factors. Conclusions Masticatory stimulation affected not only salivary secretion volume, but also metabolite concentration patterns. A low correlation between the secretion volume and these patterns supports the conclusion that the salivary metabolomic profile may be a new indicator to characterize masticatory stimulation. PMID:28813487

  20. Identifying dentists' attitudes towards prevention guidance using Q-sort methodology.

    PubMed

    Witton, R V; Moles, D R

    2015-06-01

    To gain insight into the attitudes and motivating factors of dentists working in the English National Health Service (NHS) towards prevention guidance. Q-methodology: an established hybrid quantitative/qualitative technique used in the social sciences to categorise subjects based on their views by considering factors as part of their overall decision-making profile. General Dental Practices offering care under an NHS contract. NHS dentists (n = 26) placed 36 statements about prevention guidance derived from an earlier study into a distribution grid that ranked the statements from "most agree" to "most disagree". Principal components factor analysis was applied to determine the principal patterns in the rankings of statements. Analysis indicated a total of six distinct profiles within the responses, of which three profiles had at least six dentists loading onto them. The first profile was strongly characterised by dentists who appear motivated to provide prevention but financial and time constraints prevent them from doing so. The second was characterised by dentists using prevention guidance but restricting its use to only certain patients. The third was characterised by dentists who appeared "health-focused". They placed importance on working to prevention guidance, but were keen to have greater patient and professional support in achieving this. In this group of dentists Q-methodology identified three main profiles to the delivery of prevention guidance.

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

    PubMed Central

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

    2014-01-01

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

  2. Associations Between Peer Harassment and School Risk and Protection Profiles.

    PubMed

    Gloppen, Kari M; Gower, Amy L; McMorris, Barbara J; Eisenberg, Marla E

    2017-11-01

    Peer harassment can have serious implications for students' success and well-being, and prevention programs need to consider the school context. This study aimed to: (1) identify groups of similar schools based on their risk and protective factors and demographic characteristics and (2) examine associations between school profiles and students' bullying involvement. Data came from 505 schools and 122,106 students who completed the 2013 Minnesota Student Survey. School-level risk and protective factors and demographic characteristics were included in a latent profile analysis (LPA) to identify profiles of schools. Multilevel logistic regression was used to assess associations between school profiles and peer harassment. Six qualitatively different school profiles were identified. Unadjusted models showed that schools with higher levels of risk had greater odds of peer harassment. However, after controlling for student-level risk and protection, regardless of school-level risk, students in metro-area schools with a more diverse student body reported lower odds of bullying involvement. These findings highlight the importance of the social environment into peer harassment. In addition to addressing student-level risk and protection, larger community factors and norms also need to be taken into account for developing, selecting, and implementing the most effective approaches to bullying prevention. © 2017, American School Health Association.

  3. Prevalence of stress references on college freshmen Facebook profiles.

    PubMed

    Egan, Katie G; Moreno, Megan A

    2011-10-01

    Stress is common among college students and associated with adverse health outcomes. This study used the social networking Web site Facebook to identify self-reported stress and associated conditions among college students. Public Facebook profiles of undergraduate freshman at a large Midwestern State University (n = 300) were identified using a Facebook search. Content analysis of Facebook profiles included demographic information and displayed references to stress, weight concerns, depressive symptoms, and alcohol. The mean reported age was 18.4 years, and the majority of profile owners were female (62%). Stress references were displayed on 37% of the profiles, weight concerns on 6%, depressive symptoms on 24%, and alcohol on 73%. The display of stress references was associated with female sex (odds ratio [OR], 2.81; confidence interval [CI], 1.7-4.7), weight concerns (OR, 5.36; CI, 1.87-15.34), and depressive symptoms (OR, 2.7; CI, 1.57-4.63). No associations were found between stress and alcohol references. College freshmen frequently display references to stress on Facebook profiles with prevalence rates similar to self-reported national survey data. Findings suggest a positive association between referencing stress and both weight concerns and depressive symptoms. Facebook may be a useful venue to identify students at risk for stress-related conditions and to disseminate information about campus resources to these students.

  4. PCR array analysis of gene expression profiles in chronic active Epstein-Barr virus infection.

    PubMed

    Murakami, Masanao; Hashida, Yumiko; Imajoh, Masayuki; Maeda, Akihiko; Kamioka, Mikio; Senda, Yasutaka; Sato, Tetsuya; Fujieda, Mikiya; Wakiguchi, Hiroshi; Daibata, Masanori

    2014-07-01

    To determine the host cellular gene expression profiles in chronic active Epstein-Barr virus infection (CAEBV), peripheral blood samples were obtained from three patients with CAEBV and investigated using a PCR array analysis that focused on T-cell/B-cell activation. We identified six genes with expression levels that were tenfold higher in CAEBV patients compared with those in healthy controls. These results were verified by quantitative reverse transcription-PCR. We identified four highly upregulated genes, i.e., IL-10, IL-2, IFNGR1, and INHBA. These genes may be involved in inflammatory responses and cell proliferation, and they may contribute to the development and progression of CAEBV. Copyright © 2014 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

  5. Characteristic fingerprint based on gingerol derivative analysis for discrimination of ginger (Zingiber officinale) according to geographical origin using HPLC-DAD combined with chemometrics.

    PubMed

    Yudthavorasit, Soparat; Wongravee, Kanet; Leepipatpiboon, Natchanun

    2014-09-01

    Chromatographic fingerprints of gingers from five different ginger-producing countries (China, India, Malaysia, Thailand and Vietnam) were newly established to discriminate the origin of ginger. The pungent bioactive principles of ginger, gingerols and six other gingerol-related compounds were determined and identified. Their variations in HPLC profiles create the characteristic pattern of each origin by employing similarity analysis, hierarchical cluster analysis (HCA), principal component analysis (PCA) and linear discriminant analysis (LDA). As results, the ginger profiles tended to be grouped and separated on the basis of the geographical closeness of the countries of origin. An effective mathematical model with high predictive ability was obtained and chemical markers for each origin were also identified as the characteristic active compounds to differentiate the ginger origin. The proposed method is useful for quality control of ginger in case of origin labelling and to assess food authenticity issues. Copyright © 2014 Elsevier Ltd. All rights reserved.

  6. Metabolomic analysis based on 1H-nuclear magnetic resonance spectroscopy metabolic profiles in tuberculous, malignant and transudative pleural effusion

    PubMed Central

    Wang, Cheng; Peng, Jingjin; Kuang, Yanling; Zhang, Jiaqiang; Dai, Luming

    2017-01-01

    Pleural effusion is a common clinical manifestation with various causes. Current diagnostic and therapeutic methods have exhibited numerous limitations. By involving the analysis of dynamic changes in low molecular weight catabolites, metabolomics has been widely applied in various types of disease and have provided platforms to distinguish many novel biomarkers. However, to the best of our knowledge, there are few studies regarding the metabolic profiling for pleural effusion. In the current study, 58 pleural effusion samples were collected, among which 20 were malignant pleural effusions, 20 were tuberculous pleural effusions and 18 were transudative pleural effusions. The small molecule metabolite spectrums were obtained by adopting 1H nuclear magnetic resonance technology, and pattern-recognition multi-variable statistical analysis was used to screen out different metabolites. One-way analysis of variance, and Student-Newman-Keuls and the Kruskal-Wallis test were adopted for statistical analysis. Over 400 metabolites were identified in the untargeted metabolomic analysis and 26 metabolites were identified as significantly different among tuberculous, malignant and transudative pleural effusions. These metabolites were predominantly involved in the metabolic pathways of amino acids metabolism, glycometabolism and lipid metabolism. Statistical analysis revealed that eight metabolites contributed to the distinction between the three groups: Tuberculous, malignant and transudative pleural effusion. In the current study, the feasibility of identifying small molecule biochemical profiles in different types of pleural effusion were investigated reveal novel biological insights into the underlying mechanisms. The results provide specific insights into the biology of tubercular, malignant and transudative pleural effusion and may offer novel strategies for the diagnosis and therapy of associated diseases, including tuberculosis, advanced lung cancer and congestive heart failure. PMID:28627685

  7. Integrative Analysis of Response to Tamoxifen Treatment in ER-Positive Breast Cancer Using GWAS Information and Transcription Profiling.

    PubMed

    Hicks, Chindo; Kumar, Ranjit; Pannuti, Antonio; Miele, Lucio

    2012-01-01

    Variable response and resistance to tamoxifen treatment in breast cancer patients remains a major clinical problem. To determine whether genes and biological pathways containing SNPs associated with risk for breast cancer are dysregulated in response to tamoxifen treatment, we performed analysis combining information from 43 genome-wide association studies with gene expression data from 298 ER(+) breast cancer patients treated with tamoxifen and 125 ER(+) controls. We identified 95 genes which distinguished tamoxifen treated patients from controls. Additionally, we identified 54 genes which stratified tamoxifen treated patients into two distinct groups. We identified biological pathways containing SNPs associated with risk for breast cancer, which were dysregulated in response to tamoxifen treatment. Key pathways identified included the apoptosis, P53, NFkB, DNA repair and cell cycle pathways. Combining GWAS with transcription profiling provides a unified approach for associating GWAS findings with response to drug treatment and identification of potential drug targets.

  8. Quantitative profiling of immune repertoires for minor lymphocyte counts using unique molecular identifiers.

    PubMed

    Egorov, Evgeny S; Merzlyak, Ekaterina M; Shelenkov, Andrew A; Britanova, Olga V; Sharonov, George V; Staroverov, Dmitriy B; Bolotin, Dmitriy A; Davydov, Alexey N; Barsova, Ekaterina; Lebedev, Yuriy B; Shugay, Mikhail; Chudakov, Dmitriy M

    2015-06-15

    Emerging high-throughput sequencing methods for the analyses of complex structure of TCR and BCR repertoires give a powerful impulse to adaptive immunity studies. However, there are still essential technical obstacles for performing a truly quantitative analysis. Specifically, it remains challenging to obtain comprehensive information on the clonal composition of small lymphocyte populations, such as Ag-specific, functional, or tissue-resident cell subsets isolated by sorting, microdissection, or fine needle aspirates. In this study, we report a robust approach based on unique molecular identifiers that allows profiling Ag receptors for several hundred to thousand lymphocytes while preserving qualitative and quantitative information on clonal composition of the sample. We also describe several general features regarding the data analysis with unique molecular identifiers that are critical for accurate counting of starting molecules in high-throughput sequencing applications. Copyright © 2015 by The American Association of Immunologists, Inc.

  9. Profiles of Adolescent Religiousness using Latent Profile Analysis: Implications for Psychopathology

    PubMed Central

    Longo, Gregory S.; Bray, Bethany; Kim-Spoon, Jungmeen

    2017-01-01

    Prior research has documented robust associations between adolescent religiousness/spirituality (R/S) and psychopathology outcomes including externalizing and internalizing symptomatology, yet no previous studies have examined these associations with adolescent R/S profiles using a person-centered approach. We examined if there are identifiable subgroups characterized by unique multidimensional patterns of R/S experiences and how these experiences may be related to externalizing and internalizing symptomatology. The sample consisted of 220 Appalachian adolescents between 12 and 18 years old who were primarily White and primarily Christian. Latent profile analysis revealed three profiles of adolescent R/S; high religiousness (28.4%), introjectors (47.6%), and low religiousness (24.0%). These profiles were differentially related to internalizing and externalizing symptomatology such that the high religiousness group was significantly lower than the introjectors with respect to internalizing and externalizing symptomatology and lower than the low religiousness group in externalizing symptomatology. Implications and suggestions for future research using person-centered approaches to better understand differential developmental trajectories of religious development are provided. PMID:28220955

  10. Alcohol and cannabis consumption in the French Army: determination of consumer profiles to focus on prevention and care.

    PubMed

    Rigod, Violaine; Pilard, Michel; Paul, Frédéric; Deparis, Xavier; Marimoutou, Catherine

    2011-07-01

    To ascertain the different profiles of alcohol and cannabis consumers in the French Army to improve prevention measures. A representative sample of 990 French Army staff filled in self-questionnaires in 2006. A multiple correspondence analysis identified associations between consumption and consumer profiles. The multiple correspondence analysis found three main consumer profiles: non-consumers (women and officers), moderate consumers (non-commissioned officers > 30-years old, single parents with children), and occasional multi-consumers (18-25-years-old enlisted males, who occasionally consumed cannabis and high levels of alcohol, also tobacco-addicts). Two minor profiles emerged: daily alcohol drinkers (men, > or = 30 years) and regular dependent cannabis users (identical profile to multi-consumers). Our results favor targeting the youngest to prevent the risks of high alcohol intake and cannabis consumption and addiction linked to repeated binge drinking. Systematic questionnaires on consumption habits and addiction self-evaluations during medical consultations could lead to early care.

  11. Derivative component analysis for mass spectral serum proteomic profiles.

    PubMed

    Han, Henry

    2014-01-01

    As a promising way to transform medicine, mass spectrometry based proteomics technologies have seen a great progress in identifying disease biomarkers for clinical diagnosis and prognosis. However, there is a lack of effective feature selection methods that are able to capture essential data behaviors to achieve clinical level disease diagnosis. Moreover, it faces a challenge from data reproducibility, which means that no two independent studies have been found to produce same proteomic patterns. Such reproducibility issue causes the identified biomarker patterns to lose repeatability and prevents it from real clinical usage. In this work, we propose a novel machine-learning algorithm: derivative component analysis (DCA) for high-dimensional mass spectral proteomic profiles. As an implicit feature selection algorithm, derivative component analysis examines input proteomics data in a multi-resolution approach by seeking its derivatives to capture latent data characteristics and conduct de-noising. We further demonstrate DCA's advantages in disease diagnosis by viewing input proteomics data as a profile biomarker via integrating it with support vector machines to tackle the reproducibility issue, besides comparing it with state-of-the-art peers. Our results show that high-dimensional proteomics data are actually linearly separable under proposed derivative component analysis (DCA). As a novel multi-resolution feature selection algorithm, DCA not only overcomes the weakness of the traditional methods in subtle data behavior discovery, but also suggests an effective resolution to overcoming proteomics data's reproducibility problem and provides new techniques and insights in translational bioinformatics and machine learning. The DCA-based profile biomarker diagnosis makes clinical level diagnostic performances reproducible across different proteomic data, which is more robust and systematic than the existing biomarker discovery based diagnosis. Our findings demonstrate the feasibility and power of the proposed DCA-based profile biomarker diagnosis in achieving high sensitivity and conquering the data reproducibility issue in serum proteomics. Furthermore, our proposed derivative component analysis suggests the subtle data characteristics gleaning and de-noising are essential in separating true signals from red herrings for high-dimensional proteomic profiles, which can be more important than the conventional feature selection or dimension reduction. In particular, our profile biomarker diagnosis can be generalized to other omics data for derivative component analysis (DCA)'s nature of generic data analysis.

  12. Variations in Decision-Making Profiles by Age and Gender: A Cluster-Analytic Approach.

    PubMed

    Delaney, Rebecca; Strough, JoNell; Parker, Andrew M; de Bruin, Wandi Bruine

    2015-10-01

    Using cluster-analysis, we investigated whether rational, intuitive, spontaneous, dependent, and avoidant styles of decision making (Scott & Bruce, 1995) combined to form distinct decision-making profiles that differed by age and gender. Self-report survey data were collected from 1,075 members of RAND's American Life Panel (56.2% female, 18-93 years, M age = 53.49). Three decision-making profiles were identified: affective/experiential, independent/self-controlled, and an interpersonally-oriented dependent profile. Older people were less likely to be in the affective/experiential profile and more likely to be in the independent/self-controlled profile. Women were less likely to be in the affective/experiential profile and more likely to be in the interpersonally-oriented dependent profile. Interpersonally-oriented profiles are discussed as an overlooked but important dimension of how people make important decisions.

  13. Saturated fatty acids as possible important metabolites for epithelial ovarian cancer based on the free and esterified fatty acid profiles determined by GC-MS analysis.

    PubMed

    Yin, Rui; Yang, Tongshu; Su, Hui; Ying, Li; Liu, Liyan; Sun, Changhao

    2016-09-26

    The aims were to investigate the serum free fatty acid (FFA) and esterified fatty acid (EFA) profiles and to identify biomarkers that can be used to identify patients with epithelial ovarian cancer (EOC) based on the metabolomics approach. We applied a targeted gas chromatography-mass spectrometry metabolomics approach to serum samples from 40 EOC patients and 35 healthy controls for achieving the FFA and EFA profiles. These metabolite profiles were processed using multivariate analysis to obtain potential biomarkers. And then, some independent samples were chosen to validate these potential biomarkers. There were higher saturated fatty acids and lower unsaturated fatty acids in EOC patients when compared with the healthy controls. EFA (C16:0), EFA (C18:0) and FFA (C16:0) were identified as potential biomarkers that distinguished EOC from the healthy controls. The areas under the curve from the EFA (C16:0), EFA (C18:0) and FFA (C16:0) in validated study were 0.745, 0.701, 0.682, respectively. Our study provides useful information to bridge the gaps in our understanding to the fatty acids metabolic alterations associated with EOC, and this study has demonstrated saturated fatty acid biomarkers might be helpful for the detection and characterization of EOC patients.

  14. The analysis of professional competencies of a lecturer in adult education.

    PubMed

    Žeravíková, Iveta; Tirpáková, Anna; Markechová, Dagmar

    2015-01-01

    In this article, we present the andragogical research project and evaluation of its results using nonparametric statistical methods and the semantic differential method. The presented research was realized in the years 2012-2013 in the dissertation of I. Žeravíková: Analysis of professional competencies of lecturer and creating his competence profile (Žeravíková 2013), and its purpose was based on the analysis of work activities of a lecturer to identify his most important professional competencies and to create a suggestion of competence profile of a lecturer in adult education.

  15. Drinking Patterns and Victimization among Male and Female Students in Mexico

    PubMed Central

    Strunin, Lee; Díaz-Martínez, L. Rosa; Díaz-Martínez, Alejandro; Heeren, Timothy; Winter, Michael; Kuranz, Seth; Hernández–Ávila, Carlos A.; Fernández-Varela, Héctor; Solís-Torres, Cuauhtémoc

    2015-01-01

    Aims: The purpose of this study is to estimate the prevalence of alcohol use and alcohol-related consequences, identify drinking profiles using latent profile analysis (LPA), and investigate associations between profiles and violent victimization among young people in Mexico. Methods: LPA identified profiles of drinking behavior in a survey of entering first year university students. Multinomial and logistic regression examined associations between drinking patterns, socio-demographic variables and violent victimization. Results: The LPA identified five profiles of behaviors and consequences among the 22,224 current, former and never drinkers: Non/Infrequent-No Consequences, Occasional-Few Consequences, Regular-Some Consequences, Heavy-Many Consequences and Excessive-Many Consequences drinkers. The Occasional-Few Consequences profile comprised the largest, and the Excessive-Many Consequences profile the smallest, group of drinkers. Multinomial regression showed males and older students more likely to be Heavy or Excessive-Many Consequences drinkers. Living alone was associated with higher odds, and higher maternal education with lower odds, of being a Non/Infrequent-No Consequences drinker. Heavier drinking profiles were more likely to experience violent victimization adverse consequences. Logistic regression showed male and female Heavy and Excessive-Many Consequences drinkers had the highest odds, and Non/Infrequent drinkers the lowest odds, of experiencing any victimization. Conclusion: Findings suggest changes in male and female drinking behavior and a continuation of the established pattern of infrequent but high consumption among Mexican youths. Both male and female Heavy and Excessive-Many Consequences drinkers were at elevated risk for experiencing victimization. Identifying cultural gender norms about drinking including drinker expectations and drinking context that contribute to these patterns can inform prevention efforts. PMID:25534933

  16. Molecular Profiling Reveals Biologically Discrete Subsets and Pathways of Progression in Diffuse Glioma.

    PubMed

    Ceccarelli, Michele; Barthel, Floris P; Malta, Tathiane M; Sabedot, Thais S; Salama, Sofie R; Murray, Bradley A; Morozova, Olena; Newton, Yulia; Radenbaugh, Amie; Pagnotta, Stefano M; Anjum, Samreen; Wang, Jiguang; Manyam, Ganiraju; Zoppoli, Pietro; Ling, Shiyun; Rao, Arjun A; Grifford, Mia; Cherniack, Andrew D; Zhang, Hailei; Poisson, Laila; Carlotti, Carlos Gilberto; Tirapelli, Daniela Pretti da Cunha; Rao, Arvind; Mikkelsen, Tom; Lau, Ching C; Yung, W K Alfred; Rabadan, Raul; Huse, Jason; Brat, Daniel J; Lehman, Norman L; Barnholtz-Sloan, Jill S; Zheng, Siyuan; Hess, Kenneth; Rao, Ganesh; Meyerson, Matthew; Beroukhim, Rameen; Cooper, Lee; Akbani, Rehan; Wrensch, Margaret; Haussler, David; Aldape, Kenneth D; Laird, Peter W; Gutmann, David H; Noushmehr, Houtan; Iavarone, Antonio; Verhaak, Roel G W

    2016-01-28

    Therapy development for adult diffuse glioma is hindered by incomplete knowledge of somatic glioma driving alterations and suboptimal disease classification. We defined the complete set of genes associated with 1,122 diffuse grade II-III-IV gliomas from The Cancer Genome Atlas and used molecular profiles to improve disease classification, identify molecular correlations, and provide insights into the progression from low- to high-grade disease. Whole-genome sequencing data analysis determined that ATRX but not TERT promoter mutations are associated with increased telomere length. Recent advances in glioma classification based on IDH mutation and 1p/19q co-deletion status were recapitulated through analysis of DNA methylation profiles, which identified clinically relevant molecular subsets. A subtype of IDH mutant glioma was associated with DNA demethylation and poor outcome; a group of IDH-wild-type diffuse glioma showed molecular similarity to pilocytic astrocytoma and relatively favorable survival. Understanding of cohesive disease groups may aid improved clinical outcomes. Copyright © 2016 Elsevier Inc. All rights reserved.

  17. Source apportionment of exposures to volatile organic compounds. I. Evaluation of receptor models using simulated exposure data

    NASA Astrophysics Data System (ADS)

    Miller, Shelly L.; Anderson, Melissa J.; Daly, Eileen P.; Milford, Jana B.

    Four receptor-oriented source apportionment models were evaluated by applying them to simulated personal exposure data for select volatile organic compounds (VOCs) that were generated by Monte Carlo sampling from known source contributions and profiles. The exposure sources modeled are environmental tobacco smoke, paint emissions, cleaning and/or pesticide products, gasoline vapors, automobile exhaust, and wastewater treatment plant emissions. The receptor models analyzed are chemical mass balance, principal component analysis/absolute principal component scores, positive matrix factorization (PMF), and graphical ratio analysis for composition estimates/source apportionment by factors with explicit restriction, incorporated in the UNMIX model. All models identified only the major contributors to total exposure concentrations. PMF extracted factor profiles that most closely represented the major sources used to generate the simulated data. None of the models were able to distinguish between sources with similar chemical profiles. Sources that contributed <5% to the average total VOC exposure were not identified.

  18. Methodology for fast detection of false sharing in threaded scientific codes

    DOEpatents

    Chung, I-Hsin; Cong, Guojing; Murata, Hiroki; Negishi, Yasushi; Wen, Hui-Fang

    2014-11-25

    A profiling tool identifies a code region with a false sharing potential. A static analysis tool classifies variables and arrays in the identified code region. A mapping detection library correlates memory access instructions in the identified code region with variables and arrays in the identified code region while a processor is running the identified code region. The mapping detection library identifies one or more instructions at risk, in the identified code region, which are subject to an analysis by a false sharing detection library. A false sharing detection library performs a run-time analysis of the one or more instructions at risk while the processor is re-running the identified code region. The false sharing detection library determines, based on the performed run-time analysis, whether two different portions of the cache memory line are accessed by the generated binary code.

  19. Coparenting profiles in the context of Mexican-origin teen pregnancy: links to mother-daughter relationship quality and adjustment.

    PubMed

    Perez-Brena, Norma J; Updegraff, Kimberly A; Umaña-Taylor, Adriana J; Jahromi, Laudan; Guimond, Amy

    2015-06-01

    The current study explored the multifaceted nature of the mother-adolescent coparental relationship with data from 167 Mexican-origin adolescent mothers and their own mothers at 10 months post childbirth. Profiles of mother-adolescent coparenting were created with latent profile analysis using adolescents' reports of three dimensions of coparenting (communication, involvement, and conflict). Four profiles were identified: (a) Harmonious Coparents (equal involvement, high communication, low conflict); (b) Harmonious-Adolescent Primary (adolescent is more involved than mother, high communication, low conflict); (c) Conflictual Coparents (equal involvement, high communication, high conflict); and (d) Conflictual-Adolescent Primary (adolescent is more involved than mother, moderate communication, high conflict). Families characterized by high mother-daughter conflict and psychological control prior to childbirth were more likely to belong in the Conflictual Coparents profile. In addition, adolescents' and mothers' depressive symptoms and parenting efficacy after childbirth were linked to profile membership, such that the Harmonious-Adolescent Primary profile reported the most positive adjustment patterns, whereas profiles with high coparental conflict (i.e., Conflictual Coparenting and Conflictual-Adolescent Primary profiles) showed the least positive adjustment patterns. Discussion considers the applied implications of identifying precursors to healthy and problematic mother-daughter coparenting for families of adolescent mothers in the early years of parenting. © 2014 Family Process Institute.

  20. Coparenting Profiles in the Context of Mexican-Origin Teen Pregnancy: Links to Mother-Daughter Relationship Quality and Adjustment

    PubMed Central

    Perez-Brena, Norma J.; Updegraff, Kimberly A.; Umaña-Taylor, Adriana J.; Jahromi, Laudan; Guimond, Amy

    2015-01-01

    The current study explored the multifaceted nature of the mother-adolescent coparental relationship with data from 167 Mexican-origin adolescent mothers and their own mothers at ten months post-childbirth. Profiles of mother-adolescent coparenting were created with latent profile analysis using adolescents’ reports of three dimensions of coparenting (communication, involvement and conflict). Four profiles were identified: (a) Harmonious Coparents (equal involvement, high communication, low conflict); (b) Harmonious-Adolescent Primary (adolescent is more involved than mother, high communication, low conflict); (c) Conflictual Coparents (equal involvement, high communication, high conflict); and (d) Conflictual-Adolescent Primary (adolescent is more involved than mother, moderate communication, high conflict). Families characterized by high mother-daughter conflict and psychological control prior to childbirth were more likely to belong in the Conflictual Coparents profile. In addition, adolescents’ and mothers’ depressive symptoms and parenting efficacy after childbirth were linked to profile membership, such that the Harmonious-Adolescent Primary profile reported the most positive adjustment patterns, whereas profiles with high coparental conflict (i.e., Conflictual Coparenting and Conflictual-Adolescent Primary profiles) showed the least positive adjustment patterns. Discussion considers the applied implications of identifying precursors to healthy and problematic mother-daughter coparenting for families of adolescent mothers in the early years of parenting. PMID:25438748

  1. Functional Proteomic Profiling of Secreted Serine Proteases in Health and Inflammatory Bowel Disease.

    PubMed

    Denadai-Souza, Alexandre; Bonnart, Chrystelle; Tapias, Núria Solà; Marcellin, Marlène; Gilmore, Brendan; Alric, Laurent; Bonnet, Delphine; Burlet-Schiltz, Odile; Hollenberg, Morley D; Vergnolle, Nathalie; Deraison, Céline

    2018-05-18

    While proteases are essential in gastrointestinal physiology, accumulating evidence indicates that dysregulated proteolysis plays a pivotal role in the pathophysiology of inflammatory bowel disease (IBD). Nonetheless, the identity of overactive proteases released by human colonic mucosa remains largely unknown. Studies of protease abundance have primarily investigated expression profiles, not taking into account their enzymatic activity. Herein we have used serine protease-targeted activity-based probes (ABPs) coupled with mass spectral analysis to identify active forms of proteases secreted by the colonic mucosa of healthy controls and IBD patients. Profiling of (Pro-Lys)-ABP bound proteases revealed that most of hyperactive proteases from IBD secretome are clustered at 28-kDa. We identified seven active proteases: the serine proteases cathepsin G, plasma kallikrein, plasmin, tryptase, chymotrypsin-like elastase 3 A, and thrombin and the aminopeptidase B. Only cathepsin G and thrombin were overactive in supernatants from IBD patient tissues compared to healthy controls. Gene expression analysis highlighted the transcription of genes encoding these proteases into intestinal mucosae. The functional ABP-targeted proteomic approach that we have used to identify active proteases in human colonic samples bears directly on the understanding of the role these enzymes may play in the pathophysiology of IBD.

  2. Diversity of acetic acid bacteria present in healthy grapes from the Canary Islands.

    PubMed

    Valera, Maria José; Laich, Federico; González, Sara S; Torija, Maria Jesús; Mateo, Estibaliz; Mas, Albert

    2011-11-15

    The identification of acetic acid bacteria (AAB) from sound grapes from the Canary Islands is reported in the present study. No direct recovery of bacteria was possible in the most commonly used medium, so microvinifications were performed on grapes from Tenerife, La Palma and Lanzarote islands. Up to 396 AAB were isolated from those microvinifications and identified by 16S rRNA gene sequencing and phylogenetic analysis. With this method, Acetobacter pasteurianus, Acetobacter tropicalis, Gluconobacter japonicus and Gluconacetobacter saccharivorans were identified. However, no discrimination between the closely related species Acetobacter malorum and Acetobacter cerevisiae was possible. As previously described, 16S-23S rRNA gene internal transcribed spacer (ITS) region phylogenetic analysis was required to classify isolates as one of those species. These two species were the most frequently occurring, accounting for more than 60% of the isolates. For typing the AAB isolates, both the Enterobacterial Repetitive Intergenic Consensus (ERIC)-PCR and (GTG)5-PCR techniques gave similar resolution. A total of 60 profiles were identified. Thirteen of these profiles were found in more than one vineyard, and only one profile was found on two different islands (Tenerife and La Palma). Copyright © 2011 Elsevier B.V. All rights reserved.

  3. Microarray gene expression profiling analysis combined with bioinformatics in multiple sclerosis.

    PubMed

    Liu, Mingyuan; Hou, Xiaojun; Zhang, Ping; Hao, Yong; Yang, Yiting; Wu, Xiongfeng; Zhu, Desheng; Guan, Yangtai

    2013-05-01

    Multiple sclerosis (MS) is the most prevalent demyelinating disease and the principal cause of neurological disability in young adults. Recent microarray gene expression profiling studies have identified several genetic variants contributing to the complex pathogenesis of MS, however, expressional and functional studies are still required to further understand its molecular mechanism. The present study aimed to analyze the molecular mechanism of MS using microarray analysis combined with bioinformatics techniques. We downloaded the gene expression profile of MS from Gene Expression Omnibus (GEO) and analysed the microarray data using the differentially coexpressed genes (DCGs) and links package in R and Database for Annotation, Visualization and Integrated Discovery. The regulatory impact factor (RIF) algorithm was used to measure the impact factor of transcription factor. A total of 1,297 DCGs between MS patients and healthy controls were identified. Functional annotation indicated that these DCGs were associated with immune and neurological functions. Furthermore, the RIF result suggested that IKZF1, BACH1, CEBPB, EGR1, FOS may play central regulatory roles in controlling gene expression in the pathogenesis of MS. Our findings confirm the presence of multiple molecular alterations in MS and indicate the possibility for identifying prognostic factors associated with MS pathogenesis.

  4. Identifying Taiwanese University Students' Physics Learning Profiles and Their Role in Physics Learning Self-Efficacy

    NASA Astrophysics Data System (ADS)

    Lin, Tzung-Jin; Liang, Jyh-Chong; Tsai, Chin-Chung

    2015-08-01

    The main purposes of this study were to identify Taiwanese university students' physics learning profiles in terms of their critical conceptions of learning physics and to compare their physics learning self-efficacy with the different learning profiles. A total of 250 Taiwanese undergraduates who were majoring in physics participated in this study and were invited to complete two instruments, physics learning profile and physics learning self-efficacy (PLSE). The main results indicated that, first, the two instruments developed in this study had satisfactory validity and reliability. Second, three fundamental physics learning profiles, the reproductive, transitional, and constructive profiles, were characterized based on the cluster analysis. It is also evident that the three learning profiles demonstrated different levels of self-efficacy for the five PLSE dimensions. The students with a reproductive profile tended to possess the lowest PLSE across the five dimensions. The students with a transitional profile may possess higher confidence in higher-order cognitive skills and laboratory activities than those with a reproductive profile. However, only those with a constructive profile, highlighting a comprehensive understanding of physics knowledge/concepts as well as de-emphasizing physics learning as preparing for tests and calculating and practising tutorial problems, possessed stronger PLSE in applying what they learned to real-world contexts as well as in scientifically communicating with others.

  5. Empirical Profiles of Alcohol and Marijuana Use, Drugged Driving, and Risk Perceptions.

    PubMed

    Arterberry, Brooke J; Treloar, Hayley; McCarthy, Denis M

    2017-11-01

    The present study sought to inform models of risk for drugged driving through empirically identifying patterns of marijuana use, alcohol use, and related driving behaviors. Perceived dangerousness and consequences of drugged driving were evaluated as putative influences on risk patterns. We used latent profile analysis of survey responses from 897 college students to identify patterns of substance use and drugged driving. We tested the hypotheses that low perceived danger and low perceived likelihood of negative consequences of drugged driving would identify individuals with higher-risk patterns. Findings from the latent profile analysis indicated that a four-profile model provided the best model fit. Low-level engagers had low rates of substance use and drugged driving. Alcohol-centric engagers had higher rates of alcohol use but low rates of marijuana/simultaneous use and low rates of driving after substance use. Concurrent engagers had higher rates of marijuana and alcohol use, simultaneous use, and related driving behaviors, but marijuana-centric/simultaneous engagers had the highest rates of marijuana use, co-use, and related driving behaviors. Those with higher perceived danger of driving while high were more likely to be in the low-level, alcohol-centric, or concurrent engagers' profiles; individuals with higher perceived likelihood of consequences of driving while high were more likely to be in the low-level engagers group. Findings suggested that college students' perceived dangerousness of driving after using marijuana had greater influence on drugged driving behaviors than alcohol-related driving risk perceptions. These results support targeting marijuana-impaired driving risk perceptions in young adult intervention programs.

  6. Classification and Validation of Behavioral Subtypes of Learning-Disabled Children.

    ERIC Educational Resources Information Center

    Speece, Deborah L.; And Others

    1985-01-01

    Using the Classroom Behavior Inventory, teachers rated the behaviors of 63 school-identified, learning-disabled first and second graders. Hierarchical cluster analysis techniques identified seven distinct behavioral subtypes. Internal validation techniques indicated that the subtypes were replicable and had profile patterns different from a sample…

  7. Structure-related clustering of gene expression fingerprints of thp-1 cells exposed to smaller polycyclic aromatic hydrocarbons.

    PubMed

    Wan, B; Yarbrough, J W; Schultz, T W

    2008-01-01

    This study was undertaken to test the hypothesis that structurally similar PAHs induce similar gene expression profiles. THP-1 cells were exposed to a series of 12 selected PAHs at 50 microM for 24 hours and gene expressions profiles were analyzed using both unsupervised and supervised methods. Clustering analysis of gene expression profiles revealed that the 12 tested chemicals were grouped into five clusters. Within each cluster, the gene expression profiles are more similar to each other than to the ones outside the cluster. One-methylanthracene and 1-methylfluorene were found to have the most similar profiles; dibenzothiophene and dibenzofuran were found to share common profiles with fluorine. As expression pattern comparisons were expanded, similarity in genomic fingerprint dropped off dramatically. Prediction analysis of microarrays (PAM) based on the clustering pattern generated 49 predictor genes that can be used for sample discrimination. Moreover, a significant analysis of Microarrays (SAM) identified 598 genes being modulated by tested chemicals with a variety of biological processes, such as cell cycle, metabolism, and protein binding and KEGG pathways being significantly (p < 0.05) affected. It is feasible to distinguish structurally different PAHs based on their genomic fingerprints, which are mechanism based.

  8. Exuberant and inhibited children: Person-centered profiles and links to social adjustment.

    PubMed

    Dollar, Jessica M; Stifter, Cynthia A; Buss, Kristin A

    2017-07-01

    The current study aimed to substantiate and extend our understanding regarding the existence and developmental pathways of 3 distinct temperament profiles-exuberant, inhibited, and average approach-in a sample of 3.5-year-old children (n = 121). The interactions between temperamental styles and specific types of effortful control, inhibitory control and attentional control, were also examined in predicting kindergarten peer acceptance. Latent profile analysis identified 3 temperamental styles: exuberant, inhibited, and average approach. Support was found for the adaptive role of inhibitory control for exuberant children and attentional control for inhibited children in promoting peer acceptance in kindergarten. These findings add to our current understanding of temperamental profiles by using sophisticated methodology in a slightly older, community sample, as well as the importance of examining specific types of self-regulation to identify which skills lower risk for children of different temperamental styles. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

  9. Integrative Analysis of Longitudinal Metabolomics Data from a Personal Multi-Omics Profile

    PubMed Central

    Stanberry, Larissa; Mias, George I.; Haynes, Winston; Higdon, Roger; Snyder, Michael; Kolker, Eugene

    2013-01-01

    The integrative personal omics profile (iPOP) is a pioneering study that combines genomics, transcriptomics, proteomics, metabolomics and autoantibody profiles from a single individual over a 14-month period. The observation period includes two episodes of viral infection: a human rhinovirus and a respiratory syncytial virus. The profile studies give an informative snapshot into the biological functioning of an organism. We hypothesize that pathway expression levels are associated with disease status. To test this hypothesis, we use biological pathways to integrate metabolomics and proteomics iPOP data. The approach computes the pathways’ differential expression levels at each time point, while taking into account the pathway structure and the longitudinal design. The resulting pathway levels show strong association with the disease status. Further, we identify temporal patterns in metabolite expression levels. The changes in metabolite expression levels also appear to be consistent with the disease status. The results of the integrative analysis suggest that changes in biological pathways may be used to predict and monitor the disease. The iPOP experimental design, data acquisition and analysis issues are discussed within the broader context of personal profiling. PMID:24958148

  10. Clinical Implications of Cluster Analysis-Based Classification of Acute Decompensated Heart Failure and Correlation with Bedside Hemodynamic Profiles.

    PubMed

    Ahmad, Tariq; Desai, Nihar; Wilson, Francis; Schulte, Phillip; Dunning, Allison; Jacoby, Daniel; Allen, Larry; Fiuzat, Mona; Rogers, Joseph; Felker, G Michael; O'Connor, Christopher; Patel, Chetan B

    2016-01-01

    Classification of acute decompensated heart failure (ADHF) is based on subjective criteria that crudely capture disease heterogeneity. Improved phenotyping of the syndrome may help improve therapeutic strategies. To derive cluster analysis-based groupings for patients hospitalized with ADHF, and compare their prognostic performance to hemodynamic classifications derived at the bedside. We performed a cluster analysis on baseline clinical variables and PAC measurements of 172 ADHF patients from the ESCAPE trial. Employing regression techniques, we examined associations between clusters and clinically determined hemodynamic profiles (warm/cold/wet/dry). We assessed association with clinical outcomes using Cox proportional hazards models. Likelihood ratio tests were used to compare the prognostic value of cluster data to that of hemodynamic data. We identified four advanced HF clusters: 1) male Caucasians with ischemic cardiomyopathy, multiple comorbidities, lowest B-type natriuretic peptide (BNP) levels; 2) females with non-ischemic cardiomyopathy, few comorbidities, most favorable hemodynamics; 3) young African American males with non-ischemic cardiomyopathy, most adverse hemodynamics, advanced disease; and 4) older Caucasians with ischemic cardiomyopathy, concomitant renal insufficiency, highest BNP levels. There was no association between clusters and bedside-derived hemodynamic profiles (p = 0.70). For all adverse clinical outcomes, Cluster 4 had the highest risk, and Cluster 2, the lowest. Compared to Cluster 4, Clusters 1-3 had 45-70% lower risk of all-cause mortality. Clusters were significantly associated with clinical outcomes, whereas hemodynamic profiles were not. By clustering patients with similar objective variables, we identified four clinically relevant phenotypes of ADHF patients, with no discernable relationship to hemodynamic profiles, but distinct associations with adverse outcomes. Our analysis suggests that ADHF classification using simultaneous considerations of etiology, comorbid conditions, and biomarker levels, may be superior to bedside classifications.

  11. Use of Concept Profile Analysis to Identify Difficulties in Solving Science Problems.

    ERIC Educational Resources Information Center

    Gorodetsky, Malka; Hoz, Ron

    1980-01-01

    Proposed is a new method for analyzing how concepts are used in the process of problem solving in science. Through the use of a "thinking aloud" interview technique, 21 tenth-grade students worked with a problem concerning the boiling point of water at the Dead Sea. Interview protocols were analyzed to develop students' concept profiles.…

  12. Profiles of Emergent Literacy Skills among Preschool Children Who Are at Risk for Academic Difficulties

    ERIC Educational Resources Information Center

    Cabell, Sonia Q.; Justice, Laura M.; Konold, Timothy R.; McGinty, Anita S.

    2011-01-01

    The purpose of this study was to explore patterns of within-group variability in the emergent literacy skills of preschoolers who are at risk for academic difficulties. We used the person-centered approach of cluster analysis to identify profiles of emergent literacy skills, taking into account both oral language and code-related skills.…

  13. New Insights on Developmental Dyslexia Subtypes: Heterogeneity of Mixed Reading Profiles

    PubMed Central

    Zoubrinetzky, Rachel; Bielle, Frédérique; Valdois, Sylviane

    2014-01-01

    We examined whether classifications based on reading performance are relevant to identify cognitively homogeneous subgroups of dyslexic children. Each of the 71 dyslexic participants was selected to have a mixed reading profile, i.e. poor irregular word and pseudo-word reading performance (accuracy and speed). Despite their homogeneous reading profile, the participants were found to split into four distinct cognitive subgroups, characterized by a single phonological disorder, a single visual attention span disorder, a double deficit or none of these disorders. The two subgroups characterized by single and contrasted cognitive disorders were found to exhibit a very similar reading pattern but more contrasted spelling performance (quantitative analysis). A qualitative analysis of the error types produced in reading and spelling provided some cues about the participants' underlying cognitive deficit. The overall findings disqualify subtyping based on reading profiles as a classification method to identify cognitively homogeneous subgroups of dyslexic children. They rather show an opaque relationship between the cognitive underpinnings of developmental dyslexia and their behavioral manifestations in reading and spelling. Future neuroimaging and genetic studies should take this issue into account since synthesizing over cognitively heterogeneous children would entail potential pitfalls. PMID:24918441

  14. Single-cell mRNA profiling reveals transcriptional heterogeneity among pancreatic circulating tumour cells.

    PubMed

    Lapin, Morten; Tjensvoll, Kjersti; Oltedal, Satu; Javle, Milind; Smaaland, Rune; Gilje, Bjørnar; Nordgård, Oddmund

    2017-05-31

    Single-cell mRNA profiling of circulating tumour cells may contribute to a better understanding of the biology of these cells and their role in the metastatic process. In addition, such analyses may reveal new knowledge about the mechanisms underlying chemotherapy resistance and tumour progression in patients with cancer. Single circulating tumour cells were isolated from patients with locally advanced or metastatic pancreatic cancer with immuno-magnetic depletion and immuno-fluorescence microscopy. mRNA expression was analysed with single-cell multiplex RT-qPCR. Hierarchical clustering and principal component analysis were performed to identify expression patterns. Circulating tumour cells were detected in 33 of 56 (59%) examined blood samples. Single-cell mRNA profiling of intact isolated circulating tumour cells revealed both epithelial-like and mesenchymal-like subpopulations, which were distinct from leucocytes. The profiled circulating tumour cells also expressed elevated levels of stem cell markers, and the extracellular matrix protein, SPARC. The expression of SPARC might correspond to an epithelial-mesenchymal transition in pancreatic circulating tumour cells. The analysis of single pancreatic circulating tumour cells identified distinct subpopulations and revealed elevated expression of transcripts relevant to the dissemination of circulating tumour cells to distant organ sites.

  15. Effects of age, sex, and genotype on high-sensitivity metabolomic profiles in the fruit fly, Drosophila melanogaster

    PubMed Central

    Hoffman, Jessica M; Soltow, Quinlyn A; Li, Shuzhao; Sidik, Alfire; Jones, Dean P; Promislow, Daniel E L

    2014-01-01

    Researchers have used whole-genome sequencing and gene expression profiling to identify genes associated with age, in the hope of understanding the underlying mechanisms of senescence. But there is a substantial gap from variation in gene sequences and expression levels to variation in age or life expectancy. In an attempt to bridge this gap, here we describe the effects of age, sex, genotype, and their interactions on high-sensitivity metabolomic profiles in the fruit fly, Drosophila melanogaster. Among the 6800 features analyzed, we found that over one-quarter of all metabolites were significantly associated with age, sex, genotype, or their interactions, and multivariate analysis shows that individual metabolomic profiles are highly predictive of these traits. Using a metabolomic equivalent of gene set enrichment analysis, we identified numerous metabolic pathways that were enriched among metabolites associated with age, sex, and genotype, including pathways involving sugar and glycerophospholipid metabolism, neurotransmitters, amino acids, and the carnitine shuttle. Our results suggest that high-sensitivity metabolomic studies have excellent potential not only to reveal mechanisms that lead to senescence, but also to help us understand differences in patterns of aging among genotypes and between males and females. PMID:24636523

  16. From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline.

    PubMed

    Chen, Yunshun; Lun, Aaron T L; Smyth, Gordon K

    2016-01-01

    In recent years, RNA sequencing (RNA-seq) has become a very widely used technology for profiling gene expression. One of the most common aims of RNA-seq profiling is to identify genes or molecular pathways that are differentially expressed (DE) between two or more biological conditions. This article demonstrates a computational workflow for the detection of DE genes and pathways from RNA-seq data by providing a complete analysis of an RNA-seq experiment profiling epithelial cell subsets in the mouse mammary gland. The workflow uses R software packages from the open-source Bioconductor project and covers all steps of the analysis pipeline, including alignment of read sequences, data exploration, differential expression analysis, visualization and pathway analysis. Read alignment and count quantification is conducted using the Rsubread package and the statistical analyses are performed using the edgeR package. The differential expression analysis uses the quasi-likelihood functionality of edgeR.

  17. DNA profiling analysis of endometrial and ovarian cell lines reveals misidentification, redundancy and contamination.

    PubMed

    Korch, Christopher; Spillman, Monique A; Jackson, Twila A; Jacobsen, Britta M; Murphy, Susan K; Lessey, Bruce A; Jordan, V Craig; Bradford, Andrew P

    2012-10-01

    Cell lines derived from human ovarian and endometrial cancers, and their immortalized non-malignant counterparts, are critical tools to investigate and characterize molecular mechanisms underlying gynecologic tumorigenesis, and facilitate development of novel therapeutics. To determine the extent of misidentification, contamination and redundancy, with evident consequences for the validity of research based upon these models, we undertook a systematic analysis and cataloging of endometrial and ovarian cell lines. Profiling of cell lines by analysis of DNA microsatellite short tandem repeats (STR), p53 nucleotide polymorphisms and microsatellite instability was performed. Fifty-one ovarian cancer lines were profiled with ten found to be redundant and five (A2008, OV2008, C13, SK-OV-4 and SK-OV-6) identified as cervical cancer cells. Ten endometrial cell lines were analyzed, with RL-92, HEC-1A, HEC-1B, HEC-50, KLE, and AN3CA all exhibiting unique, uncontaminated STR profiles. Multiple variants of Ishikawa and ECC-1 endometrial cancer cell lines were genotyped and analyzed by sequencing of mutations in the p53 gene. The profile of ECC-1 cells did not match the EnCa-101 tumor, from which it was reportedly derived, and all ECC-1 isolates were genotyped as Ishikawa cells, MCF-7 breast cancer cells, or a combination thereof. Two normal, immortalized endometrial epithelial cell lines, HES cells and the hTERT-EEC line, were identified as HeLa cervical carcinoma and MCF-7 breast cancer cells, respectively. Results demonstrate significant misidentification, duplication, and loss of integrity of endometrial and ovarian cancer cell lines. Authentication by STR DNA profiling is a simple and economical method to verify and validate studies undertaken with these models. Copyright © 2012 Elsevier Inc. All rights reserved.

  18. Cluster analysis of sputum cytokine-high profiles reveals diversity in T(h)2-high asthma patients.

    PubMed

    Seys, Sven F; Scheers, Hans; Van den Brande, Paul; Marijsse, Gudrun; Dilissen, Ellen; Van Den Bergh, Annelies; Goeminne, Pieter C; Hellings, Peter W; Ceuppens, Jan L; Dupont, Lieven J; Bullens, Dominique M A

    2017-02-23

    Asthma is characterized by a heterogeneous inflammatory profile and can be subdivided into T(h)2-high and T(h)2-low airway inflammation. Profiling of a broader panel of airway cytokines in large unselected patient cohorts is lacking. Patients (n = 205) were defined as being "cytokine-low/high" if sputum mRNA expression of a particular cytokine was outside the respective 10 th /90 th percentile range of the control group (n = 80). Unsupervised hierarchical clustering was used to determine clusters based on sputum cytokine profiles. Half of patients (n = 108; 52.6%) had a classical T(h)2-high ("IL-4-, IL-5- and/or IL-13-high") sputum cytokine profile. Unsupervised cluster analysis revealed 5 clusters. Patients with an "IL-4- and/or IL-13-high" pattern surprisingly did not cluster but were equally distributed among the 5 clusters. Patients with an "IL-5-, IL-17A-/F- and IL-25- high" profile were restricted to cluster 1 (n = 24) with increased sputum eosinophil as well as neutrophil counts and poor lung function parameters at baseline and 2 years later. Four other clusters were identified: "IL-5-high or IL-10-high" (n = 16), "IL-6-high" (n = 8), "IL-22-high" (n = 25). Cluster 5 (n = 132) consists of patients without "cytokine-high" pattern or patients with only high IL-4 and/or IL-13. We identified 5 unique asthma molecular phenotypes by biological clustering. Type 2 cytokines cluster with non-type 2 cytokines in 4 out of 5 clusters. Unsupervised analysis thus not supports a priori type 2 versus non-type 2 molecular phenotypes. www.clinicaltrials.gov NCT01224938. Registered 18 October 2010.

  19. Cerebrospinal fluid metabolomic profiling in tuberculous and viral meningitis: Screening potential markers for differential diagnosis.

    PubMed

    Li, Zihui; Du, Boping; Li, Jing; Zhang, Jinli; Zheng, Xiaojing; Jia, Hongyan; Xing, Aiying; Sun, Qi; Liu, Fei; Zhang, Zongde

    2017-03-01

    Tuberculous meningitis (TBM) is the most severe and frequent form of central nervous system tuberculosis. The current lack of efficient diagnostic tests makes it difficult to differentiate TBM from other common types of meningitis, especially viral meningitis (VM). Metabolomics is an important tool to identify disease-specific biomarkers. However, little metabolomic information is available on adult TBM. We used 1 H nuclear magnetic resonance-based metabolomics to investigate the metabolic features of the CSF from 18 TBM and 20 VM patients. Principal component analysis and orthogonal signal correction-partial least squares-discriminant analysis (OSC-PLS-DA) were applied to analyze profiling data. Metabolites were identified using the Human Metabolome Database and pathway analysis was performed with MetaboAnalyst 3.0. The OSC-PLS-DA model could distinguish TBM from VM with high reliability. A total of 25 key metabolites that contributed to their discrimination were identified, including some, such as betaine and cyclohexane, rarely reported before in TBM. Pathway analysis indicated that amino acid and energy metabolism was significantly different in the CSF of TBM compared with VM. Twenty-five key metabolites identified in our study may be potential biomarkers for TBM differential diagnosis and are worthy of further investigation. Copyright © 2017 Elsevier B.V. All rights reserved.

  20. Species identification of corynebacteria by cellular fatty acid analysis.

    PubMed

    Van den Velde, Sandra; Lagrou, Katrien; Desmet, Koen; Wauters, Georges; Verhaegen, Jan

    2006-02-01

    We evaluated the usefulness of cellular fatty acid analysis for the identification of corynebacteria. Therefore, 219 well-characterized strains belonging to 21 Corynebacterium species were analyzed with the Sherlock System of MIDI (Newark, DE). Most Corynebacterium species have a qualitative different fatty acid profile. Corynebacterium coyleae (subgroup 1), Corynebacterium riegelii, Corynebacterium simulans, and Corynebacterium imitans differ only quantitatively. Corynebacterium afermentans afermentans and C. coyleae (subgroup 2) have both a similar qualitative and quantitative profile. The commercially available database (CLIN 40, MIDI) identified only one third of the 219 strains correctly at the species level. We created a new database with these 219 strains. This new database was tested with 34 clinical isolates and could identify 29 strains correctly. Strains that remained unidentified were 2 Corynebacterium aurimucosum (not included in our database), 1 C. afermentans afermentans, and 2 Corynebacterium pseudodiphtheriticum. Cellular fatty acid analysis with a self-created database can be used for the identification and differentiation of corynebacteria.

  1. iTRAQ protein profile analysis of Citrus sinensis roots in response to long-term boron-deficiency.

    PubMed

    Yang, Lin-Tong; Qi, Yi-Ping; Lu, Yi-Bin; Guo, Peng; Sang, Wen; Feng, Hui; Zhang, Hong-Xing; Chen, Li-Song

    2013-11-20

    Seedlings of Citrus sinensis were fertilized with boron (B)-deficient (0μM H3BO3) or -sufficient (10μM H3BO3) nutrient solution for 15weeks. Thereafter, iTRAQ analysis was employed to compare the abundances of proteins from B-deficient and -sufficient roots. In B-deficient roots, 164 up-regulated and 225 down-regulated proteins were identified. These proteins were grouped into the following functional categories: protein metabolism, nucleic acid metabolism, stress responses, carbohydrate and energy metabolism, cell transport, cell wall and cytoskeleton metabolism, biological regulation and signal transduction, and lipid metabolism. The adaptive responses of roots to B-deficiency might include following several aspects: (a) decreasing root respiration; (b) improving the total ability to scavenge reactive oxygen species (ROS); and (c) enhancing cell transport. The differentially expressed proteins identified by iTRAQ are much larger than those detected using 2D gel electrophoresis, and many novel B-deficiency-responsive proteins involved in cell transport, biological regulation and signal transduction, stress responses and other metabolic processes were identified in this work. Our results indicate remarkable metabolic flexibility of citrus roots, which may contribute to the survival of B-deficient plants. This represents the most comprehensive analysis of protein profiles in response to B-deficiency. In this study, we identified many new proteins involved in cell transport, biological regulation and signal transduction, stress responses and other metabolic processes that were not previously known to be associated with root B-deficiency responses. Therefore, our manuscript represents the most comprehensive analysis of protein profiles in response to B-deficiency and provides new information about the plant response to B-deficiency. This article is part of a Special Issue entitled: Translational Plant Proteomics. Copyright © 2013 Elsevier B.V. All rights reserved.

  2. The Human Pancreas Proteome Defined by Transcriptomics and Antibody-Based Profiling

    PubMed Central

    Fagerberg, Linn; Hallström, Björn M.; Schwenk, Jochen M.; Uhlén, Mathias; Korsgren, Olle; Lindskog, Cecilia

    2014-01-01

    The pancreas is composed of both exocrine glands and intermingled endocrine cells to execute its diverse functions, including enzyme production for digestion of nutrients and hormone secretion for regulation of blood glucose levels. To define the molecular constituents with elevated expression in the human pancreas, we employed a genome-wide RNA sequencing analysis of the human transcriptome to identify genes with elevated expression in the human pancreas. This quantitative transcriptomics data was combined with immunohistochemistry-based protein profiling to allow mapping of the corresponding proteins to different compartments and specific cell types within the pancreas down to the single cell level. Analysis of whole pancreas identified 146 genes with elevated expression levels, of which 47 revealed a particular higher expression as compared to the other analyzed tissue types, thus termed pancreas enriched. Extended analysis of in vitro isolated endocrine islets identified an additional set of 42 genes with elevated expression in these specialized cells. Although only 0.7% of all genes showed an elevated expression level in the pancreas, this fraction of transcripts, in most cases encoding secreted proteins, constituted 68% of the total mRNA in pancreas. This demonstrates the extreme specialization of the pancreas for production of secreted proteins. Among the elevated expression profiles, several previously not described proteins were identified, both in endocrine cells (CFC1, FAM159B, RBPJL and RGS9) and exocrine glandular cells (AQP12A, DPEP1, GATM and ERP27). In summary, we provide a global analysis of the pancreas transcriptome and proteome with a comprehensive list of genes and proteins with elevated expression in pancreas. This list represents an important starting point for further studies of the molecular repertoire of pancreatic cells and their relation to disease states or treatment effects. PMID:25546435

  3. Sequencing Bands of Ribosomal Intergenic Spacer Analysis Fingerprints for Characterization and Microscale Distribution of Soil Bacterium Populations Responding to Mercury Spiking

    PubMed Central

    Ranjard, Lionel; Brothier, Elisabeth; Nazaret, Sylvie

    2000-01-01

    Two major emerging bands (a 350-bp band and a 650-bp band) within the RISA (ribosomal intergenic spacer analysis) profile of a soil bacterial community spiked with Hg(II) were selected for further identification of the populations involved in the response of the community to the added metal. The bands were cut out from polyacrylamide gels, cloned, characterized by restriction analysis, and sequenced for phylogenetic affiliation of dominant clones. The sequences were the intergenic spacer between the rrs and rrl genes and the first 130 nucleotides of the rrl gene. Comparison of sequences derived from the 350-bp band to The GenBank database permitted us to identify the bacteria as being mostly close relatives to low G+C firmicutes (Clostridium-like genera), while the 650-bp band permitted us to identify the bacteria as being mostly close relatives to β-proteobacteria (Ralstonia-like genera). Oligonucleotide probes specific for the identified dominant bacteria were designed and hybridized with the RISA profiles derived from the control and spiked communities. These studies confirmed the contribution of these populations to the community response to the metal. Hybridization of the RISA profiles from subcommunities (bacterial pools associated with different soil microenvironments) also permitted to characterize the distribution and the dynamics of these populations at a microscale level following mercury spiking. PMID:11097911

  4. Low levels of serum serotonin and amino acids identified in migraine patients.

    PubMed

    Ren, Caixia; Liu, Jia; Zhou, Juntuo; Liang, Hui; Wang, Yayun; Sun, Yinping; Ma, Bin; Yin, Yuxin

    2018-02-05

    Migraine is a highly disabling primary headache associated with a high socioeconomic burden and a generally high prevalence. The clinical management of migraine remains a challenge. This study was undertaken to identify potential serum biomarkers of migraine. Using Liquid Chromatography coupled to Mass Spectrometry (LC-MS), the metabolomic profile of migraine was compared with healthy individuals. Principal component analysis (PCA) and Orthogonal partial least squares-discriminant analysis (orthoPLS-DA) showed the metabolomic profile of migraine is distinguishable from controls. Volcano plot analysis identified 10 serum metabolites significantly decreased during migraine. One of these was serotonin, and the other 9 were amino acids. Pathway analysis and enrichment analysis showed tryptophan metabolism (serotonin metabolism), arginine and proline metabolism, and aminoacyl-tRNA biosynthesis are the three most prominently altered pathways in migraine. ROC curve analysis indicated Glycyl-l-proline, N-Methyl-dl-Alanine and l-Methionine are potential sensitive and specific biomarkers for migraine. Our results show Glycyl-l-proline, N-Methyl-dl-Alanine and l-Methionine may be as specific or more specific for migraine than serotonin which is the traditional biomarker of migraine. We propose that therapeutic manipulation of these metabolites or metabolic pathways may be helpful in the prevention and treatment of migraine. Copyright © 2018 Elsevier Inc. All rights reserved.

  5. Metabolic Disturbances in Adult-Onset Still's Disease Evaluated Using Liquid Chromatography/Mass Spectrometry-Based Metabolomic Analysis.

    PubMed

    Chen, Der-Yuan; Chen, Yi-Ming; Chien, Han-Ju; Lin, Chi-Chen; Hsieh, Chia-Wei; Chen, Hsin-Hua; Hung, Wei-Ting; Lai, Chien-Chen

    2016-01-01

    Liquid chromatography/mass spectrometry (LC/MS)-based comprehensive analysis of metabolic profiles with metabolomics approach has potential diagnostic and predictive implications. However, no metabolomics data have been reported in adult-onset Still's disease (AOSD). This study investigated the metabolomic profiles in AOSD patients and examined their association with clinical characteristics and disease outcome. Serum metabolite profiles were determined on 32 AOSD patients and 30 healthy controls (HC) using ultra-performance liquid chromatography (UPLC)/MS analysis, and the differentially expressed metabolites were quantified using multiple reactions monitoring (MRM)/MS analysis in 44 patients and 42 HC. Pure standards were utilized to confirm the presence of the differentially expressed metabolites. Eighteen differentially expressed metabolites were identified in AOSD patents using LC/MS-based analysis, of which 13 metabolites were validated by MRM/MS analysis. Among them, serum levels of lysoPC(18:2), urocanic acid and indole were significantly lower, and L-phenylalanine levels were significantly higher in AOSD patients compared with HC. Moreover, serum levels of lysoPC(18:2), PhePhe, uridine, taurine, L-threonine, and (R)-3-Hydroxy-hexadecanoic acid were significantly correlated with disease activity scores (all p<0.05) in AOSD patients. A different clustering of metabolites was associated with a different disease outcome, with significantly lower levels of isovalerylsarcosine observed in patients with chronic articular pattern (median, 77.0AU/ml) compared with monocyclic (341.5AU/ml, p<0.01) or polycyclic systemic pattern (168.0AU/ml, p<0.05). Thirteen differentially expressed metabolites identified and validated in AOSD patients were shown to be involved in five metabolic pathways. Significant associations of metabolic profiles with disease activity and outcome of AOSD suggest their involvement in AOSD pathogenesis.

  6. Metabolomics Coupled with Multivariate Data and Pathway Analysis on Potential Biomarkers in Gastric Ulcer and Intervention Effects of Corydalis yanhusuo Alkaloid

    PubMed Central

    Shuai, Wang; Yongrui, Bao; Shanshan, Guan; Bo, Liu; Lu, Chen; Lei, Wang; Xiaorong, Ran

    2014-01-01

    Metabolomics, the systematic analysis of potential metabolites in a biological specimen, has been increasingly applied to discovering biomarkers, identifying perturbed pathways, measuring therapeutic targets, and discovering new drugs. By analyzing and verifying the significant difference in metabolic profiles and changes of metabolite biomarkers, metabolomics enables us to better understand substance metabolic pathways which can clarify the mechanism of Traditional Chinese Medicines (TCM). Corydalis yanhusuo alkaloid (CA) is a major component of Qizhiweitong (QZWT) prescription which has been used for treating gastric ulcer for centuries and its mechanism remains unclear completely. Metabolite profiling was performed by high-performance liquid chromatography combined with time-of-flight mass spectrometry (HPLC/ESI-TOF-MS) and in conjunction with multivariate data analysis and pathway analysis. The statistic software Mass Profiller Prossional (MPP) and statistic method including ANOVA and principal component analysis (PCA) were used for discovering novel potential biomarkers to clarify mechanism of CA in treating acid injected rats with gastric ulcer. The changes in metabolic profiling were restored to their base-line values after CA treatment according to the PCA score plots. Ten different potential biomarkers and seven key metabolic pathways contributing to the treatment of gastric ulcer were discovered and identified. Among the pathways, sphingophospholipid metabolism and fatty acid metabolism related network were acutely perturbed. Quantitative real time polymerase chain reaction (RT-PCR) analysis were performed to evaluate the expression of genes related to the two pathways for verifying the above results. The results show that changed biomarkers and pathways may provide evidence to insight into drug action mechanisms and enable us to increase research productivity toward metabolomics drug discovery. PMID:24454691

  7. A Modified ABCDE Model of Flowering in Orchids Based on Gene Expression Profiling Studies of the Moth Orchid Phalaenopsis aphrodite

    PubMed Central

    Lee, Ann-Ying; Chen, Chun-Yi; Chang, Yao-Chien Alex; Chao, Ya-Ting; Shih, Ming-Che

    2013-01-01

    Previously we developed genomic resources for orchids, including transcriptomic analyses using next-generation sequencing techniques and construction of a web-based orchid genomic database. Here, we report a modified molecular model of flower development in the Orchidaceae based on functional analysis of gene expression profiles in Phalaenopsis aphrodite (a moth orchid) that revealed novel roles for the transcription factors involved in floral organ pattern formation. Phalaenopsis orchid floral organ-specific genes were identified by microarray analysis. Several critical transcription factors including AP3, PI, AP1 and AGL6, displayed distinct spatial distribution patterns. Phylogenetic analysis of orchid MADS box genes was conducted to infer the evolutionary relationship among floral organ-specific genes. The results suggest that gene duplication MADS box genes in orchid may have resulted in their gaining novel functions during evolution. Based on these analyses, a modified model of orchid flowering was proposed. Comparison of the expression profiles of flowers of a peloric mutant and wild-type Phalaenopsis orchid further identified genes associated with lip morphology and peloric effects. Large scale investigation of gene expression profiles revealed that homeotic genes from the ABCDE model of flower development classes A and B in the Phalaenopsis orchid have novel functions due to evolutionary diversification, and display differential expression patterns. PMID:24265826

  8. An integrated one-step system to extract, analyze and annotate all relevant information from image-based cell screening of chemical libraries.

    PubMed

    Rabal, Obdulia; Link, Wolfgang; Serelde, Beatriz G; Bischoff, James R; Oyarzabal, Julen

    2010-04-01

    Here we report the development and validation of a complete solution to manage and analyze the data produced by image-based phenotypic screening campaigns of small-molecule libraries. In one step initial crude images are analyzed for multiple cytological features, statistical analysis is performed and molecules that produce the desired phenotypic profile are identified. A naïve Bayes classifier, integrating chemical and phenotypic spaces, is built and utilized during the process to assess those images initially classified as "fuzzy"-an automated iterative feedback tuning. Simultaneously, all this information is directly annotated in a relational database containing the chemical data. This novel fully automated method was validated by conducting a re-analysis of results from a high-content screening campaign involving 33 992 molecules used to identify inhibitors of the PI3K/Akt signaling pathway. Ninety-two percent of confirmed hits identified by the conventional multistep analysis method were identified using this integrated one-step system as well as 40 new hits, 14.9% of the total, originally false negatives. Ninety-six percent of true negatives were properly recognized too. A web-based access to the database, with customizable data retrieval and visualization tools, facilitates the posterior analysis of annotated cytological features which allows identification of additional phenotypic profiles; thus, further analysis of original crude images is not required.

  9. Major carcinogenic pathways identified by gene expression analysis of peritoneal mesotheliomas following chemical treatment in F344 rats

    EPA Science Inventory

    This study was performed to characterize the gene expression profile and to identify the major carcinogenic pathways involved in rat peritoneal mesothelioma (RPM) formation following treatment of Fischer 344 rats with o-nitrotoluene (o-NT) or bromochloracetic acid (BCA). Oligo a...

  10. An approach to functionally relevant clustering of the protein universe: Active site profile‐based clustering of protein structures and sequences

    PubMed Central

    Knutson, Stacy T.; Westwood, Brian M.; Leuthaeuser, Janelle B.; Turner, Brandon E.; Nguyendac, Don; Shea, Gabrielle; Kumar, Kiran; Hayden, Julia D.; Harper, Angela F.; Brown, Shoshana D.; Morris, John H.; Ferrin, Thomas E.; Babbitt, Patricia C.

    2017-01-01

    Abstract Protein function identification remains a significant problem. Solving this problem at the molecular functional level would allow mechanistic determinant identification—amino acids that distinguish details between functional families within a superfamily. Active site profiling was developed to identify mechanistic determinants. DASP and DASP2 were developed as tools to search sequence databases using active site profiling. Here, TuLIP (Two‐Level Iterative clustering Process) is introduced as an iterative, divisive clustering process that utilizes active site profiling to separate structurally characterized superfamily members into functionally relevant clusters. Underlying TuLIP is the observation that functionally relevant families (curated by Structure‐Function Linkage Database, SFLD) self‐identify in DASP2 searches; clusters containing multiple functional families do not. Each TuLIP iteration produces candidate clusters, each evaluated to determine if it self‐identifies using DASP2. If so, it is deemed a functionally relevant group. Divisive clustering continues until each structure is either a functionally relevant group member or a singlet. TuLIP is validated on enolase and glutathione transferase structures, superfamilies well‐curated by SFLD. Correlation is strong; small numbers of structures prevent statistically significant analysis. TuLIP‐identified enolase clusters are used in DASP2 GenBank searches to identify sequences sharing functional site features. Analysis shows a true positive rate of 96%, false negative rate of 4%, and maximum false positive rate of 4%. F‐measure and performance analysis on the enolase search results and comparison to GEMMA and SCI‐PHY demonstrate that TuLIP avoids the over‐division problem of these methods. Mechanistic determinants for enolase families are evaluated and shown to correlate well with literature results. PMID:28054422

  11. An integrated systems genetics screen reveals the transcriptional structure of inherited predisposition to metastatic disease

    PubMed Central

    Faraji, Farhoud; Hu, Ying; Wu, Gang; Goldberger, Natalie E.; Walker, Renard C.; Zhang, Jinghui; Hunter, Kent W.

    2014-01-01

    Metastasis is the result of stochastic genomic and epigenetic events leading to gene expression profiles that drive tumor dissemination. Here we exploit the principle that metastatic propensity is modified by the genetic background to generate prognostic gene expression signatures that illuminate regulators of metastasis. We also identify multiple microRNAs whose germline variation is causally linked to tumor progression and metastasis. We employ network analysis of global gene expression profiles in tumors derived from a panel of recombinant inbred mice to identify a network of co-expressed genes centered on Cnot2 that predicts metastasis-free survival. Modulating Cnot2 expression changes tumor cell metastatic potential in vivo, supporting a functional role for Cnot2 in metastasis. Small RNA sequencing of the same tumor set revealed a negative correlation between expression of the Mir216/217 cluster and tumor progression. Expression quantitative trait locus analysis (eQTL) identified cis-eQTLs at the Mir216/217 locus, indicating that differences in expression may be inherited. Ectopic expression of Mir216/217 in tumor cells suppressed metastasis in vivo. Finally, small RNA sequencing and mRNA expression profiling data were integrated to reveal that miR-3470a/b target a high proportion of network transcripts. In vivo analysis of Mir3470a/b demonstrated that both promote metastasis. Moreover, Mir3470b is a likely regulator of the Cnot2 network as its overexpression down-regulated expression of network hub genes and enhanced metastasis in vivo, phenocopying Cnot2 knockdown. The resulting data from this strategy identify Cnot2 as a novel regulator of metastasis and demonstrate the power of our systems-level approach in identifying modifiers of metastasis. PMID:24322557

  12. Variations in Decision-Making Profiles by Age and Gender: A Cluster-Analytic Approach

    PubMed Central

    Delaney, Rebecca; Strough, JoNell; Parker, Andrew M.; de Bruin, Wandi Bruine

    2015-01-01

    Using cluster-analysis, we investigated whether rational, intuitive, spontaneous, dependent, and avoidant styles of decision making (Scott & Bruce, 1995) combined to form distinct decision-making profiles that differed by age and gender. Self-report survey data were collected from 1,075 members of RAND’s American Life Panel (56.2% female, 18–93 years, Mage = 53.49). Three decision-making profiles were identified: affective/experiential, independent/self-controlled, and an interpersonally-oriented dependent profile. Older people were less likely to be in the affective/experiential profile and more likely to be in the independent/self-controlled profile. Women were less likely to be in the affective/experiential profile and more likely to be in the interpersonally-oriented dependent profile. Interpersonally-oriented profiles are discussed as an overlooked but important dimension of how people make important decisions. PMID:26005238

  13. GC-FID coupled with chemometrics for quantitative and chemical fingerprinting analysis of Alpinia oxyphylla oil.

    PubMed

    Miao, Qing; Kong, Weijun; Zhao, Xiangsheng; Yang, Shihai; Yang, Meihua

    2015-01-01

    Analytical methods for quantitative analysis and chemical fingerprinting of volatile oils from Alpinia oxyphylla were established. The volatile oils were prepared by hydrodistillation, and the yields were between 0.82% and 1.33%. The developed gas chromatography-flame ionization detection (GC-FID) method showed good specificity, linearity, reproducibility, stability and recovery, and could be used satisfactorily for quantitative analysis. The results showed that the volatile oils contained 2.31-77.30 μL/mL p-cymene and 12.38-99.34 mg/mL nootkatone. A GC-FID fingerprinting method was established, and the profiles were analyzed using chemometrics. GC-MS was used to identify the principal compounds in the GC-FID profiles. The profiles of almost all the samples were consistent and stable. The harvesting time and source were major factors that affected the profile, while the volatile oil yield and the nootkatone content had minor secondary effects. Copyright © 2014 Elsevier B.V. All rights reserved.

  14. The influence of temperament and character profiles on specialty choice and well-being in medical residents

    PubMed Central

    Sievert, Martin; Zwir, Igor; Cloninger, Kevin M.; Lester, Nigel; Rozsa, Sandor

    2016-01-01

    Background Multiple factors influence the decision to enter a career in medicine and choose a specialty. Previous studies have looked at personality differences in medicine but often were unable to describe the heterogeneity that exists within each specialty. Our study used a person-centered approach to characterize the complex relations between the personality profiles of resident physicians and their choice of specialty. Methods 169 resident physicians at a large Midwestern US training hospital completed the Temperament and Character Inventory (TCI) and the Satisfaction with Life Scale (SWLS). Clusters of personality profiles were identified without regard to medical specialty, and then the personality clusters were tested for association with their choice of specialty by co-clustering analysis. Life satisfaction was tested for association with personality traits and medical specialty by linear regression and analysis of variance. Results We identified five clusters of people with distinct personality profiles, and found that these were associated with particular medical specialties Physicians with an “investigative” personality profile often chose pathology or internal medicine, those with a “commanding” personality often chose general surgery, “rescuers” often chose emergency medicine, the “dependable” often chose pediatrics, and the “compassionate” often chose psychiatry. Life satisfaction scores were not enhanced by personality-specialty congruence, but were related strongly to self-directedness regardless of specialty. Conclusions The personality profiles of physicians were strongly associated with their medical specialty choices. Nevertheless, the relationships were complex: physicians with each personality profile went into a variety of medical specialties, and physicians in each medical specialty had variable personality profiles. The plasticity and resilience of physicians were more important for their life satisfaction than was matching personality to the prototype of a particular specialty. PMID:27651982

  15. Stability and Instability of Subjective Well-Being in the Transition from Adolescence to Young Adulthood: Longitudinal Evidence from 20991 Young Australians

    PubMed Central

    Page, Andrew

    2016-01-01

    Purpose This study assessed the long-term stability and instability of subjective well-being during post-school transition (i.e., transition from adolescence to young adulthood) and evaluated the determinants of transition stability. Methods Using two cohorts from a national representative longitudinal study, the Longitudinal Study of Australian Youth (N = 20991), latent profile analysis and latent transition analysis were conducted to examine transition patterns among subjective well-being profiles for youth from age 17 to 25. Multinomial logistic regressions were conducted to evaluate whether key socio-demographic variables were associated with transition stability. Results We identified: (1) three subjective well-being profiles: Low (30%), Moderate (50%), and High (20%); and (2) three major transition patterns among these subjective well-being profiles: stable, partially-stable, and unstable. The majority of youth had stable transition patterns during the transition from adolescence to adulthood. A large percentage of youth (52%) started low in subjective well-being profile and remained in the low subjective-wellbeing profile. Our examination also revealed gender was the most pronounced indicator for transition stability during this time period, with males more likely to have unstable transition patterns than females. Conclusions Results suggest that different subjective well-being status and transition patterns can be identified in the post-high school transition to adulthood, including unstable transitions. By targeting those groups more vulnerable to transition, mental health promotion and interventions may be delivered more effectively. PMID:27232183

  16. Profiling of ARDS pulmonary edema fluid identifies a metabolically distinct subset.

    PubMed

    Rogers, Angela J; Contrepois, Kévin; Wu, Manhong; Zheng, Ming; Peltz, Gary; Ware, Lorraine B; Matthay, Michael A

    2017-05-01

    There is considerable biological and physiological heterogeneity among patients who meet standard clinical criteria for acute respiratory distress syndrome (ARDS). In this study, we tested the hypothesis that there exists a subgroup of ARDS patients who exhibit a metabolically distinct profile. We examined undiluted pulmonary edema fluid obtained at the time of endotracheal intubation from 16 clinically phenotyped ARDS patients and 13 control patients with hydrostatic pulmonary edema. Nontargeted metabolic profiling was carried out on the undiluted edema fluid. Univariate and multivariate statistical analyses including principal component analysis (PCA) and partial least squares discriminant analysis (PLS-DA) were conducted to find discriminant metabolites. Seven-hundred and sixty unique metabolites were identified in the pulmonary edema fluid of these 29 patients. We found that a subset of ARDS patients (6/16, 38%) presented a distinct metabolic profile with the overrepresentation of 235 metabolites compared with edema fluid from the other 10 ARDS patients, whose edema fluid metabolic profile was indistinguishable from those of the 13 control patients with hydrostatic edema. This "high metabolite" endotype was characterized by higher concentrations of metabolites belonging to all of the main metabolic classes including lipids, amino acids, and carbohydrates. This distinct group with high metabolite levels in the edema fluid was also associated with a higher mortality rate. Thus metabolic profiling of the edema fluid of ARDS patients supports the hypothesis that there is considerable biological heterogeneity among ARDS patients who meet standard clinical and physiological criteria for ARDS. Copyright © 2017 the American Physiological Society.

  17. Profiling of ARDS pulmonary edema fluid identifies a metabolically distinct subset

    PubMed Central

    Contrepois, Kévin; Wu, Manhong; Zheng, Ming; Peltz, Gary; Ware, Lorraine B.; Matthay, Michael A.

    2017-01-01

    There is considerable biological and physiological heterogeneity among patients who meet standard clinical criteria for acute respiratory distress syndrome (ARDS). In this study, we tested the hypothesis that there exists a subgroup of ARDS patients who exhibit a metabolically distinct profile. We examined undiluted pulmonary edema fluid obtained at the time of endotracheal intubation from 16 clinically phenotyped ARDS patients and 13 control patients with hydrostatic pulmonary edema. Nontargeted metabolic profiling was carried out on the undiluted edema fluid. Univariate and multivariate statistical analyses including principal component analysis (PCA) and partial least squares discriminant analysis (PLS-DA) were conducted to find discriminant metabolites. Seven-hundred and sixty unique metabolites were identified in the pulmonary edema fluid of these 29 patients. We found that a subset of ARDS patients (6/16, 38%) presented a distinct metabolic profile with the overrepresentation of 235 metabolites compared with edema fluid from the other 10 ARDS patients, whose edema fluid metabolic profile was indistinguishable from those of the 13 control patients with hydrostatic edema. This “high metabolite” endotype was characterized by higher concentrations of metabolites belonging to all of the main metabolic classes including lipids, amino acids, and carbohydrates. This distinct group with high metabolite levels in the edema fluid was also associated with a higher mortality rate. Thus metabolic profiling of the edema fluid of ARDS patients supports the hypothesis that there is considerable biological heterogeneity among ARDS patients who meet standard clinical and physiological criteria for ARDS. PMID:28258106

  18. A regulation probability model-based meta-analysis of multiple transcriptomics data sets for cancer biomarker identification.

    PubMed

    Xie, Xin-Ping; Xie, Yu-Feng; Wang, Hong-Qiang

    2017-08-23

    Large-scale accumulation of omics data poses a pressing challenge of integrative analysis of multiple data sets in bioinformatics. An open question of such integrative analysis is how to pinpoint consistent but subtle gene activity patterns across studies. Study heterogeneity needs to be addressed carefully for this goal. This paper proposes a regulation probability model-based meta-analysis, jGRP, for identifying differentially expressed genes (DEGs). The method integrates multiple transcriptomics data sets in a gene regulatory space instead of in a gene expression space, which makes it easy to capture and manage data heterogeneity across studies from different laboratories or platforms. Specifically, we transform gene expression profiles into a united gene regulation profile across studies by mathematically defining two gene regulation events between two conditions and estimating their occurring probabilities in a sample. Finally, a novel differential expression statistic is established based on the gene regulation profiles, realizing accurate and flexible identification of DEGs in gene regulation space. We evaluated the proposed method on simulation data and real-world cancer datasets and showed the effectiveness and efficiency of jGRP in identifying DEGs identification in the context of meta-analysis. Data heterogeneity largely influences the performance of meta-analysis of DEGs identification. Existing different meta-analysis methods were revealed to exhibit very different degrees of sensitivity to study heterogeneity. The proposed method, jGRP, can be a standalone tool due to its united framework and controllable way to deal with study heterogeneity.

  19. Integrated analysis of chromosome copy number variation and gene expression in cervical carcinoma

    PubMed Central

    Yan, Deng; Yi, Song; Chiu, Wang Chi; Qin, Liu Gui; Kin, Wong Hoi; Kwok Hung, Chung Tony; Linxiao, Han; Wai, Choy Kwong; Yi, Sui; Tao, Yang; Tao, Tang

    2017-01-01

    Objective This study was conducted to explore chromosomal copy number variations (CNV) and transcript expression and to examine pathways in cervical pathogenesis using genome-wide high resolution microarrays. Methods Genome-wide chromosomal CNVs were investigated in 6 cervical cancer cell lines by Human Genome CGH Microarray Kit (4x44K). Gene expression profiles in cervical cancer cell lines, primary cervical carcinoma and normal cervical epithelium tissues were also studied using the Whole Human Genome Microarray Kit (4x44K). Results Fifty common chromosomal CNVs were identified in the cervical cancer cell lines. Correlation analysis revealed that gene up-regulation or down-regulation is significantly correlated with genomic amplification (P=0.009) or deletion (P=0.006) events. Expression profiles were identified through cluster analysis. Gene annotation analysis pinpointed cell cycle pathways was significantly (P=1.15E-08) affected in cervical cancer. Common CNVs were associated with cervical cancer. Conclusion Chromosomal CNVs may contribute to their transcript expression in cervical cancer. PMID:29312578

  20. A graph-based network-vulnerability analysis system

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

    Swiler, L.P.; Phillips, C.; Gaylor, T.

    1998-05-03

    This paper presents a graph based approach to network vulnerability analysis. The method is flexible, allowing analysis of attacks from both outside and inside the network. It can analyze risks to a specific network asset, or examine the universe of possible consequences following a successful attack. The analysis system requires as input a database of common attacks, broken into atomic steps, specific network configuration and topology information, and an attacker profile. The attack information is matched with the network configuration information and an attacker profile to create a superset attack graph. Nodes identify a stage of attack, for example themore » class of machines the attacker has accessed and the user privilege level he or she has compromised. The arcs in the attack graph represent attacks or stages of attacks. By assigning probabilities of success on the arcs or costs representing level of effort for the attacker, various graph algorithms such as shortest path algorithms can identify the attack paths with the highest probability of success.« less

  1. A graph-based network-vulnerability analysis system

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

    Swiler, L.P.; Phillips, C.; Gaylor, T.

    1998-01-01

    This report presents a graph-based approach to network vulnerability analysis. The method is flexible, allowing analysis of attacks from both outside and inside the network. It can analyze risks to a specific network asset, or examine the universe of possible consequences following a successful attack. The analysis system requires as input a database of common attacks, broken into atomic steps, specific network configuration and topology information, and an attacker profile. The attack information is matched with the network configuration information and an attacker profile to create a superset attack graph. Nodes identify a stage of attack, for example the classmore » of machines the attacker has accessed and the user privilege level he or she has compromised. The arcs in the attack graph represent attacks or stages of attacks. By assigning probabilities of success on the arcs or costs representing level-of-effort for the attacker, various graph algorithms such as shortest-path algorithms can identify the attack paths with the highest probability of success.« less

  2. Integrated analysis of chromosome copy number variation and gene expression in cervical carcinoma.

    PubMed

    Yan, Deng; Yi, Song; Chiu, Wang Chi; Qin, Liu Gui; Kin, Wong Hoi; Kwok Hung, Chung Tony; Linxiao, Han; Wai, Choy Kwong; Yi, Sui; Tao, Yang; Tao, Tang

    2017-12-12

    This study was conducted to explore chromosomal copy number variations (CNV) and transcript expression and to examine pathways in cervical pathogenesis using genome-wide high resolution microarrays. Genome-wide chromosomal CNVs were investigated in 6 cervical cancer cell lines by Human Genome CGH Microarray Kit (4x44K). Gene expression profiles in cervical cancer cell lines, primary cervical carcinoma and normal cervical epithelium tissues were also studied using the Whole Human Genome Microarray Kit (4x44K). Fifty common chromosomal CNVs were identified in the cervical cancer cell lines. Correlation analysis revealed that gene up-regulation or down-regulation is significantly correlated with genomic amplification ( P =0.009) or deletion ( P =0.006) events. Expression profiles were identified through cluster analysis. Gene annotation analysis pinpointed cell cycle pathways was significantly ( P =1.15E-08) affected in cervical cancer. Common CNVs were associated with cervical cancer. Chromosomal CNVs may contribute to their transcript expression in cervical cancer.

  3. A latent profile analysis of Asian American men's and women's adherence to cultural values.

    PubMed

    Wong, Y Joel; Nguyen, Chi P; Wang, Shu-Yi; Chen, Weilin; Steinfeldt, Jesse A; Kim, Bryan S K

    2012-07-01

    The goal of this study was to identify diverse profiles of Asian American women's and men's adherence to values that are salient in Asian cultures (i.e., conformity to norms, family recognition through achievement, emotional self-control, collectivism, and humility). To this end, the authors conducted a latent profile analysis using the 5 subscales of the Asian American Values Scale-Multidimensional in a sample of 214 Asian Americans. The analysis uncovered a four-cluster solution. In general, Clusters 1 and 2 were characterized by relatively low and moderate levels of adherence to the 5 dimensions of cultural values, respectively. Cluster 3 was characterized by the highest level of adherence to the cultural value of family recognition through achievement, whereas Cluster 4 was typified by the highest levels of adherence to collectivism, emotional self-control, and humility. Clusters 3 and 4 were associated with higher levels of depressive symptoms than Cluster 1. Furthermore, Asian American women and Asian American men had lower odds of being in Cluster 4 and Cluster 3, respectively. These findings attest to the importance of identifying specific patterns of adherence to cultural values when examining the relationship between Asian Americans' cultural orientation and mental health status.

  4. Sex differences in discriminative power of volleyball game-related statistics.

    PubMed

    João, Paulo Vicente; Leite, Nuno; Mesquita, Isabel; Sampaio, Jaime

    2010-12-01

    To identify sex differences in volleyball game-related statistics, the game-related statistics of several World Championships in 2007 (N=132) were analyzed using the software VIS from the International Volleyball Federation. Discriminant analysis was used to identify the game-related statistics which better discriminated performances by sex. Analysis yielded an emphasis on fault serves (SC = -.40), shot spikes (SC = .40), and reception digs (SC = .31). Specific robust numbers represent that considerable variability was evident in the game-related statistics profile, as men's volleyball games were better associated with terminal actions (errors of service), and women's volleyball games were characterized by continuous actions (in defense and attack). These differences may be related to the anthropometric and physiological differences between women and men and their influence on performance profiles.

  5. NICU Network Neurobehavioral Profiles Predict Developmental Outcomes in a Low Risk Sample

    PubMed Central

    Sucharew, Heidi; Khoury, Jane C.; Xu, Yingying; Succop, Paul; Yolton, Kimberly

    2012-01-01

    Summary Latent profile analysis (LPA) has been used previously to classify neurobehavioral responses of infants prenatally exposed to cocaine and other drugs of abuse. The objective of this study was to define NICU Network Neurobehavioral Scale (NNNS) profile response patterns in a cohort of infants with no known cocaine exposure or other risks for neurobehavior deficits, and determine whether these profiles predict neurobehavioral outcomes in these low-risk infants. NNNS exams were performed on 355 low-risk infants at approximately 5 weeks after birth. LPA was used to define discrete profiles based on the standard NNNS summary scales. Associations between the infant profiles and neurobehavioral outcomes at one to three years of age were examined. Twelve of the 13 summary scales were used and three discrete NNNS profiles identified: social/easy going infants (44%), hypotonic infants (24%), and high arousal/difficult infants (32%). Statistically significant associations between NNNS profiles and later neurobehavioral outcomes were found for psychomotor development and externalizing behaviors. Hypotonic infants had both lower psychomotor development and lower externalizing scores compared to the other two profiles. In conclusion, three distinct profiles of the NNNS summary scores were identifiable using LPA among infants with no known cocaine exposure. These profile patterns were associated with early childhood neurobehavioral outcome, similar to findings reported in a study of infants with substantial cocaine exposure, demonstrating the utility of this profiling technique in both exposed and unexposed populations. PMID:22686386

  6. Small RNAome profiling from human skeletal muscle: novel miRNAs and their targets associated with cancer cachexia.

    PubMed

    Narasimhan, Ashok; Ghosh, Sunita; Stretch, Cynthia; Greiner, Russell; Bathe, Oliver F; Baracos, Vickie; Damaraju, Sambasivarao

    2017-06-01

    MicroRNAs (miRs) are small non-coding RNAs that regulate gene (mRNA) expression. Although the pathological role of miRs have been studied in muscle wasting conditions such as myotonic and muscular dystrophy, their roles in cancer cachexia (CC) are still emerging. The objectives are (i) to profile human skeletal muscle expressed miRs; (ii) to identify differentially expressed (DE) miRs between cachectic and non-cachectic cancer patients; (iii) to identify mRNA targets for the DE miRs to gain mechanistic insights; and (iv) to investigate if miRs show potential prognostic and predictive value. Study subjects were classified based on the international consensus diagnostic criteria for CC. Forty-two cancer patients were included, of which 22 were cachectic cases and 20 were non-cachectic cancer controls. Total RNA isolated from muscle biopsies were subjected to next-generation sequencing. A total of 777 miRs were profiled, and 82 miRs with read counts of ≥5 in 80% of samples were retained for analysis. We identified eight DE miRs (up-regulated, fold change of ≥1.4 at P < 0.05). A total of 191 potential mRNA targets were identified for the DE miRs using previously described human skeletal muscle mRNA expression data (n = 90), and a majority of them were also confirmed in an independent mRNA transcriptome dataset. Ingenuity pathway analysis identified pathways related to myogenesis and inflammation. qRT-PCR analysis of representative miRs showed similar direction of effect (P < 0.05), as observed in next-generation sequencing. The identified miRs also showed prognostic and predictive value. In all, we identified eight novel miRs associated with CC. © 2017 The Authors. Journal of Cachexia, Sarcopenia and Muscle published by John Wiley & Sons Ltd on behalf of the Society on Sarcopenia, Cachexia and Wasting Disorders.

  7. Cross Racial Identity Scale (CRIS) scores and profiles in African American adolescents involved with the juvenile justice system.

    PubMed

    Worrell, Frank C; Andretta, James R; Woodland, Malcolm H

    2014-10-01

    In this study, we examined the internal consistency and structural validity of Cross Racial Identity Scale (CRIS) scores in a sample of 477 African American adolescents who had been arrested in a city in the mid-Atlantic. Using cluster analysis, we also identified profiles of CRIS scores and compared adolescents with different profiles on Major Depressive Episode, Manic Episode, Generalized Anxiety Disorder, and Obsessive-Compulsive Disorder scores. Results indicated that CRIS subscale scores were reliable, and the 6-factor structure of the CRIS was supported. Five nigrescence profiles were identified: Miseducation-Pro-Black, Conflicted-Self-Hatred, Multiculturalist, Low Race Salience, and Conflicted-Anti-White. Individuals with Conflicted-Self-Hatred profiles reported significantly and meaningfully higher scores on the 4 syndromes than did their peers, and individuals with the Multiculturalist and Low Race Salience profiles reported the lowest scores. A greater percentage of individuals with Conflicted racial identity profiles had syndrome scores in the clinically significant range. The results of this study demonstrate that some of the nigrescence profiles found in college-age students generalize to adolescents. The implications of the findings for theory, research, and practice are discussed. PsycINFO Database Record (c) 2014 APA, all rights reserved.

  8. Mexican-Origin Parents’ Latent Occupational Profiles: Associations with Parent-Youth Relationships and Youth Aspirations

    PubMed Central

    Wheeler, Lorey A.; Updegraff, Kimberly A.; Umaña-Taylor, Adriana; Tein, Jenn-Yun

    2014-01-01

    This study utilized an ecological, person-centered approach to identify subgroups of families who had similar profiles across multiple dimensions of Mexican-origin mothers’ and fathers’ occupational characteristics (i.e., self-direction, hazardous conditions, physical activity) and to relate these subgroups to families’ sociocultural characteristics and youth adjustment. The study included 160 dual-earner Mexican-origin families from the urban Southwest. Mothers’ and fathers’ objective work characteristics and families’ sociocultural characteristics were assessed when youth were in early to middle adolescence; adjustment was assessed during late adolescence and early adulthood for two offspring in each family. A latent profile analysis identified 3 profiles that evidenced distinct patterns of occupational characteristics: a differentiated high physical activity profile characterized by high levels of physical activity and low levels of self-direction; an incongruent profile characterized by large differences between parents on self-direction, hazards, and physical activity; and a congruent highly self-directed profile characterized by congruence across parents on occupational characteristics. These profiles were linked to sociocultural characteristics (i.e., family income, educational attainment, and acculturation) and to relational adjustment (i.e., mother- and father-youth conflict, father warmth) and educational aspirations. Results are discussed with respect to implications of parents’ work for youth’s future family relationships and attainment. PMID:23957822

  9. Thin Versus Thick Description: Analyzing Representations of People and Their Life Worlds in the Literature of Communication Sciences and Disorders.

    PubMed

    Hengst, Julie A; Devanga, Suma; Mosier, Hillary

    2015-11-01

    Evidence-based practice relies on clinicians to translate research evidence for individual clients. This study, the initial phase of a broader research project, examines the textual resources of such translations by analyzing how people with acquired cognitive-communication disorders (ACCD) and their life worlds have been represented in Communication Sciences and Disorders (CSD) research articles. Using textual analysis, we completed a categorical analysis of 6,059 articles published between 1936 and 2012, coding for genre, population, and any evidence of thick representations of people and their life worlds, and a discourse analysis of representations used in 56 ACCD research articles, identifying thin and thick representations in 4 domains (derived from the International Classification of Functioning, Disability, and Health) and across article sections. The categorical analysis identified a higher percentage of ACCD articles with some evidence of thick representation (30%) compared with all CSD articles (12%) sampled. However, discourse analysis of ACCD research articles found that thick representations were quite limited; 34/56 articles had thin representational profiles, 19/56 had mixed profiles, and 3/56 had thick profiles. These findings document the dominance of thin representations in the CSD literature, which we suggest makes translational work more difficult. How clinicians translate such evidence will be addressed in the next research phase, an interview study of speech-language pathologists.

  10. Analysis of blood-based gene expression in idiopathic Parkinson disease.

    PubMed

    Shamir, Ron; Klein, Christine; Amar, David; Vollstedt, Eva-Juliane; Bonin, Michael; Usenovic, Marija; Wong, Yvette C; Maver, Ales; Poths, Sven; Safer, Hershel; Corvol, Jean-Christophe; Lesage, Suzanne; Lavi, Ofer; Deuschl, Günther; Kuhlenbaeumer, Gregor; Pawlack, Heike; Ulitsky, Igor; Kasten, Meike; Riess, Olaf; Brice, Alexis; Peterlin, Borut; Krainc, Dimitri

    2017-10-17

    To examine whether gene expression analysis of a large-scale Parkinson disease (PD) patient cohort produces a robust blood-based PD gene signature compared to previous studies that have used relatively small cohorts (≤220 samples). Whole-blood gene expression profiles were collected from a total of 523 individuals. After preprocessing, the data contained 486 gene profiles (n = 205 PD, n = 233 controls, n = 48 other neurodegenerative diseases) that were partitioned into training, validation, and independent test cohorts to identify and validate a gene signature. Batch-effect reduction and cross-validation were performed to ensure signature reliability. Finally, functional and pathway enrichment analyses were applied to the signature to identify PD-associated gene networks. A gene signature of 100 probes that mapped to 87 genes, corresponding to 64 upregulated and 23 downregulated genes differentiating between patients with idiopathic PD and controls, was identified with the training cohort and successfully replicated in both an independent validation cohort (area under the curve [AUC] = 0.79, p = 7.13E-6) and a subsequent independent test cohort (AUC = 0.74, p = 4.2E-4). Network analysis of the signature revealed gene enrichment in pathways, including metabolism, oxidation, and ubiquitination/proteasomal activity, and misregulation of mitochondria-localized genes, including downregulation of COX4I1 , ATP5A1 , and VDAC3 . We present a large-scale study of PD gene expression profiling. This work identifies a reliable blood-based PD signature and highlights the importance of large-scale patient cohorts in developing potential PD biomarkers. © 2017 American Academy of Neurology.

  11. Liver protein profiles in insulin receptor-knockout mice reveal novel molecules involved in the diabetes pathophysiology.

    PubMed

    Capuani, Barbara; Della-Morte, David; Donadel, Giulia; Caratelli, Sara; Bova, Luca; Pastore, Donatella; De Canio, Michele; D'Aguanno, Simona; Coppola, Andrea; Pacifici, Francesca; Arriga, Roberto; Bellia, Alfonso; Ferrelli, Francesca; Tesauro, Manfredi; Federici, Massimo; Neri, Anna; Bernardini, Sergio; Sbraccia, Paolo; Di Daniele, Nicola; Sconocchia, Giuseppe; Orlandi, Augusto; Urbani, Andrea; Lauro, Davide

    2015-05-01

    Liver has a principal role in glucose regulation and lipids homeostasis. It is under a complex control by substrates such as hormones, nutrients, and neuronal impulses. Insulin promotes glycogen synthesis, lipogenesis, and lipoprotein synthesis and inhibits gluconeogenesis, glycogenolysis, and VLDL secretion by modifying the expression and enzymatic activity of specific molecules. To understand the pathophysiological mechanisms leading to metabolic liver disease, we analyzed liver protein patterns expressed in a mouse model of diabetes by proteomic approaches. We used insulin receptor-knockout (IR(-/-)) and heterozygous (IR(+/-)) mice as a murine model of liver metabolic dysfunction associated with diabetic ketoacidosis and insulin resistance. We evaluated liver fatty acid levels by microscopic examination and protein expression profiles by orthogonal experimental strategies using protein 2-DE MALDI-TOF/TOF and peptic nLC-MS/MS shotgun profiling. Identified proteins were then loaded into Ingenuity Pathways Analysis to find possible molecular networks. Twenty-eight proteins identified by 2-DE analysis and 24 identified by nLC-MS/MS shotgun were differentially expressed among the three genotypes. Bioinformatic analysis revealed a central role of high-mobility group box 1/2 and huntigtin never reported before in association with metabolic and related liver disease. A different modulation of these proteins in both blood and hepatic tissue further suggests their role in these processes. These results provide new insight into pathophysiology of insulin resistance and hepatic steatosis and could be useful in identifying novel biomarkers to predict risk for diabetes and its complications. Copyright © 2015 the American Physiological Society.

  12. In-Silico Integration Approach to Identify a Key miRNA Regulating a Gene Network in Aggressive Prostate Cancer

    PubMed Central

    Colaprico, Antonio; Bontempi, Gianluca; Castiglioni, Isabella

    2018-01-01

    Like other cancer diseases, prostate cancer (PC) is caused by the accumulation of genetic alterations in the cells that drives malignant growth. These alterations are revealed by gene profiling and copy number alteration (CNA) analysis. Moreover, recent evidence suggests that also microRNAs have an important role in PC development. Despite efforts to profile PC, the alterations (gene, CNA, and miRNA) and biological processes that correlate with disease development and progression remain partially elusive. Many gene signatures proposed as diagnostic or prognostic tools in cancer poorly overlap. The identification of co-expressed genes, that are functionally related, can identify a core network of genes associated with PC with a better reproducibility. By combining different approaches, including the integration of mRNA expression profiles, CNAs, and miRNA expression levels, we identified a gene signature of four genes overlapping with other published gene signatures and able to distinguish, in silico, high Gleason-scored PC from normal human tissue, which was further enriched to 19 genes by gene co-expression analysis. From the analysis of miRNAs possibly regulating this network, we found that hsa-miR-153 was highly connected to the genes in the network. Our results identify a four-gene signature with diagnostic and prognostic value in PC and suggest an interesting gene network that could play a key regulatory role in PC development and progression. Furthermore, hsa-miR-153, controlling this network, could be a potential biomarker for theranostics in high Gleason-scored PC. PMID:29562723

  13. Staff nurse commitment, work relationships, and turnover intentions: a latent profile analysis.

    PubMed

    Gellatly, Ian R; Cowden, Tracy L; Cummings, Greta G

    2014-01-01

    The three-component model of organization commitment has typically been studied using a variable-centered rather than a person-centered approach, preventing a more complete understanding of how these forms of commitment are felt and expressed as a whole. Latent profile analysis was used to identify qualitatively distinct categories or profiles of staff nurses' commitment. Then, associations of the profiles with perceived work unit relations and turnover intentions were examined. Three hundred thirty-six registered nurses provided data on affective, normative, and continuance commitment, perceived work unit relations, and turnover intentions. Latent profile analysis of the nurses' commitment scores revealed six distinct profile groups. Work unit relations and turnover intentions were compared in the six profile-defined groups. Staff nurses with profiles characterized by high affective commitment and/or high normative commitment in relation to other components experienced stronger work unit relations and reported lower turnover intentions. Profiles characterized by high continuance commitment relative to other components or by low overall commitment experienced poorer work unit relations, and the turnover risk was higher. High continuance commitment in combination with high affective and normative commitment was experienced differently than high continuance commitment in combination with low affective and normative commitment. Healthcare organizations often foster commitment by using continuance commitment-enhancing strategies (e.g., offer high salaries and attractive benefits) that may inadvertently introduce behavioral risk. This work suggests the importance of changing the context in which continuance commitment occurs by strengthening the other two components.

  14. Prevalence of Stress References on College Freshmen Facebook Profiles

    PubMed Central

    EGAN, KATIE G.; MORENO, MEGAN A.

    2011-01-01

    Stress is common among college students and associated with adverse health outcomes. This study used the social networking Web site Facebook to identify self-reported stress and associated conditions among college students. Public Facebook profiles of undergraduate freshman at a large Midwestern State University (n = 300) were identified using a Facebook search. Content analysis of Facebook profiles included demographic information and displayed references to stress, weight concerns, depressive symptoms, and alcohol. The mean reported age was 18.4 years, and the majority of profile owners were female (62%). Stress references were displayed on 37% of the profiles, weight concerns on 6%, depressive symptoms on 24%, and alcohol on 73%. The display of stress references was associated with female sex (odds ratio [OR], 2.81; confidence interval [CI], 1.7–4.7), weight concerns (OR, 5.36; CI, 1.87–15.34), and depressive symptoms (OR, 2.7; CI, 1.57–4.63). No associations were found between stress and alcohol references. College freshmen frequently display references to stress on Facebook profiles with prevalence rates similar to self-reported national survey data. Findings suggest a positive association between referencing stress and both weight concerns and depressive symptoms. Facebook may be a useful venue to identify students at risk for stress-related conditions and to disseminate information about campus resources to these students. PMID:21436681

  15. Uncovering the molecular secrets of inflammatory breast cancer biology: an integrated analysis of three distinct affymetrix gene expression datasets.

    PubMed

    Van Laere, Steven J; Ueno, Naoto T; Finetti, Pascal; Vermeulen, Peter; Lucci, Anthony; Robertson, Fredika M; Marsan, Melike; Iwamoto, Takayuki; Krishnamurthy, Savitri; Masuda, Hiroko; van Dam, Peter; Woodward, Wendy A; Viens, Patrice; Cristofanilli, Massimo; Birnbaum, Daniel; Dirix, Luc; Reuben, James M; Bertucci, François

    2013-09-01

    Inflammatory breast cancer (IBC) is a poorly characterized form of breast cancer. So far, the results of expression profiling in IBC are inconclusive due to various reasons including limited sample size. Here, we present the integration of three Affymetrix expression datasets collected through the World IBC Consortium allowing us to interrogate the molecular profile of IBC using the largest series of IBC samples ever reported. Affymetrix profiles (HGU133-series) from 137 patients with IBC and 252 patients with non-IBC (nIBC) were analyzed using unsupervised and supervised techniques. Samples were classified according to the molecular subtypes using the PAM50-algorithm. Regression models were used to delineate IBC-specific and molecular subtype-independent changes in gene expression, pathway, and transcription factor activation. Four robust IBC-sample clusters were identified, associated with the different molecular subtypes (P<0.001), all of which were identified in IBC with a similar prevalence as in nIBC, except for the luminal A subtype (19% vs. 42%; P<0.001) and the HER2-enriched subtype (22% vs. 9%; P<0.001). Supervised analysis identified and validated an IBC-specific, molecular subtype-independent 79-gene signature, which held independent prognostic value in a series of 871 nIBCs. Functional analysis revealed attenuated TGF-β signaling in IBC. We show that IBC is transcriptionally heterogeneous and that all molecular subtypes described in nIBC are detectable in IBC, albeit with a different frequency. The molecular profile of IBC, bearing molecular traits of aggressive breast tumor biology, shows attenuation of TGF-β signaling, potentially explaining the metastatic potential of IBC tumor cells in an unexpected manner. ©2013 AACR.

  16. Metabolomic Profile of Ards by Nuclear Magnetic Resonance Spectroscopy in Patients with H1N1 Influenza Virus Pneumonia.

    PubMed

    Izquierdo-Garcia, Jose L; Nin, Nicolas; Jimenez-Clemente, Jorge; Horcajada, Juan P; Arenas-Miras, Maria Del Mar; Gea, Joaquim; Esteban, Andres; Ruiz-Cabello, Jesus; Lorente, Jose A

    2017-12-29

    The integrated analysis of changes in the metabolic profile could be critical for the discovery of biomarkers of lung injury, and also for generating new pathophysiological hypotheses and designing novel therapeutic targets for the acute respiratory distress syndrome (ARDS). This study aimed at developing a Nuclear Magnetic Resonance (NMR)-based approach for the identification of the metabolomic profile of ARDS in patients with H1N1 influenza virus pneumonia. Serum samples from 30 patients (derivation set) diagnosed of H1N1 influenza virus pneumonia were analysed by unsupervised Principal Component Analysis (PCA) to identify metabolic differences between patients with and without ARDS by NMR-spectroscopy. A predictive model of partial least squares discriminant analysis (PLS-DA) was developed for the identification of ARDS. PLS-DA was trained with the derivation set and tested in another set of samples from 26 patients also diagnosed of H1N1 influenza virus pneumonia (validation set). Decreased serum glucose, alanine, glutamine, methylhistidine and fatty acids concentrations, and elevated serum phenylalanine and methylguanidine concentrations, discriminated patients with ARDS versus patients without ARDS. PLS-DA model successfully identified the presence of ARDS in the validation set with a success rate of 92% (sensitivity 100% and specificity 91%). The classification functions showed a good correlation with the Sequential Organ Failure Assessment (SOFA) score (R = 0.74, p < 0.0001) and the Pa02/Fi02 ratio (R = 0.41, p = 0.03). The serum metabolomic profile is sensitive and specific to identify ARDS in patients with H1N1 influenza A pneumonia. Future studies are needed to determine the role of NMR-spectroscopy as a biomarker of ARDS.

  17. Histological analysis and identification of spermatogenesis-related genes in 2-, 6-, and 12-month-old sheep testes

    NASA Astrophysics Data System (ADS)

    Bai, Man; Sun, Limin; Zhao, Jia; Xiang, Lujie; Cheng, Xiaoyin; Li, Jiarong; Jia, Chao; Jiang, Huaizhi

    2017-10-01

    Testis development and spermatogenesis are vital factors that influence male animal fertility. In order to identify spermatogenesis-related genes and further provide a theory basis for finding biomarkers related to male sheep fertility, 2-, 6-, and 12-month-old Small Tail Han Sheep testes were selected to investigate the dynamic changes of sheep testis development. Hematoxylin-eosin routine staining and RNA-Seq technique were used to perform histological and transcriptome analysis for these testes. The results showed that 630, 102, and 322 differentially expressed genes (DEGs) were identified in 2- vs 6-month-old, 6- vs 12-month-old, and 2- vs 12-month-old testes, respectively. GO and KEGG analysis showed the following: DEGs in 2- vs 6-month-old testes were mainly related to the GO terms of sexual maturation and the pathways of multiple metabolism and biosynthesis; in 6- vs 12-month-old testes, most of the GO terms that DEGs involved in were related to metabolism and translation processes; the most significantly enriched pathway is the ribosome pathway. The union of DEGs in 2- vs 6-month-old, 6- vs 12-month-old, and 2- vs 12-month-old testes was categorized into eight profiles by series cluster. Subsequently, the eight profiles were classified into four model profiles and four co-expression networks were constructed based on the DEGs in these model profiles. Finally, 29 key regulatory genes related to spermatogenesis were identified in the four co-expression networks. The expression of 13 DEGs (CA3, APOH, MYOC, CATSPER4, SYT6, SERPINA10, DAZL, ADIPOR2, RAB13, CEP41, SPAG4, ODF1, and FRG1) was validated by RT-PCR.

  18. Characterisation of volatile profile and sensory analysis of fresh-cut "Radicchio di Chioggia" stored in air or modified atmosphere.

    PubMed

    Cozzolino, Rosaria; Martignetti, Antonella; Pellicano, Mario Paolo; Stocchero, Matteo; Cefola, Maria; Pace, Bernardo; De Giulio, Beatrice

    2016-02-01

    The volatile profile of two hybrids of "Radicchio di Chioggia", Corelli and Botticelli, stored in air or passive modified atmosphere (MAP) during 12 days of cold storage, was monitored by solid phase micro-extraction (SPME) GC-MS. Botticelli samples were also subjected to sensory analysis. Totally, 61 volatile organic compounds (VOCs) were identified in the headspace of radicchio samples. Principal component analysis (PCA) showed that fresh product possessed a metabolic content similar to that of the MAP samples after 5 and 8 days of storage. Projection to latent structures by partial least squares (PLS) regression analysis showed the volatiles content of the samples varied depending only on the packaging conditions. Specifically, 12 metabolites describing the time evolution and explaining the effects of the different storage conditions were highlighted. Finally, a PCA analysis revealed that VOCs profile significantly correlated with sensory attributes. Copyright © 2015 Elsevier Ltd. All rights reserved.

  19. Profiles of Emotional Intelligence and Learning Strategies in a Sample of Chilean Students

    ERIC Educational Resources Information Center

    García-Fernández, José M.; Inglés, Cándido J.; Suriá, Raquel; Martín, Nelly Lagos-San; Gonzálvez-Maciá, Carolina; Aparisi, David; Martínez-Monteagudo, Mari C.

    2015-01-01

    In the last few years, one of the lines of research of great interest in the field of emotional intelligence (EI) has been the analysis of the role of emotions in the educational context and, in particular, their influence on learning strategies. The aims of this study are to identify the existence of different EI profiles and to determine…

  20. 41 CFR 60-2.11 - Organizational profile.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... that may assist in identifying organizational units where women or minorities are underrepresented or.../Pacific Islanders, and American Indians/Alaskan Natives. (c) Workforce analysis. (1) A workforce analysis... Indians/Alaskan Natives. The wage rate or salary range for each job title must be given. All job titles...

  1. 41 CFR 60-2.11 - Organizational profile.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... that may assist in identifying organizational units where women or minorities are underrepresented or.../Pacific Islanders, and American Indians/Alaskan Natives. (c) Workforce analysis. (1) A workforce analysis... Indians/Alaskan Natives. The wage rate or salary range for each job title must be given. All job titles...

  2. 41 CFR 60-2.11 - Organizational profile.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... that may assist in identifying organizational units where women or minorities are underrepresented or.../Pacific Islanders, and American Indians/Alaskan Natives. (c) Workforce analysis. (1) A workforce analysis... Indians/Alaskan Natives. The wage rate or salary range for each job title must be given. All job titles...

  3. 41 CFR 60-2.11 - Organizational profile.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... that may assist in identifying organizational units where women or minorities are underrepresented or.../Pacific Islanders, and American Indians/Alaskan Natives. (c) Workforce analysis. (1) A workforce analysis... Indians/Alaskan Natives. The wage rate or salary range for each job title must be given. All job titles...

  4. Motivational and emotional profiles in university undergraduates: a self-determination theory perspective.

    PubMed

    González, Antonio; Paoloni, Verónica; Donolo, Danilo; Rinaudo, Cristina

    2012-11-01

    Previous research has focused on specific forms of self-determined motivation or discrete class-related emotions, but few studies have simultaneously examined both constructs. The aim of this study on 472 undergraduates was twofold: to perform cluster analysis to identify homogeneous groups of motivation in the sample; and to determine the profile of each cluster for emotions and academic achievement. Cluster analysis configured four groups in terms of motivation: controlled, autonomous, both high, and both low. Each cluster revealed a distinct emotional profile, autonomous motivation being the most adaptable with high scores for academic achievement and pleasant emotions and low values for unpleasant emotions. The results are discussed in the light of their implications for academic adjustment.

  5. From loquacious to reticent: understanding patient health information communication to guide consumer health IT design.

    PubMed

    Valdez, Rupa S; Guterbock, Thomas M; Fitzgibbon, Kara; Williams, Ishan C; Wellbeloved-Stone, Claire A; Bears, Jaime E; Menefee, Hannah K

    2017-07-01

    It is increasingly recognized that some patients self-manage in the context of social networks rather than alone. Consumer health information technology (IT) designed to support socially embedded self-management must be responsive to patients' everyday communication practices. There is an opportunity to improve consumer health IT design by explicating how patients currently leverage social media to support health information communication. The objective of this study was to determine types of health information communication patterns that typify Facebook users with chronic health conditions to guide consumer health IT design. Seven hundred participants with type 2 diabetes were recruited through a commercial survey access panel. Cluster analysis was used to identify distinct approaches to health information communication both on and off Facebook. Analysis of variance (ANOVA) methods were used to identify demographic and behavioral differences among profiles. Secondary analysis of qualitative interviews ( n  = 25) and analysis of open-ended survey questions were conducted to understand participant rationales for each profile. Our analysis yielded 7 distinct health information communication profiles. Five of 7 profiles had consistent patterns both on and off Facebook, while the remaining 2 demonstrated distinct practices, with no health information communication on Facebook but some off Facebook. One profile was distinct from all others in both health information communication practices and demographic composition. Rationales for following specific health information communication practices were categorized under 6 themes: altruism, instrumental support, social support, privacy and stigma, convenience, and Facebook knowledge. Facebook has been widely adopted for health information communication; This study demonstrates that Facebook has been widely adopted for health information communication. It also shows that the ways in which patients communicate health information on and off Facebook are diverse. © The Author 2017. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  6. The Impact of Time Perspective Latent Profiles on College Drinking: A Multidimensional Approach

    PubMed Central

    Braitman, Abby L.; Henson, James M.

    2015-01-01

    Background Zimbardo and Boyd’s1 time perspective, or the temporal framework individuals use to process information, has been shown to predict health behaviors such as alcohol use. Previous studies supported the predictive validity of individual dimensions of time perspective, with some dimensions acting as protective factors and others as risk factors. However, some studies produced findings contrary to the general body of literature. In addition, time perspective is a multidimensional construct, and the combination of perspectives may be more predictive than individual dimensions in isolation; consequently, multidimensional profiles are a more accurate measure of individual differences and more appropriate for predicting health behaviors. Objectives The current study identified naturally occurring profiles of time perspective and examined their association with risky alcohol use. Methods Data were collected from a college student sample (n = 431, mean age = 20.41 years) using an online survey. Time perspective profiles were identified using latent profile analysis. Results Bootstrapped regression models identified a protective class that engaged in significantly less overall drinking (β = −0.254) as well as engaging in significantly less episodic high risk drinking (β = −0.274). There was also emerging evidence of a high risk time perspective profile that was linked to more overall drinking (β = 0.198) and engaging in more high risk drinking (β = 0.245), though these differences were not significant. Conclusions/Importance These findings support examining time perspective in a multidimensional framework rather than individual dimensions in isolation. Implications include identifying students most in need of interventions, and tailoring interventions to target temporal framing in decision-making. PMID:25607806

  7. The impact of time perspective latent profiles on college drinking: a multidimensional approach.

    PubMed

    Braitman, Abby L; Henson, James M

    2015-04-01

    Zimbardo and Boyd's(1) time perspective, or the temporal framework individuals use to process information, has been shown to predict health behaviors such as alcohol use. Previous studies supported the predictive validity of individual dimensions of time perspective, with some dimensions acting as protective factors and others as risk factors. However, some studies produced findings contrary to the general body of literature. In addition, time perspective is a multidimensional construct, and the combination of perspectives may be more predictive than individual dimensions in isolation; consequently, multidimensional profiles are a more accurate measure of individual differences and more appropriate for predicting health behaviors. The current study identified naturally occurring profiles of time perspective and examined their association with risky alcohol use. Data were collected from a college student sample (n = 431, mean age = 20.41 years) using an online survey. Time perspective profiles were identified using latent profile analysis. Bootstrapped regression models identified a protective class that engaged in significantly less overall drinking (β = -0.254) as well as engaging in significantly less episodic high risk drinking (β = -0.274). There was also emerging evidence of a high risk time perspective profile that was linked to more overall drinking (β = 0.198) and engaging in more high risk drinking (β = 0.245), though these differences were not significant. CONCLUSIONS/IMPORTANCE: These findings support examining time perspective in a multidimensional framework rather than individual dimensions in isolation. Implications include identifying students most in need of interventions, and tailoring interventions to target temporal framing in decision-making.

  8. Quality Control of Wind Data from 50-MHz Doppler Radar Wind Profiler

    NASA Technical Reports Server (NTRS)

    Vacek, Austin

    2016-01-01

    Upper-level wind profiles obtained from a 50-MHz Doppler Radar Wind Profiler (DRWP) instrument at Kennedy Space Center are incorporated in space launch vehicle design and day-of-launch operations to assess wind effects on the vehicle during ascent. Automated and manual quality control (QC) techniques are implemented to remove spurious data in the upper-level wind profiles caused from atmospheric and non-atmospheric artifacts over the 2010-2012 period of record (POR). By adding the new quality controlled profiles with older profiles from 1997-2009, a robust database will be constructed of upper-level wind characteristics. Statistical analysis will determine the maximum, minimum, and 95th percentile of the wind components from the DRWP profiles over recent POR and compare against the older database. Additionally, this study identifies specific QC flags triggered during the QC process to understand how much data is retained and removed from the profiles.

  9. Quality Control of Wind Data from 50-MHz Doppler Radar Wind Profiler

    NASA Technical Reports Server (NTRS)

    Vacek, Austin

    2015-01-01

    Upper-level wind profiles obtained from a 50-MHz Doppler Radar Wind Profiler (DRWP) instrument at Kennedy Space Center are incorporated in space launch vehicle design and day-of-launch operations to assess wind effects on the vehicle during ascent. Automated and manual quality control (QC) techniques are implemented to remove spurious data in the upper-level wind profiles caused from atmospheric and non-atmospheric artifacts over the 2010-2012 period of record (POR). By adding the new quality controlled profiles with older profiles from 1997-2009, a robust database will be constructed of upper-level wind characteristics. Statistical analysis will determine the maximum, minimum, and 95th percentile of the wind components from the DRWP profiles over recent POR and compare against the older database. Additionally, this study identifies specific QC flags triggered during the QC process to understand how much data is retained and removed from the profiles.

  10. Personality Profiles of Effective Leadership Performance in Assessment Centers.

    PubMed

    Parr, Alissa D; Lanza, Stephanie T; Bernthal, Paul

    2016-01-01

    Most research examining the relationship between effective leadership and personality has focused on individual personality traits. However, profiles of personality traits more fully describe individuals, and these profiles may be important as they relate to leadership. This study used latent class analysis to examine how personality traits combine and interact to form subpopulations of leaders, and how these subpopulations relate to performance criteria. Using a sample of 2,461 executive-level leaders, six personality profiles were identified: Unpredictable Leaders with Low Diligence (7.3%); Conscientious, Backend Leaders (3.6%); Unpredictable Leaders (8.6%); Creative Communicators (20.8%); Power Players (32.4%); and Protocol Followers (27.1%). One profile performed well on all criteria in an assessment center; remaining profiles exhibited strengths and weaknesses across criteria. Implications and future directions for research are highlighted.

  11. Caregiver profiles in dementia related to quality of life, depression and perseverance time in the European Actifcare study: the importance of social health.

    PubMed

    Janssen, Eveline P C J; de Vugt, Marjolein; Köhler, Sebastian; Wolfs, Claire; Kerpershoek, Liselot; Handels, Ron L H; Orrell, Martin; Woods, Bob; Jelley, Hannah; Stephan, Astrid; Bieber, Anja; Meyer, Gabriele; Engedal, Knut; Selbaek, Geir; Wimo, Anders; Irving, Kate; Hopper, Louise; Gonçalves-Pereira, Manuel; Portolani, Elisa; Zanetti, Orazio; Verhey, Frans R

    2017-01-01

    To identify caregiver profiles of persons with mild to moderate dementia and to investigate differences between identified caregiver profiles, using baseline data of the international prospective cohort study Actifcare. A latent class analysis was used to discover different caregiver profiles based on disease related characteristics of 453 persons with dementia and their 453 informal caregivers. These profiles were compared with regard to quality of life (CarerQoL score), depressive symptoms (HADS-D score) and perseverance time. A 5-class model was identified, with the best Bayesian Information Criterion value, significant likelihood ratio test (p < 0.001), high entropy score (0.88) and substantive interpretability. The classes could be differentiated on two axes: (i) caregivers' age, relationship with persons with dementia, severity of dementia, and (ii) tendency towards stress and difficulty adapting to stress. Classes showed significant differences with all dependent variables, and were labelled 'older low strain', 'older intermediate strain', 'older high strain', 'younger low strain' and 'younger high strain'. Differences exist between types of caregivers that explain variability in quality of life, depressive symptoms and perseverance time. Our findings may give direction for tailored interventions for caregivers of persons with dementia, which may improve social health and reduce health care costs.

  12. Technical player profiles related to the physical fitness of young female volleyball players predict team performance.

    PubMed

    Dávila-Romero, C; Hernández-Mocholí, M A; García-Hermoso, A

    2015-03-01

    This study is divided into three sequential stages: identification of fitness and game performance profiles (individual player performance), an assessment of the relationship between these profiles, and an assessment of the relationship between individual player profiles and team performance during play (in championship performance). The overall study sample comprised 525 (19 teams) female volleyball players aged 12-16 years and a subsample (N.=43) used to examine study aims one and two was selected from overall sample. Anthropometric, fitness and individual player performance (actual game) data were collected in the subsample. These data were analyzed through clustering methods, ANOVA and independence chi-square test. Then, we investigated whether the proportion of players with the highest individual player performance profile might predict a team's results in the championship. Cluster analysis identified three volleyball fitness profiles (high, medium, and low) and two individual player performance profiles (high and low). The results showed a relationship between both types of profile (fitness and individual player performance). Then, linear regression revealed a moderate relationship between the number of players with a high volleyball fitness profile and a team's results in the championship (R2=0.23). The current study findings may enable coaches and trainers to manage training programs more efficiently in order to obtain tailor-made training, identify volleyball-specific physical fitness training requirements and reach better results during competitions.

  13. The integration of information and communication technology into community pharmacists practice in Barcelona.

    PubMed

    Lupiáñez-Villanueva, Francisco; Hardey, Michael; Lluch, Maria

    2014-03-01

    The study aims to identify community pharmacists' (CPs) utilization of information and communication technology (ICT); to develop and characterize a typology of CPs' utilization of ICT and to identify factors that can enhance or inhibit the use of these technologies. An online survey of the 7649 members of the Pharmacist Association of Barcelona who had a registered email account in 2006 was carried out. Factor analysis, cluster analysis and binomial logit modelling were undertaken. Multivariate analysis of the CPs' responses to the survey (648) revealed two profiles of adoption of ICT. The first profile (40.75%) represents those CPs who place high emphasis on ICT within their practice. This group is therefore referred to as 'integrated CPs'. The second profile (59.25%) represents those CPs who make less use of ICT and so are consequently labelled 'non-integrated CPs'. Statistical modelling was used to identify variables that were important in predisposing CPs to integrate ICT with their work. From the analysis it is evident that responses to questions relating to 'recommend patients going on line for health information'; 'patients discuss or share their Internet health information findings'; 'emphasis on the Internet for communication and dissemination' and 'Pharmacists Professional Association information' play a positive and significant role in the probability of being an 'integrated CP'. The integration of ICT within CPs' practices cannot be adequately understood and appreciated without examining how CPs are making use of ICT within their own practice, their organizational context and the nature of the pharmacists-client relationship.

  14. Urinary metabonomics elucidate the therapeutic mechanism of Orthosiphon stamineus in mouse crystal-induced kidney injury.

    PubMed

    Gao, Songyan; Chen, Wei; Peng, Zhongjiang; Li, Na; Su, Li; Lv, Diya; Li, Ling; Lin, Qishan; Dong, Xin; Guo, Zhiyong; Lou, Ziyang

    2015-05-26

    Orthosiphon stamineus (OS), a traditional Chinese herb, is often used for promoting urination and treating nephrolithiasis. Urolithiasis is a major worldwide public health burden due to its high incidence of recurrence and damage to renal function. However, the etiology for urolithiasis is not well understood. Metabonomics, the systematic study of small molecule metabolites present in biological samples, has become a valid and powerful tool for understanding disease phenotypes. In this study, a urinary metabolic profiling analysis was performed in a mouse model of renal calcium oxalate crystal deposition to identify potential biomarkers for crystal-induced renal damage and the anti-crystal mechanism of OS. Thirty six mice were randomly divided into six groups including Saline, Crystal, Cystone and OS at dosages of 0.5g/kg, 1g/kg, and 2g/kg. A metabonomics approach using ultra-performance liquid chromatography coupled with quadrupole-time-of-flight mass spectrometry (UHPLC-Q-TOF/MS) was developed to perform the urinary metabolic profiling analysis. Principal component analysis (PCA) and partial least squares discriminant analysis (PLS-DA) were utilized to identify differences between the metabolic profiles of mice in the saline control group and crystal group. Using partial least squares-discriminant analysis, 30 metabolites were identified as potential biomarkers of crystal-induced renal damage. Most of them were primarily involved in amino acid metabolism, taurine and hypotaurine metabolism, purine metabolism, and the citrate cycle (TCA). After the treatment with OS, the levels of 20 biomarkers had returned to the levels of the control samples. Our results suggest that OS has a protective effect for mice with crystal-induced kidney injury via the regulation of multiple metabolic pathways primarily involving amino acid, energy and choline metabolism. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  15. Investigating a multigene prognostic assay based on significant pathways for Luminal A breast cancer through gene expression profile analysis.

    PubMed

    Gao, Haiyan; Yang, Mei; Zhang, Xiaolan

    2018-04-01

    The present study aimed to investigate potential recurrence-risk biomarkers based on significant pathways for Luminal A breast cancer through gene expression profile analysis. Initially, the gene expression profiles of Luminal A breast cancer patients were downloaded from The Cancer Genome Atlas database. The differentially expressed genes (DEGs) were identified using a Limma package and the hierarchical clustering analysis was conducted for the DEGs. In addition, the functional pathways were screened using Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses and rank ratio calculation. The multigene prognostic assay was exploited based on the statistically significant pathways and its prognostic function was tested using train set and verified using the gene expression data and survival data of Luminal A breast cancer patients downloaded from the Gene Expression Omnibus. A total of 300 DEGs were identified between good and poor outcome groups, including 176 upregulated genes and 124 downregulated genes. The DEGs may be used to effectively distinguish Luminal A samples with different prognoses verified by hierarchical clustering analysis. There were 9 pathways screened as significant pathways and a total of 18 DEGs involved in these 9 pathways were identified as prognostic biomarkers. According to the survival analysis and receiver operating characteristic curve, the obtained 18-gene prognostic assay exhibited good prognostic function with high sensitivity and specificity to both the train and test samples. In conclusion the 18-gene prognostic assay including the key genes, transcription factor 7-like 2, anterior parietal cortex and lymphocyte enhancer factor-1 may provide a new method for predicting outcomes and may be conducive to the promotion of precision medicine for Luminal A breast cancer.

  16. Clinical Application of Genomic Profiling With Circulating Tumor DNA for Management of Advanced Non-Small-cell Lung Cancer in Asia.

    PubMed

    Loong, Herbert H; Raymond, Victoria M; Shiotsu, Yukimasa; Chua, Daniel T T; Teo, Peter M L; Yung, Tony; Skrzypczak, Stan; Lanman, Richard B; Mok, Tony S K

    2018-05-07

    Genomic profiling of cell-free circulating tumor DNA (ctDNA) is a potential alternative to repeat invasive biopsy in patients with advanced cancer. We report the first real-world cohort of comprehensive genomic assessments of patients with non-small-cell lung cancer (NSCLC) in a Chinese population. We performed a retrospective analysis of patients with advanced or metastatic NSCLC whose physician requested ctDNA-based genomic profiling using the Guardant360 platform from January 2016 to June 2017. Guardant360 includes all 4 major types of genomic alterations (point mutations, insertion-deletion alterations, fusions, and amplifications) in 73 genes. Genomic profiling was performed in 76 patients from Hong Kong during the 18-month study period (median age, 59.5 years; 41 men and 35 women). The histologic types included adenocarcinoma (n = 10), NSCLC, not otherwise specified (n = 58), and squamous cell carcinoma (n = 8). In the adenocarcinoma and NSCLC, not otherwise specified, combined group, 62 of the 68 patients (91%) had variants identified (range, 1-12; median, 3), of whom, 26 (42%) had ≥ 1 of the 7 National Comprehensive Cancer Network-recommended lung adenocarcinoma genomic targets. Concurrent detection of driver and resistance mutations were identified in 6 of 13 patients with EGFR driver mutations and in 3 of 5 patients with EML4-ALK fusions. All 8 patients with squamous cell carcinoma had multiple variants identified (range, 1-20; median, 6), including FGFR1 amplification and ERBB2 (HER2) amplification. PIK3CA amplification occurred in combination with either FGFR1 or ERBB2 (HER2) amplification or alone. Genomic profiling using ctDNA analysis detected alterations in most patients with advanced-stage NSCLC, with targetable aberrations and resistance mechanisms identified. This approach has demonstrated its feasibility in Asia. Copyright © 2018 Elsevier Inc. All rights reserved.

  17. Refined identification of Vibrio bacterial flora from Acanthasther planci based on biochemical profiling and analysis of housekeeping genes.

    PubMed

    Rivera-Posada, J A; Pratchett, M; Cano-Gomez, A; Arango-Gomez, J D; Owens, L

    2011-09-09

    We used a polyphasic approach for precise identification of bacterial flora (Vibrionaceae) isolated from crown-of-thorns starfish (COTS) from Lizard Island (Great Barrier Reef, Australia) and Guam (U.S.A., Western Pacific Ocean). Previous 16S rRNA gene phylogenetic analysis was useful to allocate and identify isolates within the Photobacterium, Splendidus and Harveyi clades but failed in the identification of Vibrio harveyi-like isolates. Species of the V harveyi group have almost indistinguishable phenotypes and genotypes, and thus, identification by standard biochemical tests and 16S rRNA gene analysis is commonly inaccurate. Biochemical profiling and sequence analysis of additional topA and mreB housekeeping genes were carried out for definitive identification of 19 bacterial isolates recovered from sick and wild COTS. For 8 isolates, biochemical profiles and topA and mreB gene sequence alignments with the closest relatives (GenBank) confirmed previous 16S rRNA-based identification: V. fortis and Photobacterium eurosenbergii species (from wild COTS), and V natriegens (from diseased COTS). Further phylogenetic analysis based on topA and mreB concatenated sequences served to identify the remaining 11 V harveyi-like isolates: V. owensii and V. rotiferianus (from wild COTS), and V. owensii, V. rotiferianus, and V. harveyi (from diseased COTS). This study further confirms the reliability of topA-mreB gene sequence analysis for identification of these close species, and it reveals a wider distribution range of the potentially pathogenic V. harveyi group.

  18. Genetic relatedness of Brazilian Colletotrichum truncatum isolates assessed by vegetative compatibility groups and RAPD analysis.

    PubMed

    Sant'Anna, Juliane R; Miyamoto, Cláudia T; Rosada, Lúcia J; Franco, Claudinéia C S; Kaneshima, Edilson N; Castro-Prado, Marialba A A

    2010-01-01

    The genetic variation among nine soybean-originating isolates of Colletotrichum truncatum from different Brazilian states was studied. Nitrate non-utilizing (nit) mutants were obtained with potassium chlorate and used to characterize vegetative compatibility reactions, heterokaryosis and RAPD profile. Based on pairings of nit mutants from the different isolates, five vegetative complementation groups (VCG) were identified, and barriers to the formation of heterokaryons were observed among isolates derived from the same geographic area. No complementation was observed among any of the nit mutants recovered from the isolate A, which was designed heterokaryon-self-incompatible. Based on RAPD analysis, a polymorphism was detected among the wild isolate C and their nit1 and NitM mutants. RAPD amplification, with five different primers, also showed polymorphic profiles among Brazilian C. truncatum isolates. Dendrogram analysis resulted in a similarity degree ranging between 0.331 and 0.882 among isolates and identified three RAPD groups. Despite the lack of a correlation between the RAPD analysis and the vegetative compatibility grouping, results demonstrated the potential of VCG analysis to differentiate C. truncatum isolates genotypically similar when compared by RAPD.

  19. Comparative analysis of inflamed and non-inflamed colon biopsies reveals strong proteomic inflammation profile in patients with ulcerative colitis

    PubMed Central

    2012-01-01

    Background Accurate diagnostic and monitoring tools for ulcerative colitis (UC) are missing. Our aim was to describe the proteomic profile of UC and search for markers associated with disease exacerbation. Therefore, we aimed to characterize specific proteins associated with inflamed colon mucosa from patients with acute UC using mass spectrometry-based proteomic analysis. Methods Biopsies were sampled from rectum, sigmoid colon and left colonic flexure from twenty patients with active proctosigmoiditis and from four healthy controls for proteomics and histology. Proteomic profiles of whole colonic biopsies were characterized using 2D-gel electrophoresis, and peptide mass fingerprinting using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) was applied for identification of differently expressed protein spots. Results A total of 597 spots were annotated by image analysis and 222 of these had a statistically different protein level between inflamed and non-inflamed tissue in the patient group. Principal component analysis clearly grouped non-inflamed samples separately from the inflamed samples indicating that the proteomic signature of colon mucosa with acute UC is strong. Totally, 43 individual protein spots were identified, including proteins involved in energy metabolism (triosephosphate isomerase, glycerol-3-phosphate-dehydrogenase, alpha enolase and L-lactate dehydrogenase B-chain) and in oxidative stress (superoxide dismutase, thioredoxins and selenium binding protein). Conclusions A distinct proteomic profile of inflamed tissue in UC patients was found. Specific proteins involved in energy metabolism and oxidative stress were identified as potential candidate markers for UC. PMID:22726388

  20. Parallel mRNA, proteomics and miRNA expression analysis in cell line models of the intestine.

    PubMed

    O'Sullivan, Finbarr; Keenan, Joanne; Aherne, Sinead; O'Neill, Fiona; Clarke, Colin; Henry, Michael; Meleady, Paula; Breen, Laura; Barron, Niall; Clynes, Martin; Horgan, Karina; Doolan, Padraig; Murphy, Richard

    2017-11-07

    To identify miRNA-regulated proteins differentially expressed between Caco2 and HT-29: two principal cell line models of the intestine. Exponentially growing Caco-2 and HT-29 cells were harvested and prepared for mRNA, miRNA and proteomic profiling. mRNA microarray profiling analysis was carried out using the Affymetrix GeneChip Human Gene 1.0 ST array. miRNA microarray profiling analysis was carried out using the Affymetrix Genechip miRNA 3.0 array. Quantitative Label-free LC-MS/MS proteomic analysis was performed using a Dionex Ultimate 3000 RSLCnano system coupled to a hybrid linear ion trap/Orbitrap mass spectrometer. Peptide identities were validated in Proteome Discoverer 2.1 and were subsequently imported into Progenesis QI software for further analysis. Hierarchical cluster analysis for all three parallel datasets (miRNA, proteomics, mRNA) was conducted in the R software environment using the Euclidean distance measure and Ward's clustering algorithm. The prediction of miRNA and oppositely correlated protein/mRNA interactions was performed using TargetScan 6.1. GO biological process, molecular function and cellular component enrichment analysis was carried out for the DE miRNA, protein and mRNA lists via the Pathway Studio 11.3 Web interface using their Mammalian database. Differential expression (DE) profiling comparing the intestinal cell lines HT-29 and Caco-2 identified 1795 Genes, 168 Proteins and 160 miRNAs as DE between the two cell lines. At the gene level, 1084 genes were upregulated and 711 were downregulated in the Caco-2 cell line relative to the HT-29 cell line. At the protein level, 57 proteins were found to be upregulated and 111 downregulated in the Caco-2 cell line relative to the HT-29 cell line. Finally, at the miRNAs level, 104 were upregulated and 56 downregulated in the Caco-2 cell line relative to the HT-29 cell line. Gene ontology (GO) analysis of the DE mRNA identified cell adhesion, migration and ECM organization, cellular lipid and cholesterol metabolic processes, small molecule transport and a range of responses to external stimuli, while similar analysis of the DE protein list identified gene expression/transcription, epigenetic mechanisms, DNA replication, differentiation and translation ontology categories. The DE protein and gene lists were found to share 15 biological processes including for example epithelial cell differentiation [ P value ≤ 1.81613E-08 (protein list); P ≤ 0.000434311 (gene list)] and actin filament bundle assembly [ P value ≤ 0.001582797 (protein list); P ≤ 0.002733714 (gene list)]. Analysis was conducted on the three data streams acquired in parallel to identify targets undergoing potential miRNA translational repression identified 34 proteins, whose respective mRNAs were detected but no change in expression was observed. Of these 34 proteins, 27 proteins downregulated in the Caco-2 cell line relative to the HT-29 cell line and predicted to be targeted by 19 unique anti-correlated/upregulated microRNAs and 7 proteins upregulated in the Caco-2 cell line relative to the HT-29 cell line and predicted to be targeted by 15 unique anti-correlated/downregulated microRNAs. This first study providing "tri-omics" analysis of the principal intestinal cell line models Caco-2 and HT-29 has identified 34 proteins potentially undergoing miRNA translational repression.

  1. Parallel mRNA, proteomics and miRNA expression analysis in cell line models of the intestine

    PubMed Central

    O’Sullivan, Finbarr; Keenan, Joanne; Aherne, Sinead; O’Neill, Fiona; Clarke, Colin; Henry, Michael; Meleady, Paula; Breen, Laura; Barron, Niall; Clynes, Martin; Horgan, Karina; Doolan, Padraig; Murphy, Richard

    2017-01-01

    AIM To identify miRNA-regulated proteins differentially expressed between Caco2 and HT-29: two principal cell line models of the intestine. METHODS Exponentially growing Caco-2 and HT-29 cells were harvested and prepared for mRNA, miRNA and proteomic profiling. mRNA microarray profiling analysis was carried out using the Affymetrix GeneChip Human Gene 1.0 ST array. miRNA microarray profiling analysis was carried out using the Affymetrix Genechip miRNA 3.0 array. Quantitative Label-free LC-MS/MS proteomic analysis was performed using a Dionex Ultimate 3000 RSLCnano system coupled to a hybrid linear ion trap/Orbitrap mass spectrometer. Peptide identities were validated in Proteome Discoverer 2.1 and were subsequently imported into Progenesis QI software for further analysis. Hierarchical cluster analysis for all three parallel datasets (miRNA, proteomics, mRNA) was conducted in the R software environment using the Euclidean distance measure and Ward’s clustering algorithm. The prediction of miRNA and oppositely correlated protein/mRNA interactions was performed using TargetScan 6.1. GO biological process, molecular function and cellular component enrichment analysis was carried out for the DE miRNA, protein and mRNA lists via the Pathway Studio 11.3 Web interface using their Mammalian database. RESULTS Differential expression (DE) profiling comparing the intestinal cell lines HT-29 and Caco-2 identified 1795 Genes, 168 Proteins and 160 miRNAs as DE between the two cell lines. At the gene level, 1084 genes were upregulated and 711 were downregulated in the Caco-2 cell line relative to the HT-29 cell line. At the protein level, 57 proteins were found to be upregulated and 111 downregulated in the Caco-2 cell line relative to the HT-29 cell line. Finally, at the miRNAs level, 104 were upregulated and 56 downregulated in the Caco-2 cell line relative to the HT-29 cell line. Gene ontology (GO) analysis of the DE mRNA identified cell adhesion, migration and ECM organization, cellular lipid and cholesterol metabolic processes, small molecule transport and a range of responses to external stimuli, while similar analysis of the DE protein list identified gene expression/transcription, epigenetic mechanisms, DNA replication, differentiation and translation ontology categories. The DE protein and gene lists were found to share 15 biological processes including for example epithelial cell differentiation [P value ≤ 1.81613E-08 (protein list); P ≤ 0.000434311 (gene list)] and actin filament bundle assembly [P value ≤ 0.001582797 (protein list); P ≤ 0.002733714 (gene list)]. Analysis was conducted on the three data streams acquired in parallel to identify targets undergoing potential miRNA translational repression identified 34 proteins, whose respective mRNAs were detected but no change in expression was observed. Of these 34 proteins, 27 proteins downregulated in the Caco-2 cell line relative to the HT-29 cell line and predicted to be targeted by 19 unique anti-correlated/upregulated microRNAs and 7 proteins upregulated in the Caco-2 cell line relative to the HT-29 cell line and predicted to be targeted by 15 unique anti-correlated/downregulated microRNAs. CONCLUSION This first study providing “tri-omics” analysis of the principal intestinal cell line models Caco-2 and HT-29 has identified 34 proteins potentially undergoing miRNA translational repression. PMID:29151691

  2. The Role of Vitamin D in the Transcriptional Program of Human Pregnancy

    PubMed Central

    Al-Garawi, Amal; Carey, Vincent J.; Chhabra, Divya; Morrow, Jarrett; Lasky-Su, Jessica; Qiu, Weiliang; Laranjo, Nancy; Litonjua, Augusto A.; Weiss, Scott T.

    2016-01-01

    Background Patterns of gene expression of human pregnancy are poorly understood. In a trial of vitamin D supplementation in pregnant women, peripheral blood transcriptomes were measured longitudinally on 30 women and used to characterize gene co-expression networks. Objective Studies suggest that increased maternal Vitamin D levels may reduce the risk of asthma in early life, yet the underlying mechanisms have not been examined. In this study, we used a network-based approach to examine changes in gene expression profiles during the course of normal pregnancy and evaluated their association with maternal Vitamin D levels. Design The VDAART study is a randomized clinical trial of vitamin D supplementation in pregnancy for reduction of pediatric asthma risk. The trial enrolled 881 women at 10–18 weeks of gestation. Longitudinal gene expression measures were obtained on thirty pregnant women, using RNA isolated from peripheral blood samples obtained in the first and third trimesters. Differentially expressed genes were identified using significance of analysis of microarrays (SAM), and clustered using a weighted gene co-expression network analysis (WGCNA). Gene-set enrichment was performed to identify major biological pathways. Results Comparison of transcriptional profiles between first and third trimesters of pregnancy identified 5839 significantly differentially expressed genes (FDR<0.05). Weighted gene co-expression network analysis clustered these transcripts into 14 co-expression modules of which two showed significant correlation with maternal vitamin D levels. Pathway analysis of these two modules revealed genes enriched in immune defense pathways and extracellular matrix reorganization as well as genes enriched in notch signaling and transcription factor networks. Conclusion Our data show that gene expression profiles of healthy pregnant women change during the course of pregnancy and suggest that maternal Vitamin D levels influence transcriptional profiles. These alterations of the maternal transcriptome may contribute to fetal immune imprinting and reduce allergic sensitization in early life. Trial Registration clinicaltrials.gov NCT00920621 PMID:27711190

  3. Metabolic Profiles of Obesity in American Indians: The Strong Heart Family Study.

    PubMed

    Zhao, Qi; Zhu, Yun; Best, Lyle G; Umans, Jason G; Uppal, Karan; Tran, ViLinh T; Jones, Dean P; Lee, Elisa T; Howard, Barbara V; Zhao, Jinying

    2016-01-01

    Obesity is a typical metabolic disorder resulting from the imbalance between energy intake and expenditure. American Indians suffer disproportionately high rates of obesity and diabetes. The goal of this study is to identify metabolic profiles of obesity in 431 normoglycemic American Indians participating in the Strong Heart Family Study. Using an untargeted liquid chromatography-mass spectrometry, we detected 1,364 distinct m/z features matched to known compounds in the current metabolomics databases. We conducted multivariate analysis to identify metabolic profiles for obesity, adjusting for standard obesity indicators. After adjusting for covariates and multiple testing, five metabolites were associated with body mass index and seven were associated with waist circumference. Of them, three were associated with both. Majority of the obesity-related metabolites belongs to lipids, e.g., fatty amides, sphingolipids, prenol lipids, and steroid derivatives. Other identified metabolites are amino acids or peptides. Of the nine identified metabolites, five metabolites (oleoylethanolamide, mannosyl-diinositol-phosphorylceramide, pristanic acid, glutamate, and kynurenine) have been previously implicated in obesity or its related pathways. Future studies are warranted to replicate these findings in larger populations or other ethnic groups.

  4. Metabolic Profiles of Obesity in American Indians: The Strong Heart Family Study

    PubMed Central

    Best, Lyle G.; Umans, Jason G.; Uppal, Karan; Tran, ViLinh T.; Jones, Dean P.; Lee, Elisa T.; Howard, Barbara V.; Zhao, Jinying

    2016-01-01

    Obesity is a typical metabolic disorder resulting from the imbalance between energy intake and expenditure. American Indians suffer disproportionately high rates of obesity and diabetes. The goal of this study is to identify metabolic profiles of obesity in 431 normoglycemic American Indians participating in the Strong Heart Family Study. Using an untargeted liquid chromatography–mass spectrometry, we detected 1,364 distinct m/z features matched to known compounds in the current metabolomics databases. We conducted multivariate analysis to identify metabolic profiles for obesity, adjusting for standard obesity indicators. After adjusting for covariates and multiple testing, five metabolites were associated with body mass index and seven were associated with waist circumference. Of them, three were associated with both. Majority of the obesity-related metabolites belongs to lipids, e.g., fatty amides, sphingolipids, prenol lipids, and steroid derivatives. Other identified metabolites are amino acids or peptides. Of the nine identified metabolites, five metabolites (oleoylethanolamide, mannosyl-diinositol-phosphorylceramide, pristanic acid, glutamate, and kynurenine) have been previously implicated in obesity or its related pathways. Future studies are warranted to replicate these findings in larger populations or other ethnic groups. PMID:27434237

  5. Dietary pattern as identified by factorial analysis and its association with lipid profile and fasting plasma glucose among Iranian individuals with spinal cord injury.

    PubMed

    Sabour, Hadis; Soltani, Zahra; Latifi, Sahar; Javidan, Abbas Norouzi

    2016-07-01

    Plasma lipids (triglyceride (TG), total cholesterol (TC), high-density lipoprotein (HDL-C) and low-density lipoprotein (LDL-C)) may be associated with dietary intakes. The purpose of this study was to identify the most common food patterns among Iranian persons with spinal cord injury (SCI) and investigate their associations with lipid profile. Cross-sectional. Tertiary rehabilitation center. Referred individuals to Brain and Spinal Injury Research Center (BASIR) from 2011 to 2014. Dietary intakes were assessed by 24-hour dietary recall interviews in three non-consecutive days. Principal component analysis (PCA) was used to identify dietary patterns. Total of 100 persons (83 male and 17 female) entered the study. Four food patterns were detected. The most common dietary pattern (Pattern 1) included processed meat, sweets desserts and soft drink and was similar to 'Western' food pattern described previously. Pattern 1 was related to higher levels of TC and LDL-C (r = 0.09; P = 0.04 and r = 0.11; P = 0.03 for TC and LDL-C, respectively) only in male participants. Pattern 2 which included tea, nuts, vegetable oil and sugars had a positive association with TC level (r = 0.11; P = 0.02) again in male participants. Pattern 3 which represented a healthy food pattern showed no significant influence on lipid profiles. In this study, the four most common dietary patterns among Iranian individuals with SCI have been identified. Western food pattern was the most common diet and was associated with increased TC and LDL-C. The healthy food pattern, in which the major source of calories was protein, was not associated with variance in lipid profile.

  6. Body Mass Index Is Better than Other Anthropometric Indices for Identifying Dyslipidemia in Chinese Children with Obesity

    PubMed Central

    Jing, Jin; Ma, Jun; Chen, Yajun; Li, Xiuhong; Yang, Wenhan; Guo, Li; Jin, Yu

    2016-01-01

    Background Body mass index (BMI), waist circumference (WC), and waist-to-hip ratio (WHR) are used in screening and predicting obesity in adults. However, the best identifier of metabolic complications in children with obesity remains unclear. This study evaluated lipid profile distribution and investigated the best anthropometric parameter in association with lipid disorders in children with obesity. Methods A total of 2243 school children aged 7–17 years were enrolled in Guangzhou, China, in 2014. The anthropometric indices and lipid profiles were measured. Dyslipidemia was defined according to the US Guidelines for Cardiovascular Health and Risk Reduction in Children and Adolescents. The association between anthropometry (BMI, WC, and WHR) and lipid profile values was examined using chi-square analysis and discriminant function analysis. Information about demography, physical activity, and dietary intake was provided by the participant children and their parents. Results Children aged 10–14 and 15–17 years old generally had higher triglyceride values but lower median concentration of total cholesterol, high-density lipoprotein cholesterol, and low-density lipoprotein cholesterol compared with children aged 7–9 years old (all P < 0.001). These lipid parameters fluctuated in children aged 10–14 years old. The combination of age groups, BMI, WC and WHR achieved 65.1% accuracy in determining dyslipidemic disorders. BMI correctly identified 77% of the total dyslipidemic disorders in obese children, which was higher than that by WHR (70.8%) (P< 0.05). Conclusion The distribution of lipid profiles in Chinese children differed between younger and older age groups, and the tendency of these lipid levels remarkably fluctuated during 10 to 14 years old. BMI had better practical utility in identifying dyslipidemia among school-aged children with obesity compared with other anthropometric measures. PMID:26963377

  7. Body Mass Index Is Better than Other Anthropometric Indices for Identifying Dyslipidemia in Chinese Children with Obesity.

    PubMed

    Zhu, Yanna; Shao, Zixian; Jing, Jin; Ma, Jun; Chen, Yajun; Li, Xiuhong; Yang, Wenhan; Guo, Li; Jin, Yu

    2016-01-01

    Body mass index (BMI), waist circumference (WC), and waist-to-hip ratio (WHR) are used in screening and predicting obesity in adults. However, the best identifier of metabolic complications in children with obesity remains unclear. This study evaluated lipid profile distribution and investigated the best anthropometric parameter in association with lipid disorders in children with obesity. A total of 2243 school children aged 7-17 years were enrolled in Guangzhou, China, in 2014. The anthropometric indices and lipid profiles were measured. Dyslipidemia was defined according to the US Guidelines for Cardiovascular Health and Risk Reduction in Children and Adolescents. The association between anthropometry (BMI, WC, and WHR) and lipid profile values was examined using chi-square analysis and discriminant function analysis. Information about demography, physical activity, and dietary intake was provided by the participant children and their parents. Children aged 10-14 and 15-17 years old generally had higher triglyceride values but lower median concentration of total cholesterol, high-density lipoprotein cholesterol, and low-density lipoprotein cholesterol compared with children aged 7-9 years old (all P < 0.001). These lipid parameters fluctuated in children aged 10-14 years old. The combination of age groups, BMI, WC and WHR achieved 65.1% accuracy in determining dyslipidemic disorders. BMI correctly identified 77% of the total dyslipidemic disorders in obese children, which was higher than that by WHR (70.8%) (P< 0.05). The distribution of lipid profiles in Chinese children differed between younger and older age groups, and the tendency of these lipid levels remarkably fluctuated during 10 to 14 years old. BMI had better practical utility in identifying dyslipidemia among school-aged children with obesity compared with other anthropometric measures.

  8. Profiles of Intrinsic and Extrinsic Motivations in Elementary School: A Longitudinal Analysis

    ERIC Educational Resources Information Center

    Corpus, Jennifer Henderlong; Wormington, Stephanie V.

    2014-01-01

    The authors used a person-centered, longitudinal approach to identify and evaluate naturally occurring combinations of intrinsic and extrinsic motivations among 490 third- through fifth-grade students. Cluster analysis revealed 3 groups, characterized by high levels of both motivations ("high quantity"): high intrinsic motivation but low…

  9. Criminal profiling as expert witness evidence: The implications of the profiler validity research.

    PubMed

    Kocsis, Richard N; Palermo, George B

    The use and development of the investigative tool colloquially known as criminal profiling has steadily increased over the past five decades throughout the world. Coupled with this growth has been a diversification in the suggested range of applications for this technique. Possibly the most notable of these has been the attempted transition of the technique from a tool intended to assist police investigations into a form of expert witness evidence admissible in legal proceedings. Whilst case law in various jurisdictions has considered with mutual disinclination the evidentiary admissibility of criminal profiling, a disjunction has evolved between these judicial examinations and the scientifically vetted research testing the accuracy (i.e., validity) of the technique. This article offers an analysis of the research directly testing the validity of the criminal profiling technique and the extant legal principles considering its evidentiary admissibility. This analysis reveals that research findings concerning the validity of criminal profiling are surprisingly compatible with the extant legal principles. The overall conclusion is that a discrete form of crime behavioural analysis is supported by the profiler validity research and could be regarded as potentially admissible expert witness evidence. Finally, a number of theoretical connections are also identified concerning the skills and qualifications of individuals who may feasibly provide such expert testimony. Copyright © 2016 Elsevier Ltd. All rights reserved.

  10. Tuberculosis patients co-infected with Mycobacterium bovis and Mycobacterium tuberculosis in an urban area of Brazil.

    PubMed

    Silva, Marcio Roberto; Rocha, Adalgiza da Silva; da Costa, Ronaldo Rodrigues; de Alencar, Andrea Padilha; de Oliveira, Vania Maria; Fonseca Júnior, Antônio Augusto; Sales, Mariana Lázaro; Issa, Marina de Azevedo; Filho, Paulo Martins Soares; Pereira, Omara Tereza Vianello; dos Santos, Eduardo Calazans; Mendes, Rejane Silva; Ferreira, Angela Maria de Jesus; Mota, Pedro Moacyr Pinto Coelho; Suffys, Philip Noel; Guimarães, Mark Drew Crosland

    2013-05-01

    In this cross-sectional study, mycobacteria specimens from 189 tuberculosis (TB) patients living in an urban area in Brazil were characterised from 2008-2010 using phenotypic and molecular speciation methods (pncA gene and oxyR pseudogene analysis). Of these samples, 174 isolates simultaneously grew on Löwenstein-Jensen (LJ) and Stonebrink (SB)-containing media and presented phenotypic and molecular profiles of Mycobacterium tuberculosis, whereas 12 had molecular profiles of M. tuberculosis based on the DNA analysis of formalin-fixed paraffin wax-embedded tissue samples (paraffin blocks). One patient produced two sputum isolates, the first of which simultaneously grew on LJ and SB media and presented phenotypic and molecular profiles of M. tuberculosis, and the second of which only grew on SB media and presented phenotypic profiles of Mycobacterium bovis. One patient provided a bronchial lavage isolate, which simultaneously grew on LJ and SB media and presented phenotypic and molecular profiles of M. tuberculosis, but had molecular profiles of M. bovis from paraffin block DNA analysis, and one sample had molecular profiles of M. tuberculosis and M. bovis identified from two distinct paraffin blocks. Moreover, we found a low prevalence (1.6%) of M. bovis among these isolates, which suggests that local health service procedures likely underestimate its real frequency and that it deserves more attention from public health officials.

  11. Obesogenic family types identified through latent profile analysis.

    PubMed

    Martinson, Brian C; VazquezBenitez, Gabriela; Patnode, Carrie D; Hearst, Mary O; Sherwood, Nancy E; Parker, Emily D; Sirard, John; Pasch, Keryn E; Lytle, Leslie

    2011-10-01

    Obesity may cluster in families due to shared physical and social environments. This study aims to identify family typologies of obesity risk based on family environments. Using 2007-2008 data from 706 parent/youth dyads in Minnesota, we applied latent profile analysis and general linear models to evaluate associations between family typologies and body mass index (BMI) of youth and parents. Three typologies described most families with 18.8% "Unenriched/Obesogenic," 16.9% "Risky Consumer," and 64.3% "Healthy Consumer/Salutogenic." After adjustment for demographic and socioeconomic factors, parent BMI and youth BMI Z-scores were higher in unenriched/obesogenic families (BMI difference = 2.7, p < 0.01 and BMI Z-score difference = 0.51, p < 0.01, respectively) relative to the healthy consumer/salutogenic typology. In contrast, parent BMI and youth BMI Z-scores were similar in the risky consumer families relative to those in healthy consumer/salutogenic type. We can identify family types differing in obesity risks with implications for public health interventions.

  12. Transcriptome meta-analysis reveals common differential and global gene expression profiles in cystic fibrosis and other respiratory disorders and identifies CFTR regulators.

    PubMed

    Clarke, Luka A; Botelho, Hugo M; Sousa, Lisete; Falcao, Andre O; Amaral, Margarida D

    2015-11-01

    A meta-analysis of 13 independent microarray data sets was performed and gene expression profiles from cystic fibrosis (CF), similar disorders (COPD: chronic obstructive pulmonary disease, IPF: idiopathic pulmonary fibrosis, asthma), environmental conditions (smoking, epithelial injury), related cellular processes (epithelial differentiation/regeneration), and non-respiratory "control" conditions (schizophrenia, dieting), were compared. Similarity among differentially expressed (DE) gene lists was assessed using a permutation test, and a clustergram was constructed, identifying common gene markers. Global gene expression values were standardized using a novel approach, revealing that similarities between independent data sets run deeper than shared DE genes. Correlation of gene expression values identified putative gene regulators of the CF transmembrane conductance regulator (CFTR) gene, of potential therapeutic significance. Our study provides a novel perspective on CF epithelial gene expression in the context of other lung disorders and conditions, and highlights the contribution of differentiation/EMT and injury to gene signatures of respiratory disease. Copyright © 2015 Elsevier Inc. All rights reserved.

  13. Molecular events of apical bud formation in white spruce, Picea glauca.

    PubMed

    El Kayal, Walid; Allen, Carmen C G; Ju, Chelsea J-T; Adams, Eri; King-Jones, Susanne; Zaharia, L Irina; Abrams, Suzanne R; Cooke, Janice E K

    2011-03-01

    Bud formation is an adaptive trait that temperate forest trees have acquired to facilitate seasonal synchronization. We have characterized transcriptome-level changes that occur during bud formation of white spruce [Picea glauca (Moench) Voss], a primarily determinate species in which preformed stem units contained within the apical bud constitute most of next season's growth. Microarray analysis identified 4460 differentially expressed sequences in shoot tips during short day-induced bud formation. Cluster analysis revealed distinct temporal patterns of expression, and functional classification of genes in these clusters implied molecular processes that coincide with anatomical changes occurring in the developing bud. Comparing expression profiles in developing buds under long day and short day conditions identified possible photoperiod-responsive genes that may not be essential for bud development. Several genes putatively associated with hormone signalling were identified, and hormone quantification revealed distinct profiles for abscisic acid (ABA), cytokinins, auxin and their metabolites that can be related to morphological changes to the bud. Comparison of gene expression profiles during bud formation in different tissues revealed 108 genes that are differentially expressed only in developing buds and show greater transcript abundance in developing buds than other tissues. These findings provide a temporal roadmap of bud formation in white spruce. © 2011 Blackwell Publishing Ltd.

  14. Dlx1 and Rgs5 in the Ductus Arteriosus: Vessel-Specific Genes Identified by Transcriptional Profiling of Laser-Capture Microdissected Endothelial and Smooth Muscle Cells

    PubMed Central

    Bökenkamp, Regina; van Brempt, Ronald; van Munsteren, Jacoba Cornelia; van den Wijngaert, Ilse; de Hoogt, Ronald; Finos, Livio; Goeman, Jelle; Groot, Adriana Cornelia Gittenberger-de; Poelmann, Robert Eugen; Blom, Nicolaas Andreas; DeRuiter, Marcus Cornelis

    2014-01-01

    Closure of the ductus arteriosus (DA) is a crucial step in the transition from fetal to postnatal life. Patent DA is one of the most common cardiovascular anomalies in children with significant clinical consequences especially in premature infants. We aimed to identify genes that specify the DA in the fetus and differentiate it from the aorta. Comparative microarray analysis of laser-captured microdissected endothelial (ECs) and vascular smooth muscle cells (SMCs) from the DA and aorta of fetal rats (embryonic day 18 and 21) identified vessel-specific transcriptional profiles. We found a strong age-dependency of gene expression. Among the genes that were upregulated in the DA the regulator of the G-protein coupled receptor 5 (Rgs5) and the transcription factor distal-less homeobox 1 (Dlx1) exhibited the highest and most significant level of differential expression. The aorta showed a significant preferential expression of the Purkinje cell protein 4 (Pcp4) gene. The results of the microarray analysis were validated by real-time quantitative PCR and immunohistochemistry. Our study confirms vessel-specific transcriptional profiles in ECs and SMCs of rat DA and aorta. Rgs5 and Dlx1 represent novel molecular targets for the regulation of DA maturation and closure. PMID:24489801

  15. Identifying technical aliases in SELDI mass spectra of complex mixtures of proteins

    PubMed Central

    2013-01-01

    Background Biomarker discovery datasets created using mass spectrum protein profiling of complex mixtures of proteins contain many peaks that represent the same protein with different charge states. Correlated variables such as these can confound the statistical analyses of proteomic data. Previously we developed an algorithm that clustered mass spectrum peaks that were biologically or technically correlated. Here we demonstrate an algorithm that clusters correlated technical aliases only. Results In this paper, we propose a preprocessing algorithm that can be used for grouping technical aliases in mass spectrometry protein profiling data. The stringency of the variance allowed for clustering is customizable, thereby affecting the number of peaks that are clustered. Subsequent analysis of the clusters, instead of individual peaks, helps reduce difficulties associated with technically-correlated data, and can aid more efficient biomarker identification. Conclusions This software can be used to pre-process and thereby decrease the complexity of protein profiling proteomics data, thus simplifying the subsequent analysis of biomarkers by decreasing the number of tests. The software is also a practical tool for identifying which features to investigate further by purification, identification and confirmation. PMID:24010718

  16. Classification of juices and fermented beverages made from unripe, ripe and senescent apples based on the aromatic profile using chemometrics.

    PubMed

    Braga, Cíntia Maia; Zielinski, Acácio Antonio Ferreira; Silva, Karolline Marques da; de Souza, Frederico Koch Fernandes; Pietrowski, Giovana de Arruda Moura; Couto, Marcelo; Granato, Daniel; Wosiacki, Gilvan; Nogueira, Alessandro

    2013-11-15

    The aim of this study was to assess differences between apple juices and fermented apple beverages elaborated with fruits from different varieties and at different ripening stages in the aroma profile by using chemometrics. Ripening influenced the aroma composition of the apple juice and fermented apple. For all varieties, senescent fruits provided more aromatic fermented apple beverages. However, no significant difference was noticed in samples made of senescent or ripe fruits of the Lisgala variety. Regarding the juices, ripe Gala apple had the highest total aroma concentration. Ethanal was the major compound identified in all the samples, with values between 11.83mg/L (unripe Lisgala juice) and 81.05mg/L (ripe Gala juice). 3-Methyl-1-butanol was the major compound identified in the fermented juices. Principal component analysis (PCA) and hierarchical cluster analysis (HCA) were applied and classified the juices and fermented juices based on physicochemical and aroma profile, demonstrating their applicability as tools to monitor the quality of apple-based products. Copyright © 2013 Elsevier Ltd. All rights reserved.

  17. Coping profiles, perceived stress and health-related behaviors: a cluster analysis approach.

    PubMed

    Doron, Julie; Trouillet, Raphael; Maneveau, Anaïs; Ninot, Grégory; Neveu, Dorine

    2015-03-01

    Using cluster analytical procedure, this study aimed (i) to determine whether people could be differentiated on the basis of coping profiles (or unique combinations of coping strategies); and (ii) to examine the relationships between these profiles and perceived stress and health-related behaviors. A sample of 578 French students (345 females, 233 males; M(age)= 21.78, SD(age)= 2.21) completed the Perceived Stress Scale-14 ( Bruchon-Schweitzer, 2002), the Brief COPE ( Muller and Spitz, 2003) and a series of items measuring health-related behaviors. A two-phased cluster analytic procedure (i.e. hierarchical and non-hierarchical-k-means) was employed to derive clusters of coping strategy profiles. The results yielded four distinctive coping profiles: High Copers, Adaptive Copers, Avoidant Copers and Low Copers. The results showed that clusters differed significantly in perceived stress and health-related behaviors. High Copers and Avoidant Copers displayed higher levels of perceived stress and engaged more in unhealthy behavior, compared with Adaptive Copers and Low Copers who reported lower levels of stress and engaged more in healthy behaviors. These findings suggested that individuals' relative reliance on some strategies and de-emphasis on others may be a more advantageous way of understanding the manner in which individuals cope with stress. Therefore, cluster analysis approach may provide an advantage over more traditional statistical techniques by identifying distinct coping profiles that might best benefit from interventions. Future research should consider coping profiles to provide a deeper understanding of the relationships between coping strategies and health outcomes and to identify risk groups. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  18. Global Membrane Protein Interactome Analysis using In vivo Crosslinking and Mass Spectrometry-based Protein Correlation Profiling*

    PubMed Central

    Larance, Mark; Kirkwood, Kathryn J.; Tinti, Michele; Brenes Murillo, Alejandro; Ferguson, Michael A. J.; Lamond, Angus I.

    2016-01-01

    We present a methodology using in vivo crosslinking combined with HPLC-MS for the global analysis of endogenous protein complexes by protein correlation profiling. Formaldehyde crosslinked protein complexes were extracted with high yield using denaturing buffers that maintained complex solubility during chromatographic separation. We show this efficiently detects both integral membrane and membrane-associated protein complexes,in addition to soluble complexes, allowing identification and analysis of complexes not accessible in native extracts. We compare the protein complexes detected by HPLC-MS protein correlation profiling in both native and formaldehyde crosslinked U2OS cell extracts. These proteome-wide data sets of both in vivo crosslinked and native protein complexes from U2OS cells are freely available via a searchable online database (www.peptracker.com/epd). Raw data are also available via ProteomeXchange (identifier PXD003754). PMID:27114452

  19. A transcriptional profile of the decidua in preeclampsia

    PubMed Central

    LØSET, Mari; MUNDAL, Siv B.; JOHNSON, Matthew P.; FENSTAD, Mona H.; FREED, Katherine A.; LIAN, Ingrid A.; EIDE, Irina P.; BJØRGE, Line; BLANGERO, John; MOSES, Eric K.; AUSTGULEN, Rigmor

    2010-01-01

    OBJECTIVE To obtain insight into possible mechanisms underlying preeclampsia using genome-wide transcriptional profiling in decidua basalis. STUDY DESIGN Genome-wide transcriptional profiling was performed on decidua basalis tissue from preeclamptic (n = 37) and normal pregnancies (n = 58). Differentially expressed genes were identified and merged into canonical pathways and networks. RESULTS Of the 26,504 expressed transcripts detected, 455 were differentially expressed (P <0.05, FDR P <0.1). Both novel (ARL5B, SLITRK4) and previously reported preeclampsia-associated genes (PLA2G7, HMOX1) were identified. Pathway analysis revealed that ‘tryptophan metabolism’, ‘endoplasmic reticulum stress’, ‘linoleic acid metabolism’, ‘notch signaling’, ‘fatty acid metabolism’, ‘arachidonic acid metabolism’ and ‘NRF2-mediated oxidative stress response’ were overrepresented canonical pathways. CONCLUSION In the present study single genes, canonical pathways and gene-gene networks that are likely to play an important role in the pathogenesis of preeclampsia, have been identified. Future functional studies are needed to accomplish a greater understanding of the mechanisms involved. PMID:20934677

  20. Single-cell multimodal profiling reveals cellular epigenetic heterogeneity.

    PubMed

    Cheow, Lih Feng; Courtois, Elise T; Tan, Yuliana; Viswanathan, Ramya; Xing, Qiaorui; Tan, Rui Zhen; Tan, Daniel S W; Robson, Paul; Loh, Yuin-Han; Quake, Stephen R; Burkholder, William F

    2016-10-01

    Sample heterogeneity often masks DNA methylation signatures in subpopulations of cells. Here, we present a method to genotype single cells while simultaneously interrogating gene expression and DNA methylation at multiple loci. We used this targeted multimodal approach, implemented on an automated, high-throughput microfluidic platform, to assess primary lung adenocarcinomas and human fibroblasts undergoing reprogramming by profiling epigenetic variation among cell types identified through genotyping and transcriptional analysis.

  1. Molecular Targeted Therapies of Childhood Choroid Plexus Carcinoma

    DTIC Science & Technology

    2011-10-01

    were analyzed in PGS, using the benign human choroid plexus papilloma (CPP) samples as an expression baseline reference. This analysis highlights...Task 1: Generation of additional human and mouse CPC genomic profiles (timeframe: months 1-5). The goal of these studies is to expand our...number of genomic profiles (DNA and mRNA arrays) of both human and mouse CPCs to provide a comprehensive dataset with which to identify key candidate

  2. Molecular profiling identifies prognostic markers of stage IA lung adenocarcinoma.

    PubMed

    Zhang, Jie; Shao, Jinchen; Zhu, Lei; Zhao, Ruiying; Xing, Jie; Wang, Jun; Guo, Xiaohui; Tu, Shichun; Han, Baohui; Yu, Keke

    2017-09-26

    We previously showed that different pathologic subtypes were associated with different prognostic values in patients with stage IA lung adenocarcinoma (AC). We hypothesize that differential gene expression profiles of different subtypes may be valuable factors for prognosis in stage IA lung adenocarcinoma. We performed microarray gene expression profiling on tumor tissues micro-dissected from patients with acinar and solid predominant subtypes of stage IA lung adenocarcinoma. These patients had undergone a lobectomy and mediastinal lymph node dissection at the Shanghai Chest Hospital, Shanghai, China in 2012. No patient had preoperative treatment. We performed the Gene Set Enrichment Analysis (GSEA) analysis to look for gene expression signatures associated with tumor subtypes. The histologic subtypes of all patients were classified according to the 2015 WHO lung Adenocarcinoma classification. We found that patients with the solid predominant subtype are enriched for genes involved in RNA polymerase activity as well as inactivation of the p53 pathway. Further, we identified a list of genes that may serve as prognostic markers for stage IA lung adenocarcinoma. Validation in the TCGA database shows that these genes are correlated with survival, suggesting that they are novel prognostic factors for stage IA lung adenocarcinoma. In conclusion, we have uncovered novel prognostic factors for stage IA lung adenocarcinoma using gene expression profiling in combination with histopathology subtyping.

  3. HS-GC/MS volatile profile of different varieties of garlic and their behavior under heating.

    PubMed

    Molina-Calle, María; Priego-Capote, Feliciano; de Castro, María D Luque

    2016-05-01

    Garlic is one of the most used seasonings in the world whose beneficial health effects, mainly ascribed to organosulfur compounds, are shared with the rest of the Allium family. The fact that many of these compounds are volatile makes the evaluation of the volatile profile of garlic interesting. For this purpose, three garlic varieties-White, Purple, and Chinese-cultivated in the South of Spain were analyzed by a method based on a headspace (HS) device coupled to a gas chromatograph and mass detector (HS-GC/MS). The main temperatures in the HS were optimized to achieve the highest concentration of volatiles. A total number of 45 volatiles were tentatively identified (among them 17 were identified for the first time in garlic); then, all were classified, also for the first time, and their relative concentration in three garlic varieties was used to evaluate differences among them and to study their profiles according to the heating time. Chinese garlic was found to be the richest variety in sulfur volatiles, while the three varieties presented a similar trend under preset heating times allowing differentiation between varieties and heating time using principal component analysis. Graphical Abstract HS-GC/MS analysis of the volatile profile of garlic.

  4. Exploring Game Performance in the National Basketball Association Using Player Tracking Data

    PubMed Central

    Calleja-González, Julio; Jiménez Sáiz, Sergio; Schelling i del Alcázar, Xavi; Balciunas, Mindaugas

    2015-01-01

    Recent player tracking technology provides new information about basketball game performance. The aim of this study was to (i) compare the game performances of all-star and non all-star basketball players from the National Basketball Association (NBA), and (ii) describe the different basketball game performance profiles based on the different game roles. Archival data were obtained from all 2013-2014 regular season games (n = 1230). The variables analyzed included the points per game, minutes played and the game actions recorded by the player tracking system. To accomplish the first aim, the performance per minute of play was analyzed using a descriptive discriminant analysis to identify which variables best predict the all-star and non all-star playing categories. The all-star players showed slower velocities in defense and performed better in elbow touches, defensive rebounds, close touches, close points and pull-up points, possibly due to optimized attention processes that are key for perceiving the required appropriate environmental information. The second aim was addressed using a k-means cluster analysis, with the aim of creating maximal different performance profile groupings. Afterwards, a descriptive discriminant analysis identified which variables best predict the different playing clusters. The results identified different playing profile of performers, particularly related to the game roles of scoring, passing, defensive and all-round game behavior. Coaching staffs may apply this information to different players, while accounting for individual differences and functional variability, to optimize practice planning and, consequently, the game performances of individuals and teams. PMID:26171606

  5. Exploring Game Performance in the National Basketball Association Using Player Tracking Data.

    PubMed

    Sampaio, Jaime; McGarry, Tim; Calleja-González, Julio; Jiménez Sáiz, Sergio; Schelling I Del Alcázar, Xavi; Balciunas, Mindaugas

    2015-01-01

    Recent player tracking technology provides new information about basketball game performance. The aim of this study was to (i) compare the game performances of all-star and non all-star basketball players from the National Basketball Association (NBA), and (ii) describe the different basketball game performance profiles based on the different game roles. Archival data were obtained from all 2013-2014 regular season games (n = 1230). The variables analyzed included the points per game, minutes played and the game actions recorded by the player tracking system. To accomplish the first aim, the performance per minute of play was analyzed using a descriptive discriminant analysis to identify which variables best predict the all-star and non all-star playing categories. The all-star players showed slower velocities in defense and performed better in elbow touches, defensive rebounds, close touches, close points and pull-up points, possibly due to optimized attention processes that are key for perceiving the required appropriate environmental information. The second aim was addressed using a k-means cluster analysis, with the aim of creating maximal different performance profile groupings. Afterwards, a descriptive discriminant analysis identified which variables best predict the different playing clusters. The results identified different playing profile of performers, particularly related to the game roles of scoring, passing, defensive and all-round game behavior. Coaching staffs may apply this information to different players, while accounting for individual differences and functional variability, to optimize practice planning and, consequently, the game performances of individuals and teams.

  6. An examination of heavy drinking, depressed mood, drinking related constructs, and consequences among high-risk college students using a person-centered approach.

    PubMed

    Geisner, Irene M; Mallett, Kimberly; Varvil-Weld, Lindsey; Ackerman, Sarah; Trager, Bradley M; Turrisi, Rob

    2018-03-01

    Research has identified college students who experience depressed mood and consume alcohol are at an increased risk for experiencing alcohol problems. The present study identified profiles of differential alcohol use, depression, key psychosocial indicators of drinking (e.g., normative perceptions) and examined the relationship between these profiles and alcohol-related consequences. Students with a history of risky drinking and elevated depressed mood (n=311; 62.4% female) completed a web-based survey assessing typical and peak drinking, depressive symptoms, descriptive norms, drinking to cope motives, protective behavioral strategies, and alcohol-related consequences. Latent profile analysis was used to classify participants into distinct profiles focusing on alcohol use patterns and level of depressed mood and drinking related constructs. Profiles were then compared based on their association with reported rates of alcohol-related consequences. Four profiles emerged: 1) Mild Depression, Heavy Drinkers; 2) Mild Depression, Severe Drinkers; 3) Moderate Depression, Heavy Drinkers; and 4) Moderate Depression, Severe Drinkers. Findings revealed significant differences between the four profiles on both risky drinking and alcohol-related consequences. These findings suggest the importance of assessing and addressing depressive symptoms among college students in order to reduce rates of risky drinking and alcohol-related consequences. Copyright © 2017 Elsevier Ltd. All rights reserved.

  7. Kidney transplant patients' attitudes towards self-management support: A Q-methodological study.

    PubMed

    Grijpma, J W; Tielen, M; van Staa, A L; Maasdam, L; van Gelder, T; Berger, S P; Busschbach, J J; Betjes, M G H; Weimar, W; Massey, E K

    2016-05-01

    Kidney transplant recipients face many self-management challenges. We aimed to identify profiles of attitudes towards self-management support (SMS) shortly after kidney transplantation. Profiles were generated using Q-methodology: In face-to-face interviews participants rank-ordered opinion statements on aspects of SMS according to agreement. Socio-demographic and medical characteristics were assessed using a questionnaire. By-person factor analysis was used to analyze the rankings and qualitative data was used to support choice of profiles. The resulting factors represent clusters of patients with similar attitudes towards SMS. Forty-three patients (mean age=56; 77% male) participated. Four profiles were identified: (A) transplant-focused and obedient; (B) holistic and collaborative; (C) life-focused and self-determined; and (D) was bipolar. The positive pole (D+) minimalizing and disengaged and the negative pole (D-) coping-focused and needy represent opposing viewpoints within the same profile. Socio-demographic and medical characteristics were not related to profile membership. Each profile represents a specific attitude on post-transplant life, responsibility for health and decision-making, SMS needs, and preferences for SMS. Patients vary in their attitude, needs and preferences for SMS indicating the necessity of providing personalized support after kidney transplantation. Health professionals should explore patients' SMS needs and adapt support accordingly. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  8. Monitoring the ripening process of Cheddar cheese based on hydrophilic component profiling using gas chromatography-mass spectrometry.

    PubMed

    Ochi, H; Sakai, Y; Koishihara, H; Abe, F; Bamba, T; Fukusaki, E

    2013-01-01

    We proposed an application methodology that combines metabolic profiling with multiple appropriate multivariate analyses and verified it on the industrial scale of the ripening process of Cheddar cheese to make practical use of hydrophilic low-molecular-weight compound profiling using gas chromatography-mass spectrometry to design optimal conditions and quality monitoring of the cheese ripening process. Principal components analysis provided an overview of the effect of sodium chloride content and kind of lactic acid bacteria starter on the metabolic profile in the ripening process of Cheddar cheese and orthogonal partial least squares-discriminant analysis unveiled the difference in characteristic metabolites. When the sodium chloride contents were different (1.6 and 0.2%) but the same lactic acid bacteria starter was used, the 2 cheeses were classified by orthogonal partial least squares-discriminant analysis from their metabolic profiles, but were not given perfect discrimination. Not much difference existed in the metabolic profile between the 2 cheeses. Compounds including lactose, galactose, lactic acid, 4-aminobutyric acid, and phosphate were identified as contents that differed between the 2 cheeses. On the other hand, in the case of the same salt content of 1.6%, but different kinds of lactic acid bacteria starter, an excellent distinctive discrimination model was obtained, which showed that the difference of lactic acid bacteria starter caused an obvious difference in metabolic profiles. Compounds including lactic acid, lactose, urea, 4-aminobutyric acid, galactose, phosphate, proline, isoleucine, glycine, alanine, lysine, leucine, valine, and pyroglutamic acid were identified as contents that differed between the 2 cheeses. Then, a good sensory prediction model for "rich flavor," which was defined as "thick and rich, including umami taste and soy sauce-like flavor," was constructed based on the metabolic profile during ripening using partial least squares regression analysis. The amino acids proline, leucine, valine, isoleucine, pyroglutamic acid, alanine, glutamic acid, glycine, lysine, tyrosine, serine, phenylalanine, methionine, aspartic acid, and ornithine were extracted as ripening process markers. The present study is not limited to Cheddar cheese and can be applied to various maturation-type natural cheeses. This study provides the technical platform for designing optimal conditions and quality monitoring of the cheese ripening process. Copyright © 2013 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

  9. Protein profile in HBx transfected cells: a comparative iTRAQ-coupled 2D LC-MS/MS analysis.

    PubMed

    Feng, Huixing; Li, Xi; Niu, Dandan; Chen, Wei Ning

    2010-06-16

    The x protein of HBV (HBx) has been involved in the development of hepatocellular carcinoma (HCC), with a possible link to individual genotypes. Nevertheless, the underlying mechanism remains obscure. In this study, we aim to identify the HBx-induced protein profile in HepG2 cells by LC-MS/MS proteomics analysis. Our results indicated that proteins were differentially expressed in HepG2 cells transfected by HBx of various genotypes. Proteins associated with cytoskeleton were found to be either up-regulated (MACF1, HMGB1, Annexin A2) or down-regulated (Lamin A/C). These may in turn result in the decrease of focal adhesion and increase of cell migration in response to HBx. Levels of other cellular proteins with reported impact on the function of extracellular matrix (ECM) proteins and cell migration, including Ca(2+)-binding proteins (S100A11, S100A6, and S100A4) and proteasome protein (PSMA3), were affected by HBx. The differential protein profile identified in this study was also supported by our functional assay which indicated that cell migration was enhanced by HBx. Our preliminary study provided a new platform to establish a comprehensive cellular protein profile by LC-MS/MS proteomics analysis. Further downstream functional assays, including our reported cell migration assay, should provide new insights in the association between HCC and HBx. Copyright 2009 Elsevier B.V. All rights reserved.

  10. The integration of Information and Communication Technology into nursing.

    PubMed

    Lupiáñez-Villanueva, Francisco; Hardey, Michael; Torrent, Joan; Ficapal, Pilar

    2011-02-01

    To identify and characterise different profiles of nurses' utilization of Information and Communication Technology (ICT) and the Internet and to identify factors that can enhance or inhibit the use of these technologies within nursing. An online survey of the 13,588 members of the Nurses Association of Barcelona who had a registered email account in 2006 was carried out. Factor analysis, cluster analysis and binomial logit model was undertaken. Although most of the nurses (76.70%) are utilizing the Internet within their daily work, multivariate statistics analysis revealed two profiles of the adoption of ICT. The first profile (4.58%) represents those nurses who value ICT and the Internet so that it forms an integral part of their practice. This group is thus referred to as 'integrated nurses'. The second profile (95.42%) represents those nurses who place less emphasis on ICT and the Internet and are consequently labelled 'non-integrated nurses'. From the statistical modelling, it was observed that undertaking research activities an emphasis on international information and a belief that health information available on the Internet was 'very relevant' play a positive and significant role in the probability of being an integrated nurse. The emerging world of the 'integrated nurse' cannot be adequately understood without examining how nurses make use of ICT and the Internet within nursing practice and the way this is shaped by institutional, technical and professional opportunities and constraints. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

  11. Motivational Cluster Profiles of Adolescent Athletes: An Examination of Differences in Physical-Self Perception

    PubMed Central

    Çağlar, Emine; Aşçı, F. Hülya

    2010-01-01

    The primary purpose of the present study was to identify motivational profiles of adolescent athletes using cluster analysis in non-Western culture. A second purpose was to examine relationships between physical self-perception differences of adolescent athletes and motivational profiles. One hundred and thirty six male (Mage = 17.46, SD = 1.25 years) and 80 female adolescent athletes (Mage = 17.61, SD = 1.19 years) from a variety of team sports including basketball, soccer, volleyball, and handball volunteered to participate in this study. The Sport Motivation Scale (SMS) and Physical Self-Perception Profile (PSPP) were administered to all participants. Hierarchical cluster analysis revealed a four-cluster solution for this sample: amotivated, low motivated, moderate motivated, and highly motivated. A 4 x 5 (Cluster x PSPP Subscales) MANOVA revealed no significant main effect of motivational clusters on physical self-perception levels (p > 0.05). As a result, findings of the present study showed that motivational types of the adolescent athletes constituted four different motivational clusters. Highly and moderate motivated athletes consistently scored higher than amotivated athletes on the perceived sport competence, physical condition, and physical self-worth subscales of PSPP. This study identified motivational profiles of competitive youth-sport participants. Key points Highly motivated athletes have a tendency to perceive themselves competent in psychomotor domains as compared to the amotivated athletes As the athletes feel more competent in psychomotor domain, they are more intrinsically motivated. The information about motivational profiles of adolescent athletes could be used for developing strategies and interventions designed to improve the strength and quality of sport participants’ motivation. PMID:24149690

  12. Schizosaccharomyces pombe Polysome Profile Analysis and RNA Purification.

    PubMed

    Wolf, Dieter A; Bähler, Jürg; Wise, Jo Ann

    2017-04-03

    Polysome profile analysis is widely used by investigators studying the mechanism and regulation of translation. The method described here uses high-velocity centrifugation of whole cell extracts on linear sucrose gradients to separate 40S and 60S ribosomal subunits from 80S monosomes and polysomes. Cycloheximide is included in the lysis buffer to "freeze" polysomes by blocking translation. After centrifugation, the gradient is fractionated and RNA (and/or protein) is prepared from each fraction for subsequent analysis of individual species using northern or western blots. The entire RNA population in each fraction can be analyzed by hybridization to microarrays or by high-throughput RNA sequencing, and the proteins present can be identified by mass spectrometry analysis. © 2017 Cold Spring Harbor Laboratory Press.

  13. Differential analysis between somatic mutation and germline variation profiles reveals cancer-related genes.

    PubMed

    Przytycki, Pawel F; Singh, Mona

    2017-08-25

    A major aim of cancer genomics is to pinpoint which somatically mutated genes are involved in tumor initiation and progression. We introduce a new framework for uncovering cancer genes, differential mutation analysis, which compares the mutational profiles of genes across cancer genomes with their natural germline variation across healthy individuals. We present DiffMut, a fast and simple approach for differential mutational analysis, and demonstrate that it is more effective in discovering cancer genes than considerably more sophisticated approaches. We conclude that germline variation across healthy human genomes provides a powerful means for characterizing somatic mutation frequency and identifying cancer driver genes. DiffMut is available at https://github.com/Singh-Lab/Differential-Mutation-Analysis .

  14. An Agile Functional Analysis of Metagenomic Data Using SUPER-FOCUS.

    PubMed

    Silva, Genivaldo Gueiros Z; Lopes, Fabyano A C; Edwards, Robert A

    2017-01-01

    One of the main goals in metagenomics is to identify the functional profile of a microbial community from unannotated shotgun sequencing reads. Functional annotation is important in biological research because it enables researchers to identify the abundance of functional genes of the organisms present in the sample, answering the question, "What can the organisms in the sample do?" Most currently available approaches do not scale with increasing data volumes, which is important because both the number and lengths of the reads provided by sequencing platforms keep increasing. Here, we present SUPER-FOCUS, SUbsystems Profile by databasE Reduction using FOCUS, an agile homology-based approach using a reduced reference database to report the subsystems present in metagenomic datasets and profile their abundances. SUPER-FOCUS was tested with real metagenomes, and the results show that it accurately predicts the subsystems present in the profiled microbial communities, is computationally efficient, and up to 1000 times faster than other tools. SUPER-FOCUS is freely available at http://edwards.sdsu.edu/SUPERFOCUS .

  15. Global volatile profile of virgin olive oils flavoured by aromatic/medicinal plants.

    PubMed

    Perestrelo, R; Silva, C; Silva, P; Câmara, J S

    2017-07-15

    The global volatile profile of commercial virgin olive oils and flavoured olive oils with aromatic/medicinal plants, was established using liquid-liquid microextraction (LLME) and headspace solid-phase microextraction (HS-SPME) combined with gas chromatography-quadrupole mass spectrometry (GC-qMS). More than 60 volatile organic compounds (VOCs belonging to different groups were identified using both methods. Olive oils volatile profile was slightly influenced by maceration process, which occurred at room temperature (20±2°C) for 15days. The predominant differences were observed in terpenoids group, since some of them were only identified in the flavoured olive oils, while others showed an increase with the maceration process. VOCs mass transfer from plants to olive oils could explain the observed results. Principal components analysis (PCA) applied to LLME/GC-qMS data allowed to distinguish the olive oils. The flavoured oils would increase the use of olive oil among consumers as consequence of the improvement of its aromatic profile and healthy properties. Copyright © 2017 Elsevier Ltd. All rights reserved.

  16. Analysis of Exhaled Breath Volatile Organic Compounds in Inflammatory Bowel Disease: A Pilot Study.

    PubMed

    Hicks, Lucy C; Huang, Juzheng; Kumar, Sacheen; Powles, Sam T; Orchard, Timothy R; Hanna, George B; Williams, Horace R T

    2015-09-01

    Distinguishing between the inflammatory bowel diseases [IBD], Crohn's disease [CD] and ulcerative colitis [UC], is important for determining management and prognosis. Selected ion flow tube mass spectrometry [SIFT-MS] may be used to analyse volatile organic compounds [VOCs] in exhaled breath: these may be altered in disease states, and distinguishing breath VOC profiles can be identified. The aim of this pilot study was to identify, quantify, and analyse VOCs present in the breath of IBD patients and controls, potentially providing insights into disease pathogenesis and complementing current diagnostic algorithms. SIFT-MS breath profiling of 56 individuals [20 UC, 18 CD, and 18 healthy controls] was undertaken. Multivariate analysis included principal components analysis and partial least squares discriminant analysis with orthogonal signal correction [OSC-PLS-DA]. Receiver operating characteristic [ROC] analysis was performed for each comparative analysis using statistically significant VOCs. OSC-PLS-DA modelling was able to distinguish both CD and UC from healthy controls and from one other with good sensitivity and specificity. ROC analysis using combinations of statistically significant VOCs [dimethyl sulphide, hydrogen sulphide, hydrogen cyanide, ammonia, butanal, and nonanal] gave integrated areas under the curve of 0.86 [CD vs healthy controls], 0.74 [UC vs healthy controls], and 0.83 [CD vs UC]. Exhaled breath VOC profiling was able to distinguish IBD patients from controls, as well as to separate UC from CD, using both multivariate and univariate statistical techniques. Copyright © 2015 European Crohn’s and Colitis Organisation (ECCO). Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  17. Systemic Metabolomic Changes in Blood Samples of Lung Cancer Patients Identified by Gas Chromatography Time-of-Flight Mass Spectrometry

    PubMed Central

    Miyamoto, Suzanne; Taylor, Sandra L.; Barupal, Dinesh K.; Taguchi, Ayumu; Wohlgemuth, Gert; Wikoff, William R.; Yoneda, Ken Y.; Gandara, David R.; Hanash, Samir M.; Kim, Kyoungmi; Fiehn, Oliver

    2015-01-01

    Lung cancer is a leading cause of cancer deaths worldwide. Metabolic alterations in tumor cells coupled with systemic indicators of the host response to tumor development have the potential to yield blood profiles with clinical utility for diagnosis and monitoring of treatment. We report results from two separate studies using gas chromatography time-of-flight mass spectrometry (GC-TOF MS) to profile metabolites in human blood samples that significantly differ from non-small cell lung cancer (NSCLC) adenocarcinoma and other lung cancer cases. Metabolomic analysis of blood samples from the two studies yielded a total of 437 metabolites, of which 148 were identified as known compounds and 289 identified as unknown compounds. Differential analysis identified 15 known metabolites in one study and 18 in a second study that were statistically different (p-values <0.05). Levels of maltose, palmitic acid, glycerol, ethanolamine, glutamic acid, and lactic acid were increased in cancer samples while amino acids tryptophan, lysine and histidine decreased. Many of the metabolites were found to be significantly different in both studies, suggesting that metabolomics appears to be robust enough to find systemic changes from lung cancer, thus showing the potential of this type of analysis for lung cancer detection. PMID:25859693

  18. Safer sexual practices among African American women: intersectional socialisation and sexual assertiveness.

    PubMed

    Brown, Danice L; Blackmon, Sha'Kema; Shiflett, Alexandra

    2018-06-01

    Scholars have posited that childhood socialisation experiences may play a key role in influencing behaviours and attitudes that contribute to the acquisition of HIV. This study examined the links between past ethnic-racial and gender socialisation, sexual assertiveness and the safe sexual practices of African American college women utilising a cluster analytic approach. After identifying separate racial-gender and ethnic-gender socialisation profiles, results indicated that ethnic-gender socialisation cluster profiles were directly associated with sexual assertiveness and safer sex behaviour. Greater levels of ethnic socialisation and low traditional gender role socialisation were found to be associated with greater sexual assertiveness and safer sex behaviour. Further analysis showed that sexual assertiveness mediated the links between the identified ethnic-gender socialisation profiles and safer sex behaviour. Implications for policy and programme development are discussed.

  19. A typology of pain coping strategies in pediatric patients with chronic abdominal pain.

    PubMed

    Walker, Lynn S; Baber, Kari Freeman; Garber, Judy; Smith, Craig A

    2008-07-15

    This study aimed to identify clinically meaningful profiles of pain coping strategies used by youth with chronic abdominal pain (CAP). Participants (n=699) were pediatric patients (ages 8-18 years) and their parents. Patients completed the Pain Response Inventory (PRI) and measures of somatic and depressive symptoms, disability, pain severity and pain efficacy, and perceived competence. Parents rated their children's pain severity and coping efficacy. Hierarchical cluster analysis based on the 13 PRI subscales identified pain coping profiles in Sample 1 (n=311) that replicated in Sample 2 (n=388). Evidence was found of external validity and distinctiveness of the profiles. The findings support a typology of pain coping that reflects the quality of patients' pain mastery efforts and interpersonal relationships associated with pain coping. Results are discussed in relation to developmental processes, attachment styles, and treatment implications.

  20. Analysis of protein profiles in diabetic rat blood plasma that induced by alloxan

    NASA Astrophysics Data System (ADS)

    Hidayati, Dewi; Abdulgani, Nurlita; Setiyawan, Hengki; Trisnawati, Indah; Ashuri, Nova Maulidina; Sa'adah, Noor Nailis

    2017-06-01

    Proteomics is the study to identify the proteins involved in physiological metabolic pathway. The protein profiles of blood plasma from alloxan-induced diabetic rats has investigated using Sodium Dodecyl Sulphate Polyacrylamide Gel Electrophoresis (SDS-PAGE). Data were analyzed descriptively based on variations of the type and intensity of the protein. There were identified the similarity of protein variant between diabetic and control rats included ankyrin (200kDa), IgG (150kDa), nephrin (136 kDa), IDE (112 kDA), albumin (66 kDa), prealbumin (55 kDA), CICP (43 kDa), ApoA-V (39 kDa), GAPDH (35 kDa), C-RP (27,1 kDa), leptin (16 kDa) and apelin (13 kDa). However, the apelin profile at diabetic rats shows the higher intensity than control.

  1. Segmenting by Risk Perceptions: Predicting Young Adults’ Genetic-Belief Profiles with Health and Opinion-Leader Covariates

    PubMed Central

    Smith, Rachel A.; Greenberg, Marisa; Parrott, Roxanne L.

    2014-01-01

    With a growing interest in using genetic information to motivate young adults’ health behaviors, audience segmentation is needed for effective campaign design. Using latent class analysis, this study identifies segments based on young adults’ (N = 327) beliefs about genetic threats to their health and personal efficacy over genetic influences on their health. A four-class model was identified. The model indicators fit the risk perception attitude framework (Rimal & Real, 2003), but the covariates (e.g., current health behaviors) did not. In addition, opinion leader qualities covaried with one profile: those in this profile engaged in fewer preventative behaviors and more dangerous treatment options, and also liked to persuade others, making them a particularly salient group for campaign efforts. The implications for adult-onset disorders, like alpha-1 antitrypsin deficiency are discussed. PMID:24111749

  2. Analyzing gene expression time-courses based on multi-resolution shape mixture model.

    PubMed

    Li, Ying; He, Ye; Zhang, Yu

    2016-11-01

    Biological processes actually are a dynamic molecular process over time. Time course gene expression experiments provide opportunities to explore patterns of gene expression change over a time and understand the dynamic behavior of gene expression, which is crucial for study on development and progression of biology and disease. Analysis of the gene expression time-course profiles has not been fully exploited so far. It is still a challenge problem. We propose a novel shape-based mixture model clustering method for gene expression time-course profiles to explore the significant gene groups. Based on multi-resolution fractal features and mixture clustering model, we proposed a multi-resolution shape mixture model algorithm. Multi-resolution fractal features is computed by wavelet decomposition, which explore patterns of change over time of gene expression at different resolution. Our proposed multi-resolution shape mixture model algorithm is a probabilistic framework which offers a more natural and robust way of clustering time-course gene expression. We assessed the performance of our proposed algorithm using yeast time-course gene expression profiles compared with several popular clustering methods for gene expression profiles. The grouped genes identified by different methods are evaluated by enrichment analysis of biological pathways and known protein-protein interactions from experiment evidence. The grouped genes identified by our proposed algorithm have more strong biological significance. A novel multi-resolution shape mixture model algorithm based on multi-resolution fractal features is proposed. Our proposed model provides a novel horizons and an alternative tool for visualization and analysis of time-course gene expression profiles. The R and Matlab program is available upon the request. Copyright © 2016 Elsevier Inc. All rights reserved.

  3. A Latent Profile Analysis of Aggression and Victimization Across Relationship Types Among Veterans Who Use Substances.

    PubMed

    Anderson, RaeAnn E; Bonar, Erin E; Walton, Maureen A; Goldstick, Jason E; Rauch, Sheila A M; Epstein-Ngo, Quyen M; Chermack, Stephen T

    2017-07-01

    This study examined patterns of violence victimization and aggression in both intimate partner and nonpartner relationships among U.S. military veterans using latent profile analysis to identify subtypes of violence involvement. Participants were 839 substance use treatment-seeking veterans (93% male) from a large Veterans Affairs Medical Center who completed screening measures for a randomized controlled trial. Past-year violence involvement, including both intimate partner violence (IPV) and nonpartner violence (NPV), was common in the sample, although NPV occurred at somewhat higher rates. When we included either IPV or NPV aggression or victimization, more than 40% reported involvement with physical violence, 30% with violence involving injury, and 86% with psychological aggression. Latent profile analysis including both aggression and victimization in partner and nonpartner relationships indicated a four-profile solution: no/low violence (NLV; n = 377), predominantly IPV (n = 219), predominantly NPV (n = 134), and high general violence (HGV; n = 109). Multinomial logistic regression analyses revealed that, compared with the NLV group, the remaining three groups differed in age, cocaine use, posttraumatic stress disorder (PTSD) symptoms, and legal involvement. Legal issues appeared to differentiate the profiles most, with the predominantly NPV and HGV profiles reporting more instances of driving under the influence and the HGV profile reporting legal problems related to aggression. IPV and NPV are fairly common among veterans seeking substance use treatment. The clinical characteristics of violence profiles indicate that cocaine use, PTSD symptoms, and legal involvement are treatment needs that vary with violence profile and may be useful for clinical decision making.

  4. Transcriptome-wide identification and expression profiles of the WRKY transcription factor family in Broomcorn millet (Panicum miliaceum L.).

    PubMed

    Yue, Hong; Wang, Meng; Liu, Siyan; Du, Xianghong; Song, Weining; Nie, Xiaojun

    2016-05-10

    WRKY genes, as the most pivotal transcription factors in plants, play the indispensable roles in regulating various physiological processes, including plant growth and development as well as in response to stresses. Broomcorn millet is one of the most important crops in drought areas worldwide. However, the WRKY gene family in broomcorn millet remains unknown. A total of 32 PmWRKY genes were identified in this study using computational prediction method. Structural analysis found that PmWRKY proteins contained a highly conserved motif WRKYGQK and two common variant motifs, namely WRKYGKK and WRKYGEK. Phylogenetic analysis of PmWRKYs together with the homologous genes from the representative species could classify them into three groups, with the number of 1, 15, and 16, respectively. Finally, the transcriptional profiles of these 32 PmWRKY genes in various tissues or under different abiotic stresses were systematically investigated using qRT-PCR analysis. Results showed that the expression level of 22 PmWRKY genes varied significantly under one or more abiotic stress treatments, which could be defined as abiotic stress-responsive genes. This was the first study to identify the organization and transcriptional profiles of PmWRKY genes, which not only facilitates the functional analysis of the PmWRKY genes, and also lays the foundation to reveal the molecular mechanism of stress tolerance in this important crop.

  5. The use of fatty acid methyl esters as biomarkers to determine aerobic, facultatively aerobic and anaerobic communities in wastewater treatment systems.

    PubMed

    Quezada, Maribel; Buitrón, Germán; Moreno-Andrade, Iván; Moreno, Gloria; López-Marín, Luz M

    2007-01-01

    The use of fatty acid methyl esters (FAME) as biomarkers to identify groups of microorganisms was studied. A database was constructed using previously published results that identify FAME biomarkers for aerobic, anaerobic and facultatively aerobic bacteria. FAME profiles obtained from pure cultures were utilized to confirm the predicted presence of biomarkers. Principal component analysis demonstrated that the FAME profiles can be used to determine the incidence of these bacterial groups. The presence of aerobic, anaerobic and facultatively aerobic bacteria in the communities, in four bioreactors being used to treat different wastewaters, was investigated by applying FAME biomarkers.

  6. Automatic identification of bacterial types using statistical imaging methods

    NASA Astrophysics Data System (ADS)

    Trattner, Sigal; Greenspan, Hayit; Tepper, Gapi; Abboud, Shimon

    2003-05-01

    The objective of the current study is to develop an automatic tool to identify bacterial types using computer-vision and statistical modeling techniques. Bacteriophage (phage)-typing methods are used to identify and extract representative profiles of bacterial types, such as the Staphylococcus Aureus. Current systems rely on the subjective reading of plaque profiles by human expert. This process is time-consuming and prone to errors, especially as technology is enabling the increase in the number of phages used for typing. The statistical methodology presented in this work, provides for an automated, objective and robust analysis of visual data, along with the ability to cope with increasing data volumes.

  7. Personality Profiles of Effective Leadership Performance in Assessment Centers

    PubMed Central

    Parr, Alissa D.; Lanza, Stephanie T.; Bernthal, Paul

    2016-01-01

    Most research examining the relationship between effective leadership and personality has focused on individual personality traits. However, profiles of personality traits more fully describe individuals, and these profiles may be important as they relate to leadership. This study used latent class analysis to examine how personality traits combine and interact to form subpopulations of leaders, and how these subpopulations relate to performance criteria. Using a sample of 2,461 executive-level leaders, six personality profiles were identified: Unpredictable Leaders with Low Diligence (7.3%); Conscientious, Backend Leaders (3.6%); Unpredictable Leaders (8.6%); Creative Communicators (20.8%); Power Players (32.4%); and Protocol Followers (27.1%). One profile performed well on all criteria in an assessment center; remaining profiles exhibited strengths and weaknesses across criteria. Implications and future directions for research are highlighted. PMID:27746587

  8. Alkaloid profiles and acetylcholinesterase inhibitory activities of Fumaria species from Bulgaria.

    PubMed

    Vrancheva, Radka Z; Ivanov, Ivan G; Aneva, Ina Y; Dincheva, Ivayla N; Badjakov, Ilian K; Pavlov, Atanas I

    2016-01-01

    GC-MS analysis of alkaloid profiles of five Fumaria species, naturally grown in Bulgaria (F. officinalis, F. thuretii, F. kralikii, F. rostellata and F. schrammii) and analysis of acetylcholinesterase inhibitory activity of alkaloid extracts were performed. Fourteen isoquinoline alkaloids were identified, with the principle ones being protopine, cryptopine, sinactine, parfumine, fumariline, fumarophycine, and fumaritine. Protopine contents, defined by HPLC analysis varied between 210.6 ± 8.8 μg/g DW (F. schrammii) and 334.5 ± 7.1 μg/g DW. (F. rostellata). While all of the investigated alkaloid extracts significantly inhibited acetylcholinesterase activity, the F. kralikii demonstrated the highest level of inhibition (IC(50) 0.13 ± 0.01 mg extract/mL).

  9. Molecular Identification of Unusual Pathogenic Yeast Isolates by Large Ribosomal Subunit Gene Sequencing: 2 Years of Experience at the United Kingdom Mycology Reference Laboratory▿

    PubMed Central

    Linton, Christopher J.; Borman, Andrew M.; Cheung, Grace; Holmes, Ann D.; Szekely, Adrien; Palmer, Michael D.; Bridge, Paul D.; Campbell, Colin K.; Johnson, Elizabeth M.

    2007-01-01

    Rapid identification of yeast isolates from clinical samples is particularly important given their innately variable antifungal susceptibility profiles. We present here an analysis of the utility of PCR amplification and sequence analysis of the hypervariable D1/D2 region of the 26S rRNA gene for the identification of yeast species submitted to the United Kingdom Mycology Reference Laboratory over a 2-year period. A total of 3,033 clinical isolates were received from 2004 to 2006 encompassing 50 different yeast species. While more than 90% of the isolates, corresponding to the most common Candida species, could be identified by using the AUXACOLOR2 yeast identification kit, 153 isolates (5%), comprised of 47 species, could not be identified by using this system and were subjected to molecular identification via 26S rRNA gene sequencing. These isolates included some common species that exhibited atypical biochemical and phenotypic profiles and also many rarer yeast species that are infrequently encountered in the clinical setting. All 47 species requiring molecular identification were unambiguously identified on the basis of D1/D2 sequences, and the molecular identities correlated well with the observed biochemical profiles of the various organisms. Together, our data underscore the utility of molecular techniques as a reference adjunct to conventional methods of yeast identification. Further, we show that PCR amplification and sequencing of the D1/D2 region reliably identifies more than 45 species of clinically significant yeasts and can also potentially identify new pathogenic yeast species. PMID:17251397

  10. Plasma metabolic profiling analysis of nephrotoxicity induced by acyclovir using metabonomics coupled with multivariate data analysis.

    PubMed

    Zhang, Xiuxiu; Li, Yubo; Zhou, Huifang; Fan, Simiao; Zhang, Zhenzhu; Wang, Lei; Zhang, Yanjun

    2014-08-01

    Acyclovir (ACV) is an antiviral agent. However, its use is limited by adverse side effect, particularly by its nephrotoxicity. Metabonomics technology can provide essential information on the metabolic profiles of biofluids and organs upon drug administration. Therefore, in this study, mass spectrometry-based metabonomics coupled with multivariate data analysis was used to identify the plasma metabolites and metabolic pathways related to nephrotoxicity caused by intraperitoneal injection of low (50mg/kg) and high (100mg/kg) doses of acyclovir. Sixteen biomarkers were identified by metabonomics and nephrotoxicity results revealed the dose-dependent effect of acyclovir on kidney tissues. The present study showed that the top four metabolic pathways interrupted by acyclovir included the metabolisms of arachidonic acid, tryptophan, arginine and proline, and glycerophospholipid. This research proves the established metabonomic approach can provide information on changes in metabolites and metabolic pathways, which can be applied to in-depth research on the mechanism of acyclovir-induced kidney injury. Copyright © 2014 Elsevier B.V. All rights reserved.

  11. Cassava (Manihot esculenta Krantz) genome harbors KNOX genes differentially expressed during storage root development.

    PubMed

    Guo, D; Li, H L; Tang, X; Peng, S Q

    2014-12-18

    In plants, homeodomain proteins play a critical role in regulating various aspects of plant growth and development. KNOX proteins are members of the homeodomain protein family. The KNOX transcription factors have been reported from Arabidopsis, rice, and other higher plants. The recent publication of the draft genome sequence of cassava (Manihot esculenta Krantz) has allowed a genome-wide search for M. esculenta KNOX (MeKNOX) transcription factors and the comparison of these positively identified proteins with their homologs in model plants. In the present study, we identified 12 MeKNOX genes in the cassava genome and grouped them into two distinct subfamilies based on their domain composition and phylogenetic analysis. Furthermore, semi-quantitative reverse transcription polymerase chain reaction analysis was performed to elucidate the expression profiles of these genes in different tissues and during various stages of root development. The analysis of MeKNOX expression profiles of indicated that 12 MeKNOX genes display differential expressions either in their transcript abundance or expression patterns.

  12. Mass spectrometry based proteomics profiling as diagnostic tool in oncology: current status and future perspective.

    PubMed

    Findeisen, Peter; Neumaier, Michael

    2009-01-01

    Proteomics analysis has been heralded as a novel tool for identifying new and specific biomarkers that may improve diagnosis and monitoring of various disease states. Recent years have brought a number of proteomics profiling technologies. Although proteomics profiling has resulted in the detection of disease-associated differences and modification of proteins, current proteomics technologies display certain limitations that are hampering the introduction of these new technologies into clinical laboratory diagnostics and routine applications. In this review, we summarize current advances in mass spectrometry based biomarker discovery. The promises and challenges of this new technology are discussed with particular emphasis on diagnostic perspectives of mass-spectrometry based proteomics profiling for malignant diseases.

  13. Investigation of the aroma of commercial peach (Prunus persica L. Batsch) types by Proton Transfer Reaction-Mass Spectrometry (PTR-MS) and sensory analysis.

    PubMed

    Bianchi, Tiago; Weesepoel, Yannick; Koot, Alex; Iglesias, Ignasi; Eduardo, Iban; Gratacós-Cubarsí, Marta; Guerrero, Luis; Hortós, Maria; van Ruth, Saskia

    2017-09-01

    The aim of this study was to investigate the aroma and sensory profiles of various types of peaches (Prunus persica L. Batsch.). Forty-three commercial cultivars comprising peaches, flat peaches, nectarines, and canning peaches (pavías) were grown over two consecutive harvest years. Fruits were assessed for chemical aroma and sensory profiles. Chemical aroma profile was obtained by proton transfer reaction-mass spectrometry (PTR-MS) and spectral masses were tentatively identified with PTR-Time of Flight-MS (PTR-Tof-MS). Sensory analysis was performed at commercial maturity considering seven aroma/flavor attributes. The four types of peaches showed both distinct chemical aroma and sensory profiles. Flat peaches and canning peaches showed most distinct patterns according to discriminant analysis. The sensory data were related to the volatile compounds by partial least square regression. γ-Hexalactone, γ-octalactone, hotrienol, acetic acid and ethyl acetate correlated positively, and benzeneacetaldehyde, trimethylbenzene and acetaldehyde negatively to the intensities of aroma and ripe fruit sensory scores. Copyright © 2017 Elsevier Ltd. All rights reserved.

  14. Identification of suitable genes contributes to lung adenocarcinoma clustering by multiple meta-analysis methods.

    PubMed

    Yang, Ze-Hui; Zheng, Rui; Gao, Yuan; Zhang, Qiang

    2016-09-01

    With the widespread application of high-throughput technology, numerous meta-analysis methods have been proposed for differential expression profiling across multiple studies. We identified the suitable differentially expressed (DE) genes that contributed to lung adenocarcinoma (ADC) clustering based on seven popular multiple meta-analysis methods. Seven microarray expression profiles of ADC and normal controls were extracted from the ArrayExpress database. The Bioconductor was used to perform the data preliminary preprocessing. Then, DE genes across multiple studies were identified. Hierarchical clustering was applied to compare the classification performance for microarray data samples. The classification efficiency was compared based on accuracy, sensitivity and specificity. Across seven datasets, 573 ADC cases and 222 normal controls were collected. After filtering out unexpressed and noninformative genes, 3688 genes were remained for further analysis. The classification efficiency analysis showed that DE genes identified by sum of ranks method separated ADC from normal controls with the best accuracy, sensitivity and specificity of 0.953, 0.969 and 0.932, respectively. The gene set with the highest classification accuracy mainly participated in the regulation of response to external stimulus (P = 7.97E-04), cyclic nucleotide-mediated signaling (P = 0.01), regulation of cell morphogenesis (P = 0.01) and regulation of cell proliferation (P = 0.01). Evaluation of DE genes identified by different meta-analysis methods in classification efficiency provided a new perspective to the choice of the suitable method in a given application. Varying meta-analysis methods always present varying abilities, so synthetic consideration should be taken when providing meta-analysis methods for particular research. © 2015 John Wiley & Sons Ltd.

  15. Gene expression profiles of breast biopsies from healthy women identify a group with claudin-low features.

    PubMed

    Haakensen, Vilde D; Lingjaerde, Ole Christian; Lüders, Torben; Riis, Margit; Prat, Aleix; Troester, Melissa A; Holmen, Marit M; Frantzen, Jan Ole; Romundstad, Linda; Navjord, Dina; Bukholm, Ida K; Johannesen, Tom B; Perou, Charles M; Ursin, Giske; Kristensen, Vessela N; Børresen-Dale, Anne-Lise; Helland, Aslaug

    2011-11-01

    Increased understanding of the variability in normal breast biology will enable us to identify mechanisms of breast cancer initiation and the origin of different subtypes, and to better predict breast cancer risk. Gene expression patterns in breast biopsies from 79 healthy women referred to breast diagnostic centers in Norway were explored by unsupervised hierarchical clustering and supervised analyses, such as gene set enrichment analysis and gene ontology analysis and comparison with previously published genelists and independent datasets. Unsupervised hierarchical clustering identified two separate clusters of normal breast tissue based on gene-expression profiling, regardless of clustering algorithm and gene filtering used. Comparison of the expression profile of the two clusters with several published gene lists describing breast cells revealed that the samples in cluster 1 share characteristics with stromal cells and stem cells, and to a certain degree with mesenchymal cells and myoepithelial cells. The samples in cluster 1 also share many features with the newly identified claudin-low breast cancer intrinsic subtype, which also shows characteristics of stromal and stem cells. More women belonging to cluster 1 have a family history of breast cancer and there is a slight overrepresentation of nulliparous women in cluster 1. Similar findings were seen in a separate dataset consisting of histologically normal tissue from both breasts harboring breast cancer and from mammoplasty reductions. This is the first study to explore the variability of gene expression patterns in whole biopsies from normal breasts and identified distinct subtypes of normal breast tissue. Further studies are needed to determine the specific cell contribution to the variation in the biology of normal breasts, how the clusters identified relate to breast cancer risk and their possible link to the origin of the different molecular subtypes of breast cancer.

  16. An Analysis of Cognitive Style Profiles and Related Science Achievement Among Secondary School Students.

    ERIC Educational Resources Information Center

    Ogden, William R.; Brewster, Patricia M.

    The purpose of this study was to identify cognitive styles for successful and unsuccessful science students at the secondary level. Additional purposes were to identify common and unique elements in these composite cognitive styles and to substantiate the description of the groups of successful and unsuccessful science students according to the…

  17. Analysis of the differential gene and protein expression profile of the rolled leaf mutant of transgenic rice (Oryza sativa L.).

    PubMed

    Zhu, Qiuqiang; Yu, Shuguang; Chen, Guanshui; Ke, Lanlan; Pan, Daren

    2017-01-01

    The importance of leaf rolling in rice (Oryza sativa L.) has been widely recognized. Although several studies have investigated rice leaf rolling and identified some related genes, knowledge of the molecular mechanism underlying rice leaf rolling, especially outward leaf rolling, is limited. Therefore, in this study, differential proteomics and gene expression profiling were used to analyze rolled leaf mutant of transgenic rice in order to investigate differentially expressed genes and proteins related to rice leaf rolling. To this end, 28 differentially expressed proteins related to rolling leaf traits were isolated and identified. Digital expression profiling detected 10 genes related to rice leaf rolling. Some of the proteins and genes detected are involved in lipid metabolism, which is related to the development of bulliform cells, such as phosphoinositide phospholipase C, Mgll gene, and At4g26790 gene. The "omics"-level techniques were useful for simultaneously isolating several proteins and genes related to rice leaf rolling. In addition, the results of the analysis of differentially expressed proteins and genes were closely consistent with those from a corresponding functional analysis of cellular mechanisms; our study findings might form the basis for further research on the molecular mechanisms underlying rice leaf rolling.

  18. MMPI-2: Cluster Analysis of Personality Profiles in Perinatal Depression—Preliminary Evidence

    PubMed Central

    Grillo, Alessandra; Lauriola, Marco; Giacchetti, Nicoletta

    2014-01-01

    Background. To assess personality characteristics of women who develop perinatal depression. Methods. The study started with a screening of a sample of 453 women in their third trimester of pregnancy, to which was administered a survey data form, the Edinburgh Postnatal Depression Scale (EPDS) and the Minnesota Multiphasic Personality Inventory 2 (MMPI-2). A clinical group of subjects with perinatal depression (PND, 55 subjects) was selected; clinical and validity scales of MMPI-2 were used as predictors in hierarchical cluster analysis carried out. Results. The analysis identified three clusters of personality profile: two “clinical” clusters (1 and 3) and an “apparently common” one (cluster 2). The first cluster (39.5%) collects structures of personality with prevalent obsessive or dependent functioning tending to develop a “psychasthenic” depression; the third cluster (13.95%) includes women with prevalent borderline functioning tending to develop “dysphoric” depression; the second cluster (46.5%) shows a normal profile with a “defensive” attitude, probably due to the presence of defense mechanisms or to the fear of stigma. Conclusion. Characteristics of personality have a key role in clinical manifestations of perinatal depression; it is important to detect them to identify mothers at risk and to plan targeted therapeutic interventions. PMID:25574499

  19. Facial trauma as physical violence markers against elderly Brazilians: A comparative analysis between genders.

    PubMed

    de Sousa, Rayanne Izabel Maciel; de Macedo Bernardino, Ítalo; Castro, Ricardo Dias; Cavalcanti, Alessandro Leite; Bento, Patricia Meira; d'Ávila, Sérgio

    2016-01-01

    The aim of this study was to characterize the profile of elderly Brazilians with injuries resulting from physical violence and identify victimization differences. A descriptive and exploratory study was conducted involving the analysis of medico-legal and social records of 259 elderly victims of physical violence treated at an Institute of Forensic Medicine and Dentistry over four years (from January 2008 to December 2011). The forensic service database was evaluated by researchers properly trained and calibrated to perform this function between January and March 2013. Socio-demographic variables of victims, aggression characteristics, aggressor's profile and types of lesions were evaluated. Descriptive and multivariate statistics using Multiple Correspondence Analysis (MCA) were performed. The prevalence of facial trauma was 42.9%. Based on the MCA results, two groups with different victimization profiles were identified: married men aged 70-79 years, victims of community violence at night, suffering facial injuries; and single, widowed or separated women aged 60-69 years, victims of domestic violence during the day, suffering trauma in other areas of the body. The results suggest that there is a high prevalence of facial injuries among elderly Brazilians victims of physical violence and there are important differences related to victimization characteristics according to gender. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  20. Molecular phenotyping of severe asthma using pattern recognition of bronchoalveolar lavage-derived cytokines.

    PubMed

    Brasier, Allan R; Victor, Sundar; Boetticher, Gary; Ju, Hyunsu; Lee, Chang; Bleecker, Eugene R; Castro, Mario; Busse, William W; Calhoun, William J

    2008-01-01

    Asthma is a heterogeneous clinical disorder. Methods for objective identification of disease subtypes will focus on clinical interventions and help identify causative pathways. Few studies have explored phenotypes at a molecular level. We sought to discriminate asthma phenotypes on the basis of cytokine profiles in bronchoalveolar lavage (BAL) samples from patients with mild-moderate and severe asthma. Twenty-five cytokines were measured in BAL samples of 84 patients (41 severe, 43 mild-moderate) using bead-based multiplex immunoassays. The normalized data were subjected to statistical and informatics analysis. Four groups of asthmatic profiles could be identified on the basis of unsupervised analysis (hierarchical clustering) that were independent of treatment. One group, enriched in patients with severe asthma, showed differences in BAL cellular content, reductions in baseline pulmonary function, and enhanced response to methacholine provocation. Ten cytokines were identified that accurately predicted this group. Classification methods for predicting methacholine sensitivity were developed. The best model analysis predicted hyperresponders with 88% accuracy in 10 trials by using a 10-fold cross-validation. The cytokines that contributed to this model were IL-2, IL-4, and IL-5. On the basis of this classifier, 3 distinct hyperresponder classes were identified that varied in BAL eosinophil count and PC20 methacholine. Cytokine expression patterns in BAL can be used to identify distinct types of asthma and identify distinct subsets of methacholine hyperresponders. Further biomarker discovery in BAL may be informative.

  1. Bioinformatics approaches for cross-species liver cancer analysis based on microarray gene expression profiling

    PubMed Central

    Fang, H; Tong, W; Perkins, R; Shi, L; Hong, H; Cao, X; Xie, Q; Yim, SH; Ward, JM; Pitot, HC; Dragan, YP

    2005-01-01

    Background The completion of the sequencing of human, mouse and rat genomes and knowledge of cross-species gene homologies enables studies of differential gene expression in animal models. These types of studies have the potential to greatly enhance our understanding of diseases such as liver cancer in humans. Genes co-expressed across multiple species are most likely to have conserved functions. We have used various bioinformatics approaches to examine microarray expression profiles from liver neoplasms that arise in albumin-SV40 transgenic rats to elucidate genes, chromosome aberrations and pathways that might be associated with human liver cancer. Results In this study, we first identified 2223 differentially expressed genes by comparing gene expression profiles for two control, two adenoma and two carcinoma samples using an F-test. These genes were subsequently mapped to the rat chromosomes using a novel visualization tool, the Chromosome Plot. Using the same plot, we further mapped the significant genes to orthologous chromosomal locations in human and mouse. Many genes expressed in rat 1q that are amplified in rat liver cancer map to the human chromosomes 10, 11 and 19 and to the mouse chromosomes 7, 17 and 19, which have been implicated in studies of human and mouse liver cancer. Using Comparative Genomics Microarray Analysis (CGMA), we identified regions of potential aberrations in human. Lastly, a pathway analysis was conducted to predict altered human pathways based on statistical analysis and extrapolation from the rat data. All of the identified pathways have been known to be important in the etiology of human liver cancer, including cell cycle control, cell growth and differentiation, apoptosis, transcriptional regulation, and protein metabolism. Conclusion The study demonstrates that the hepatic gene expression profiles from the albumin-SV40 transgenic rat model revealed genes, pathways and chromosome alterations consistent with experimental and clinical research in human liver cancer. The bioinformatics tools presented in this paper are essential for cross species extrapolation and mapping of microarray data, its analysis and interpretation. PMID:16026603

  2. Preconception reflections, postconception intentions: the before and after of birth control in Australian adolescent females.

    PubMed

    Smith, Jennifer Lawson; Skinner, S Rachel; Fenwick, Jennifer

    2013-08-01

    Background The relationship between pregnancy intentions and contraceptive behaviour is difficult to establish. This study explored the contraceptive histories of teenagers with a recent experience of pregnancy to generate qualitative profiles of pregnancy intentions. Subsequent intentions in relation to birth control were also examined. A purposive sample of female teenagers aged 14-19 years was recruited from various clinical and community-based antenatal and postnatal services and termination services across the Perth metropolitan area. The current analysis was based on a total of 56 semistructured interviews. A two-staged process of thematic analysis was conducted to identify commonalities emerging from the narrative data. Three pregnancy intention profiles were identified: 1) unplanned, unwanted, unlikely; 2) planned, wanted, likely; and 3) unplanned, ambivalent, likely. Each profile represents variation in pathways to pregnancy based on teenagers' accounts of pregnancy desires, personal responsibility over contraceptive use, and perceptions of pregnancy risk. Regardless of the way that pregnancy was resolved (i.e. termination or childbirth), similar postconception intentions surrounding birth control emerged through a shared discourse of pregnancy avoidance across the sample. Exploring adolescents' understandings of the decisions and behaviours that lead to pregnancy will assist in the development of more accurate assessment tools to identify those at risk of unplanned and unwanted pregnancies. Our research also suggests that the provision of contraceptive counselling immediately after conception, followed by ongoing support, may help to maintain strong intentions to delay further pregnancies as identified in our study.

  3. Aeromonas hydrophila and Aeromonas veronii Predominate among Potentially Pathogenic Ciprofloxacin- and Tetracycline-Resistant Aeromonas Isolates from Lake Erie

    PubMed Central

    Shinko, Jasmine; Augustyniak, Alexander; Gee, Christopher; Andraso, Greg

    2014-01-01

    Members of the genus Aeromonas are ubiquitous in nature and have increasingly been implicated in numerous diseases of humans and other animal taxa. Although some species of aeromonads are human pathogens, their presence, density, and relative abundance are rarely considered in assessing water quality. The objectives of this study were to identify Aeromonas species within Lake Erie, determine their antibiotic resistance patterns, and assess their potential pathogenicity. Aeromonas strains were isolated from Lake Erie water by use of Aeromonas selective agar with and without tetracycline and ciprofloxacin. All isolates were analyzed for hemolytic ability and cytotoxicity against human epithelial cells and were identified to the species level by using 16S rRNA gene restriction fragment length polymorphisms and phylogenetic analysis based on gyrB gene sequences. A molecular virulence profile was identified for each isolate, using multiplex PCR analysis of six virulence genes. We demonstrated that Aeromonas comprised 16% of all culturable bacteria from Lake Erie. Among 119 Aeromonas isolates, six species were identified, though only two species (Aeromonas hydrophila and A. veronii) predominated among tetracycline- and ciprofloxacin-resistant isolates. Additionally, both of these species demonstrated pathogenic phenotypes in vitro. Virulence gene profiles demonstrated a high prevalence of aerolysin and serine protease genes among A. hydrophila and A. veronii isolates, a genetic profile which corresponded with pathogenic phenotypes. Together, our findings demonstrate increased antibiotic resistance among potentially pathogenic strains of aeromonads, illustrating an emerging potential health concern. PMID:24242249

  4. A graph-based system for network-vulnerability analysis

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

    Swiler, L.P.; Phillips, C.

    1998-06-01

    This paper presents a graph-based approach to network vulnerability analysis. The method is flexible, allowing analysis of attacks from both outside and inside the network. It can analyze risks to a specific network asset, or examine the universe of possible consequences following a successful attack. The graph-based tool can identify the set of attack paths that have a high probability of success (or a low effort cost) for the attacker. The system could be used to test the effectiveness of making configuration changes, implementing an intrusion detection system, etc. The analysis system requires as input a database of common attacks,more » broken into atomic steps, specific network configuration and topology information, and an attacker profile. The attack information is matched with the network configuration information and an attacker profile to create a superset attack graph. Nodes identify a stage of attack, for example the class of machines the attacker has accessed and the user privilege level he or she has compromised. The arcs in the attack graph represent attacks or stages of attacks. By assigning probabilities of success on the arcs or costs representing level-of-effort for the attacker, various graph algorithms such as shortest-path algorithms can identify the attack paths with the highest probability of success.« less

  5. DNA analysis in Disaster Victim Identification.

    PubMed

    Montelius, Kerstin; Lindblom, Bertil

    2012-06-01

    DNA profiling and matching is one of the primary methods to identify missing persons in a disaster, as defined by the Interpol Disaster Victim Identification Guide. The process to identify a victim by DNA includes: the collection of the best possible ante-mortem (AM) samples, the choice of post-mortem (PM) samples, DNA-analysis, matching and statistical weighting of the genetic relationship or match. Each disaster has its own scenario, and each scenario defines its own methods for identification of the deceased.

  6. Application of conductive polymer analysis for wood and woody plant identifications

    Treesearch

    A. Dan Wilson; D.G. Lester; Charisse S. Oberle

    2005-01-01

    An electronic aroma detection (EAD) technology known as conductive polymer analysis (CPA) was evaluated as a means of identifying and discriminating woody samples of angiosperms and gymnosperms using an analytical instrument (electronic nose) that characterizes the aroma profiles of volatiles released from excised wood into sampled headspace. The instrument measures...

  7. Analysis of baseline gene expression levels from toxicogenomics study control animals to identify sources of variation and predict responses to chemicals

    EPA Science Inventory

    The use of gene expression profiling to predict chemical mode of action would be enhanced by better characterization of variance due to individual, environmental, and technical factors. Meta-analysis of microarray data from untreated or vehicle-treated animals within the control ...

  8. Computer planning tools applied to a cable logging research study

    Treesearch

    Chris B. LeDoux; Penn A. Peters

    1985-01-01

    Contemporary harvest planning software was used in planning the layout of cable logging units for a production study of the Clearwater Yarder in upstate New York. Planning software, including payload analysis and digital terrain models, allowed researchers to identify layout and yarding problems before the experiment. Analysis of proposed ground profiles pinpointed the...

  9. The development of the Problematic Online Gaming Questionnaire (POGQ).

    PubMed

    Demetrovics, Zsolt; Urbán, Róbert; Nagygyörgy, Katalin; Farkas, Judit; Griffiths, Mark D; Pápay, Orsolya; Kökönyei, Gyöngyi; Felvinczi, Katalin; Oláh, Attila

    2012-01-01

    Online gaming has become increasingly popular. However, this has led to concerns that these games might induce serious problems and/or lead to dependence for a minority of players. The aim of this study was to uncover and operationalize the components of problematic online gaming. A total of 3415 gamers (90% males; mean age 21 years), were recruited through online gaming websites. A combined method of exploratory factor analysis (EFA) and confirmatory factor analysis (CFA) was applied. Latent profile analysis was applied to identify persons at-risk. EFA revealed a six-factor structure in the background of problematic online gaming that was also confirmed by a CFA. For the assessment of the identified six dimensions--preoccupation, overuse, immersion, social isolation, interpersonal conflicts, and withdrawal--the 18-item Problematic Online Gaming Questionnaire (POGQ) proved to be exceedingly suitable. Based on the latent profile analysis, 3.4% of the gamer population was considered to be at high risk, while another 15.2% was moderately problematic. The POGQ seems to be an adequate measurement tool for the differentiated assessment of gaming related problems on six subscales.

  10. Analysis of microRNA profile of Anopheles sinensis by deep sequencing and bioinformatic approaches.

    PubMed

    Feng, Xinyu; Zhou, Xiaojian; Zhou, Shuisen; Wang, Jingwen; Hu, Wei

    2018-03-12

    microRNAs (miRNAs) are small non-coding RNAs widely identified in many mosquitoes. They are reported to play important roles in development, differentiation and innate immunity. However, miRNAs in Anopheles sinensis, one of the Chinese malaria mosquitoes, remain largely unknown. We investigated the global miRNA expression profile of An. sinensis using Illumina Hiseq 2000 sequencing. Meanwhile, we applied a bioinformatic approach to identify potential miRNAs in An. sinensis. The identified miRNA profiles were compared and analyzed by two approaches. The selected miRNAs from the sequencing result and the bioinformatic approach were confirmed with qRT-PCR. Moreover, target prediction, GO annotation and pathway analysis were carried out to understand the role of miRNAs in An. sinensis. We identified 49 conserved miRNAs and 12 novel miRNAs by next-generation high-throughput sequencing technology. In contrast, 43 miRNAs were predicted by the bioinformatic approach, of which two were assigned as novel. Comparative analysis of miRNA profiles by two approaches showed that 21 miRNAs were shared between them. Twelve novel miRNAs did not match any known miRNAs of any organism, indicating that they are possibly species-specific. Forty miRNAs were found in many mosquito species, indicating that these miRNAs are evolutionally conserved and may have critical roles in the process of life. Both the selected known and novel miRNAs (asi-miR-281, asi-miR-184, asi-miR-14, asi-miR-nov5, asi-miR-nov4, asi-miR-9383, and asi-miR-2a) could be detected by quantitative real-time PCR (qRT-PCR) in the sequenced sample, and the expression patterns of these miRNAs measured by qRT-PCR were in concordance with the original miRNA sequencing data. The predicted targets for the known and the novel miRNAs covered many important biological roles and pathways indicating the diversity of miRNA functions. We also found 21 conserved miRNAs and eight counterparts of target immune pathway genes in An. sinensis based on the analysis of An. gambiae. Our results provide the first lead to the elucidation of the miRNA profile in An. sinensis. Unveiling the roles of mosquito miRNAs will undoubtedly lead to a better understanding of mosquito biology and mosquito-pathogen interactions. This work lays the foundation for the further functional study of An. sinensis miRNAs and will facilitate their application in vector control.

  11. Dynamic motif occupancy (DynaMO) analysis identifies transcription factors and their binding sites driving dynamic biological processes

    PubMed Central

    Kuang, Zheng; Ji, Zhicheng

    2018-01-01

    Abstract Biological processes are usually associated with genome-wide remodeling of transcription driven by transcription factors (TFs). Identifying key TFs and their spatiotemporal binding patterns are indispensable to understanding how dynamic processes are programmed. However, most methods are designed to predict TF binding sites only. We present a computational method, dynamic motif occupancy analysis (DynaMO), to infer important TFs and their spatiotemporal binding activities in dynamic biological processes using chromatin profiling data from multiple biological conditions such as time-course histone modification ChIP-seq data. In the first step, DynaMO predicts TF binding sites with a random forests approach. Next and uniquely, DynaMO infers dynamic TF binding activities at predicted binding sites using their local chromatin profiles from multiple biological conditions. Another landmark of DynaMO is to identify key TFs in a dynamic process using a clustering and enrichment analysis of dynamic TF binding patterns. Application of DynaMO to the yeast ultradian cycle, mouse circadian clock and human neural differentiation exhibits its accuracy and versatility. We anticipate DynaMO will be generally useful for elucidating transcriptional programs in dynamic processes. PMID:29325176

  12. A High Resolution Seismic Sequence Analysis of the Malta Plateau

    DTIC Science & Technology

    1999-05-01

    the SACLANTCEN Programme of Work. The document has been approved for release by The Director, SACLANTCEN. Jan L . Spoelstra Director NATO...the Plio- Quatemary. To the southwest of Sicily, Di Stefano et al. (1993) identified six sequence boundaries and estimated the ages by the...the location of the seismic reflection profiles in Di Stefano et al. (1993) do not overlap any of the profiles in this study and use a lower frequency

  13. Cognitive factors affecting children's nonsymbolic and symbolic magnitude judgment abilities: A latent profile analysis.

    PubMed

    Chew, Cindy S; Forte, Jason D; Reeve, Robert A

    2016-12-01

    Early math abilities are claimed to be linked to magnitude representation ability. Some claim that nonsymbolic magnitude abilities scaffold the acquisition of symbolic (Arabic number) magnitude abilities and influence math ability. Others claim that symbolic magnitude abilities, and ipso facto math abilities, are independent of nonsymbolic abilities and instead depend on the ability to process number symbols (e.g., 2, 7). Currently, the issue of whether symbolic abilities are or are not related to nonsymbolic abilities, and the cognitive factors associated with nonsymbolic-symbolic relationships, remains unresolved. We suggest that different nonsymbolic-symbolic relationships reside within the general magnitude ability distribution and that different cognitive abilities are likely associated with these different relationships. We further suggest that the different nonsymbolic-symbolic relationships and cognitive abilities in combination differentially predict math abilities. To test these claims, we used latent profile analysis to identify nonsymbolic-symbolic judgment patterns of 124, 5- to 7-year-olds. We also assessed four cognitive factors (visuospatial working memory [VSWM], naming numbers, nonverbal IQ, and basic reaction time [RT]) and two math abilities (number transcoding and single-digit addition abilities). Four nonsymbolic-symbolic ability profiles were identified. Naming numbers, VSWM, and basic RT abilities were differentially associated with the different ability profiles and in combination differentially predicted math abilities. Findings show that different patterns of nonsymbolic-symbolic magnitude abilities can be identified and suggest that an adequate account of math development should specify the inter-relationship between cognitive factors and nonsymbolic-symbolic ability patterns. Copyright © 2016 Elsevier Inc. All rights reserved.

  14. Fatty acid methyl ester analysis to identify sources of soil in surface water.

    PubMed

    Banowetz, Gary M; Whittaker, Gerald W; Dierksen, Karen P; Azevedo, Mark D; Kennedy, Ann C; Griffith, Stephen M; Steiner, Jeffrey J

    2006-01-01

    Efforts to improve land-use practices to prevent contamination of surface waters with soil are limited by an inability to identify the primary sources of soil present in these waters. We evaluated the utility of fatty acid methyl ester (FAME) profiles of dry reference soils for multivariate statistical classification of soils collected from surface waters adjacent to agricultural production fields and a wooded riparian zone. Trials that compared approaches to concentrate soil from surface water showed that aluminum sulfate precipitation provided comparable yields to that obtained by vacuum filtration and was more suitable for handling large numbers of samples. Fatty acid methyl ester profiles were developed from reference soils collected from contrasting land uses in different seasons to determine whether specific fatty acids would consistently serve as variables in multivariate statistical analyses to permit reliable classification of soils. We used a Bayesian method and an independent iterative process to select appropriate fatty acids and found that variable selection was strongly impacted by the season during which soil was collected. The apparent seasonal variation in the occurrence of marker fatty acids in FAME profiles from reference soils prevented preparation of a standardized set of variables. Nevertheless, accurate classification of soil in surface water was achieved utilizing fatty acid variables identified in seasonally matched reference soils. Correlation analysis of entire chromatograms and subsequent discriminant analyses utilizing a restricted number of fatty acid variables showed that FAME profiles of soils exposed to the aquatic environment still had utility for classification at least 1 wk after submersion.

  15. Gene Expression Profiling in Pachyonychia Congenita Skin

    PubMed Central

    Cao, Yu-An; Hickerson, Robyn P.; Seegmiller, Brandon L.; Grapov, Dmitry; Gross, Maren M.; Bessette, Marc R.; Phinney, Brett S.; Flores, Manuel A.; Speaker, Tycho J.; Vermeulen, Annaleen; Bravo, Albert A.; Bruckner, Anna L.; Milstone, Leonard M.; Schwartz, Mary E.; Rice, Robert H.; Kaspar, Roger L.

    2015-01-01

    Background Pachyonychia congenita (PC) is a skin disorder resulting from mutations in keratin (K) proteins including K6a, K6b, K16, and K17. One of the major symptoms is painful plantar keratoderma. The pathogenic sequelae resulting from the keratin mutations remain unclear. Objective To better understand PC pathogenesis. Methods RNA profiling was performed on biopsies taken from PC-involved and uninvolved plantar skin of seven genotyped PC patients (two K6a, one K6b, three K16, and one K17) as well as from control volunteers. Protein profiling was generated from tape-stripping samples. Results A comparison of PC-involved skin biopsies to adjacent uninvolved plantar skin identified 112 differentially-expressed mRNAs common to patient groups harboring K6 (i.e., both K6a and K6b) and K16 mutations. Among these mRNAs, 25 encode structural proteins including keratins, small proline-rich and late cornified envelope proteins, 20 are related to metabolism and 16 encode proteases, peptidases, and their inhibitors including kallikrein-related peptidases (KLKs), and serine protease inhibitors (SERPINs). mRNAs were also identified to be differentially expressed only in K6 (81) or K16 (141) patient samples. Furthermore, 13 mRNAs were identified that may be involved in pain including nociception and neuropathy. Protein profiling, comparing three K6a plantar tape-stripping samples to non-PC controls, showed changes in the PC corneocytes similar, but not identical, to the mRNA analysis. Conclusion Many differentially-expressed genes identified in PC-involved skin encode components critical for skin barrier homeostasis including keratinocyte proliferation, differentiation, cornification, and desquamation. The profiling data provide a foundation for unraveling the pathogenesis of PC and identifying targets for developing effective PC therapeutics. PMID:25656049

  16. Proteomics of gliomas: Initial biomarker discovery and evolution of technology

    PubMed Central

    Kalinina, Juliya; Peng, Junmin; Ritchie, James C.; Van Meir, Erwin G.

    2011-01-01

    Gliomas are a group of aggressive brain tumors that diffusely infiltrate adjacent brain tissues, rendering them largely incurable, even with multiple treatment modalities and agents. Mostly asymptomatic at early stages, they present in several subtypes with astrocytic or oligodendrocytic features and invariably progress to malignant forms. Gliomas are difficult to classify precisely because of interobserver variability during histopathologic grading. Identifying biological signatures of each glioma subtype through protein biomarker profiling of tumor or tumor-proximal fluids is therefore of high priority. Such profiling not only may provide clues regarding tumor classification but may identify clinical biomarkers and pathologic targets for the development of personalized treatments. In the past decade, differential proteomic profiling techniques have utilized tumor, cerebrospinal fluid, and plasma from glioma patients to identify the first candidate diagnostic, prognostic, predictive, and therapeutic response markers, highlighting the potential for glioma biomarker discovery. The number of markers identified, however, has been limited, their reproducibility between studies is unclear, and none have been validated for clinical use. Recent technological advancements in methodologies for high-throughput profiling, which provide easy access, rapid screening, low sample consumption, and accurate protein identification, are anticipated to accelerate brain tumor biomarker discovery. Reliable tools for biomarker verification forecast translation of the biomarkers into clinical diagnostics in the foreseeable future. Herein we update the reader on the recent trends and directions in glioma proteomics, including key findings and established and emerging technologies for analysis, together with challenges we are still facing in identifying and verifying potential glioma biomarkers. PMID:21852429

  17. Socioeconomic Differences in the Risk Profiles of Susceptibility and Ever Use of Tobacco Among Indian Urban Youth: A Latent Class Approach

    PubMed Central

    2014-01-01

    Purpose: To empirically determine the socioeconomic differences in risk profiles of susceptibility and ever use of tobacco among adolescents in India and to investigate the association between the risk profiles and the psychosocial factors for tobacco use. Methods: Students in 16 private (higher socioeconomic status [SES]; n = 4,489) and 16 government (lower SES; n = 7,153) schools in two large cities in India were surveyed about their tobacco use and related psychosocial factors in 2004. Latent class analysis was used to identify homogenous, mutually exclusive typologies existing within the data. Results: Overall, 3 and 4 latent classes of susceptibility and ever use of tobacco best described students in higher- and lower- SES schools, respectively. Profiles with various combinations of susceptibility and ever use of tobacco were differentially related to psychosocial factors, with lower- SES students being more vulnerable to increased levels of tobacco use than higher- SES students. Conclusions: Acknowledging the multiple dimensions of tobacco use behaviors and identifying constellations of risk behaviors will enable more accurate understanding of etiological processes and will provide information for refining and targeting preventive interventions. Additionally, identifying the socioeconomic differences in susceptibility and ever use risk profiles and their psychosocial correlates will enable policy makers to address these inequities through improved allocation of resources. PMID:24271966

  18. Barcode DNA length polymorphisms vs fatty acid profiling for adulteration detection in olive oil.

    PubMed

    Uncu, Ali Tevfik; Uncu, Ayse Ozgur; Frary, Anne; Doganlar, Sami

    2017-04-15

    The aim of this study was to compare the performance of a DNA-barcode assay with fatty acid profile analysis to authenticate the botanical origin of olive oil. To achieve this aim, we performed a PCR-capillary electrophoresis (PCR-CE) approach on olive oil: seed oil blends using the plastid trnL (UAA) intron barcode. In parallel to genomic analysis, we subjected the samples to gas chromatography analysis of fatty acid composition. While the PCR-CE assay proved equally efficient as gas chromatography analysis in detecting adulteration with soybean, palm, rapeseed, sunflower, sesame, cottonseed and peanut oils, it was superior to the widely utilized analytical chemistry approach in revealing the adulterant species and detecting small quantities of corn and safflower oils in olive oil. Moreover, the DNA-based test correctly identified all tested olive oil: hazelnut oil blends whereas it was not feasible to detect hazelnut oil adulteration through fatty acid profile analysis. Thus, the present research has shown the feasibility of a PCR-CE barcode assay to detect adulteration in olive oil. Copyright © 2016 Elsevier Ltd. All rights reserved.

  19. The expression profiling and ontology analysis of non-coding RNAs in dexamethasone induced steatosis in hepatoma cell.

    PubMed

    Liu, Fengqiong; Gong, Ruijie; Lv, Xiaofei; Li, Huangyuan

    2018-04-15

    Increasing amounts of evidence have indicated that non-coding RNAs (ncRNAs) have important regulatory potential in various biological processes. However, the contribution of ncRNAs, especially long non-coding RNAs (lncRNAs) to drug induced steatosis remain largely unknown. The aim of this study is to investigate miRNA, lncRNA and mRNA expression profiles and their potential roles in the process of drug induced steatosis. Microarray expression profiles of miRNAs, lncRNAs and mRNAs were determined in dexamethasone treated HepG2 cell as well as control cell. Differential expression, pathway and gene network analyses were developed to identify possible functional RNA molecules in dexamethasone induced steatosis. Compared with control HepG2 cell, 652 lncRNAs (528 up-regulated and 124 down-regulated), 655 mRNAs (527 upregulated and 128 down-regulated) and 114 miRNAs (55 miRNAs up-regulated and 59 down-regulated) were differentially expressed in dexamethasone treated HepG2 cell. Pathway analysis showed that the fatty acid biosynthesis, insulin resistance, PPAR signaling pathway, regulation of lipolysis in adipocytes, carbohydrate digestion and absorption, steroid hormone biosynthesis signaling pathways had a close relationship with dexamethasone induced steatosis. 10 highly dysregulated mRNAs and 20 miRNAs, which are closely related to lipid metabolism, were identified and validated by PCR, which followed by ceRNA analysis. CeRNA network analysis identified 5 lipid metabolism related genes, including CYP7A1, CYP11A1, PDK4, ABHD5, ACSL1. It also identified 12 miRNAs (miR-23a-3p, miR-519d-3p, miR-4328, miR-15b-5p etc.) and 177 lncRNAs (ENST00000508884, ENST00000608794, ENST00000568457 etc.). Our results provide a foundation and an expansive view of the roles and mechanisms of ncRNAs in dexamethasone induced steatosis. Copyright © 2018 Elsevier B.V. All rights reserved.

  20. Identification of a 'Candidatus Phytoplasma hispanicum'-related strain, associated with yellows-type diseases, in smoke-tree sharpshooter (Homalodisca liturata Ball).

    PubMed

    Servín-Villegas, Rosalía; Caamal-Chan, Maria Goretty; Chavez-Medina, Alicia; Loera-Muro, Abraham; Barraza, Aarón; Medina-Hernández, Diana; Holguín-Peña, Ramón Jaime

    2018-04-11

    The 16SrXIII group from phytoplasma bacteria were identified in salivary glands from Homalodisca liturata, which were collected in El Comitán on the Baja California peninsula in Mexico. We were able to positively identify 15 16S rRNA gene sequences with the corresponding signature sequence of 'CandidatusPhytoplasma' (CAAGAYBATKATGTKTAGCYGGDCT) and in silico restriction fragment length polymorphism (RFLP) profiles (F value estimations) coupled with a phylogenetic analysis to confirm their relatedness to 'CandidatusPhytoplasma hispanicum', which in turn belongs to the 16SrXIII group. A restriction analysis was carried out with AluI and EcoRI to confirm that the five sequences belongs to subgroup D. The rest of the sequences did not exhibit any known RFLP profile related to a subgroup reported in the 16SrXIII group.

  1. Identification of discriminant proteins through antibody profiling, methods and apparatus for identifying an individual

    DOEpatents

    Apel, William A.; Thompson, Vicki S; Lacey, Jeffrey A.; Gentillon, Cynthia A.

    2016-08-09

    A method for determining a plurality of proteins for discriminating and positively identifying an individual based from a biological sample. The method may include profiling a biological sample from a plurality of individuals against a protein array including a plurality of proteins. The protein array may include proteins attached to a support in a preselected pattern such that locations of the proteins are known. The biological sample may be contacted with the protein array such that a portion of antibodies in the biological sample reacts with and binds to the proteins forming immune complexes. A statistical analysis method, such as discriminant analysis, may be performed to determine discriminating proteins for distinguishing individuals. Proteins of interest may be used to form a protein array. Such a protein array may be used, for example, to compare a forensic sample from an unknown source with a sample from a known source.

  2. Identification of discriminant proteins through antibody profiling, methods and apparatus for identifying an individual

    DOEpatents

    Thompson, Vicki S; Lacey, Jeffrey A; Gentillon, Cynthia A; Apel, William A

    2015-03-03

    A method for determining a plurality of proteins for discriminating and positively identifying an individual based from a biological sample. The method may include profiling a biological sample from a plurality of individuals against a protein array including a plurality of proteins. The protein array may include proteins attached to a support in a preselected pattern such that locations of the proteins are known. The biological sample may be contacted with the protein array such that a portion of antibodies in the biological sample reacts with and binds to the proteins forming immune complexes. A statistical analysis method, such as discriminant analysis, may be performed to determine discriminating proteins for distinguishing individuals. Proteins of interest may be used to form a protein array. Such a protein array may be used, for example, to compare a forensic sample from an unknown source with a sample from a known source.

  3. High-throughput deep screening and identification of four peripheral leucocyte microRNAs as novel potential combination biomarkers for preeclampsia

    PubMed Central

    Wang, Yonghong; Yang, Xukui; Yang, Yuanyuan; Wang, Wenjun; Zhao, Meiling; Liu, Huiqiang; Li, Dongyan; Hao, Min

    2016-01-01

    Objective: To identify the specific microRNA (miRNA) biomarkers of preeclampsia (PE), the miRNA profiles analysis were performed. Study Design: The blood samples were obtained from five PE patients and five normal healthy pregnant women. The small RNA profiles were analyzed to identify miRNA expression levels and find out miRNAs that may associate with PE. The quantitative reverse transcriptase–PCR (qRT-PCR) assay was used to validate differentially expressed peripheral leucocyte miRNAs in a new cohort. Result: The data analysis showed that 10 peripheral leucocyte miRNAs were significantly differently expressed in severe PE patients. Four differently expressed miRNAs were successfully validated using qRT-PCR method. Conclusion: We successfully constructed a model with high accuracy to predict PE. A combination of four peripheral leucocyte miRNAs has great potential to serve as diagnostic biomarkers of PE. PMID:26675000

  4. A Healthcare Utilization Analysis Framework for Hot Spotting and Contextual Anomaly Detection

    PubMed Central

    Hu, Jianying; Wang, Fei; Sun, Jimeng; Sorrentino, Robert; Ebadollahi, Shahram

    2012-01-01

    Patient medical records today contain vast amount of information regarding patient conditions along with treatment and procedure records. Systematic healthcare resource utilization analysis leveraging such observational data can provide critical insights to guide resource planning and improve the quality of care delivery while reducing cost. Of particular interest to providers are hot spotting: the ability to identify in a timely manner heavy users of the systems and their patterns of utilization so that targeted intervention programs can be instituted, and anomaly detection: the ability to identify anomalous utilization cases where the patients incurred levels of utilization that are unexpected given their clinical characteristics which may require corrective actions. Past work on medical utilization pattern analysis has focused on disease specific studies. We present a framework for utilization analysis that can be easily applied to any patient population. The framework includes two main components: utilization profiling and hot spotting, where we use a vector space model to represent patient utilization profiles, and apply clustering techniques to identify utilization groups within a given population and isolate high utilizers of different types; and contextual anomaly detection for utilization, where models that map patient’s clinical characteristics to the utilization level are built in order to quantify the deviation between the expected and actual utilization levels and identify anomalies. We demonstrate the effectiveness of the framework using claims data collected from a population of 7667 diabetes patients. Our analysis demonstrates the usefulness of the proposed approaches in identifying clinically meaningful instances for both hot spotting and anomaly detection. In future work we plan to incorporate additional sources of observational data including EMRs and disease registries, and develop analytics models to leverage temporal relationships among medical encounters to provide more in-depth insights. PMID:23304306

  5. A healthcare utilization analysis framework for hot spotting and contextual anomaly detection.

    PubMed

    Hu, Jianying; Wang, Fei; Sun, Jimeng; Sorrentino, Robert; Ebadollahi, Shahram

    2012-01-01

    Patient medical records today contain vast amount of information regarding patient conditions along with treatment and procedure records. Systematic healthcare resource utilization analysis leveraging such observational data can provide critical insights to guide resource planning and improve the quality of care delivery while reducing cost. Of particular interest to providers are hot spotting: the ability to identify in a timely manner heavy users of the systems and their patterns of utilization so that targeted intervention programs can be instituted, and anomaly detection: the ability to identify anomalous utilization cases where the patients incurred levels of utilization that are unexpected given their clinical characteristics which may require corrective actions. Past work on medical utilization pattern analysis has focused on disease specific studies. We present a framework for utilization analysis that can be easily applied to any patient population. The framework includes two main components: utilization profiling and hot spotting, where we use a vector space model to represent patient utilization profiles, and apply clustering techniques to identify utilization groups within a given population and isolate high utilizers of different types; and contextual anomaly detection for utilization, where models that map patient's clinical characteristics to the utilization level are built in order to quantify the deviation between the expected and actual utilization levels and identify anomalies. We demonstrate the effectiveness of the framework using claims data collected from a population of 7667 diabetes patients. Our analysis demonstrates the usefulness of the proposed approaches in identifying clinically meaningful instances for both hot spotting and anomaly detection. In future work we plan to incorporate additional sources of observational data including EMRs and disease registries, and develop analytics models to leverage temporal relationships among medical encounters to provide more in-depth insights.

  6. Identifying Risk and Protective Factors in Recidivist Juvenile Offenders: A Decision Tree Approach

    PubMed Central

    Ortega-Campos, Elena; García-García, Juan; Gil-Fenoy, Maria José; Zaldívar-Basurto, Flor

    2016-01-01

    Research on juvenile justice aims to identify profiles of risk and protective factors in juvenile offenders. This paper presents a study of profiles of risk factors that influence young offenders toward committing sanctionable antisocial behavior (S-ASB). Decision tree analysis is used as a multivariate approach to the phenomenon of repeated sanctionable antisocial behavior in juvenile offenders in Spain. The study sample was made up of the set of juveniles who were charged in a court case in the Juvenile Court of Almeria (Spain). The period of study of recidivism was two years from the baseline. The object of study is presented, through the implementation of a decision tree. Two profiles of risk and protective factors are found. Risk factors associated with higher rates of recidivism are antisocial peers, age at baseline S-ASB, problems in school and criminality in family members. PMID:27611313

  7. Fuel spill identification using solid-phase extraction and solid-phase microextraction. 1. Aviation turbine fuels.

    PubMed

    Lavine, B K; Brzozowski, D M; Ritter, J; Moores, A J; Mayfield, H T

    2001-12-01

    The water-soluble fraction of aviation jet fuels is examined using solid-phase extraction and solid-phase microextraction. Gas chromatographic profiles of solid-phase extracts and solid-phase microextracts of the water-soluble fraction of kerosene- and nonkerosene-based jet fuels reveal that each jet fuel possesses a unique profile. Pattern recognition analysis reveals fingerprint patterns within the data characteristic of fuel type. By using a novel genetic algorithm (GA) that emulates human pattern recognition through machine learning, it is possible to identify features characteristic of the chromatographic profile of each fuel class. The pattern recognition GA identifies a set of features that optimize the separation of the fuel classes in a plot of the two largest principal components of the data. Because principal components maximize variance, the bulk of the information encoded by the selected features is primarily about the differences between the fuel classes.

  8. Contextual Risk Profiles and Trajectories of Adolescent Dating Violence Perpetration.

    PubMed

    Reyes, H Luz McNaughton; Foshee, Vangie A; Markiewitz, Nathan; Chen, May S; Ennett, Susan T

    2018-04-09

    Social ecological and developmental system perspectives suggest that interactions among factors within and across multiple contexts (e.g., neighborhood, peer, family) must be considered in explaining dating violence perpetration. Yet, to date, most extant research on dating violence has focused on individual, rather than contextual predictors, and used variable-centered approaches that fail to capture the configurations of factors that may jointly explain involvement in dating violence. The current study used a person-centered approach, latent profile analysis, to identify key configurations (or profiles) of contextual risk and protective factors for dating violence perpetration across the neighborhood, school, friend and family contexts. We then examine the longitudinal associations between these contextual risk profiles, assessed during middle school, and trajectories of psychological and physical dating violence perpetration across grades 8 through 12. Five contextual risk profiles were identified: school, neighborhood, and family risk; school and family risk; school and friend risk; school and neighborhood risk; and low risk. The highest levels of psychological and physical perpetration across grades 8 through 12 were among adolescents in the profile characterized by high levels of school, neighborhood, and family risk. Results suggest that early interventions to reduce violence exposure and increase social regulation across multiple social contexts may be effective in reducing dating violence perpetration across adolescence.

  9. Distilling Heterogeneity among Children with Disruptive Behavior: Associations between Symptom Patterns and Social Functioning.

    PubMed

    Aitken, Madison; Henry, Shanelle; Andrade, Brendan F

    2017-10-16

    Children with disruptive behavior (DB) are a heterogeneous group who exhibit several characteristics that may contribute to poor social functioning. The present study identified profiles of reactive aggression, proactive aggression, callous-unemotional (CU) traits, and prosocial behavior in a sample of children with DB. Associations with social functioning (social interaction, social status) were then examined, along with sex differences in profile membership. Parent ratings of 304 clinic-referred children ages 6-12 years with DB were analyzed using latent profile analysis. Five profiles were identified: 1) Moderate prosocial behavior, reactive aggression, and CU, and low proactive aggression (labelled Moderate); 2) Relatively high prosocial behavior and low reactive and proactive aggression and CU traits (Prosocial); 3) High prosocial behavior and reactive aggression, moderate proactive aggression, and low-moderate CU (Reactive-Prosocial); 4) Low prosocial behavior, high CU, high-moderate reactive aggression, and low-moderate proactive aggression (Reactive-CU); and 5) Low prosocial behavior and high reactive and proactive aggression and CU (Aggressive-CU). Profiles characterized by CU traits, reactive aggression, and low prosocial behavior were associated with the most problematic parent-rated social interaction and social status. The results highlight the need to differentiate profiles of psychopathology in children with DB to better address factors most associated with social functioning.

  10. Identification of pathogenic genes related to rheumatoid arthritis through integrated analysis of DNA methylation and gene expression profiling.

    PubMed

    Zhang, Lei; Ma, Shiyun; Wang, Huailiang; Su, Hang; Su, Ke; Li, Longjie

    2017-11-15

    The purpose of our study was to identify new pathogenic genes used for exploring the pathogenesis of rheumatoid arthritis (RA). To screen pathogenic genes of RA, an integrated analysis was performed by using the microarray datasets in RA derived from the Gene Expression Omnibus (GEO) database. The functional annotation and potential pathways of differentially expressed genes (DEGs) were further discovered by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. Afterwards, the integrated analysis of DNA methylation and gene expression profiling was used to screen crucial genes. In addition, we used RT-PCR and MSP to verify the expression levels and methylation status of these crucial genes in 20 synovial biopsy samples obtained from 10 RA model mice and 10 normal mice. BCL11B, CCDC88C, FCRLA and APOL6 were both up-regulated and hypomethylated in RA according to integrated analysis, RT-PCR and MSP verification. Four crucial genes (BCL11B, CCDC88C, FCRLA and APOL6) identified and analyzed in this study might be closely connected with the pathogenesis of RA. Copyright © 2017. Published by Elsevier B.V.

  11. Objective Classification of Radar Profile Types, and Their Relationship to Lightning Occurrence

    NASA Technical Reports Server (NTRS)

    Boccippio, Dennis

    2003-01-01

    A cluster analysis technique is used to identify 16 "archetypal" vertical radar profile types from a large, globally representative sample of profiles from the TRMM Precipitation Radar. These include nine convective types (7 of these deep convective) and seven stratiform types (5 of these clearly glaciated). Radar profile classification provides an alternative to conventional deep convective storm metrics, such as 30 dBZ echo height, maximum reflectivity or VIL. As expected, the global frequency of occurrence of deep convective profile types matches satellite-observed total lightning production, including to very small scall local features. Each location's "mix" of profile types provides an objective description of the local convective spectrum, and in turn, is a first step in objectively classifying convective regimes. These classifiers are tested as inputs to a neural network which attempts to predict lightning occurrence based on radar-only storm observations, and performance is compared with networks using traditional radar metrics as inputs.

  12. A geodemographic analysis of the Denplan patient population in the North West Region.

    PubMed

    Tickle, M; Blinkhorn, A S; Brown, P J; Matthews, R

    2000-11-11

    To provide a preliminary descriptive investigation of Denplan patients in the North West Region, by plotting the age/gender and payment banding distribution, and to identify the area types where Denplan patients live and the areas in the North West Region where Denplan practices are most likely to thrive. North West Region of England The study included Denplan patients resident in the North West Region. Age/gender and payment banding frequency distributions were constructed. A market penetration ranking report using the Target Market level of the Super Profiles geodemographic classification was produced by a spreadsheet analysis in Microsoft Excel. A Lorenz curve was plotted to graphically represent the output of the market penetration analysis. Following the market penetration analysis the enumeration districts (EDs) of the six top ranked Target Markets in the North West Region were identified and mapped out across the Region. Finally, the number and percentage of EDs in the six top ranked Target Markets were identified for each health authority in the Region. 47,106 patients were registered with Denplan. In all but one 5-year age band (16-20-year-olds) female patients were in the majority. Patients were concentrated (40.5%) into the 40-55 age group. Nearly 50% (22,329) of patients were allocated to the second lowest payment banding. Under 0.5% of patients (N = 199) were categorised into the highest payment band. The Target Markets at the top of the penetration ranking were more affluent in nature, with a strong rural element and an older demographic profile as part of their descriptive titles. At the bottom of the ranking deprived area types with young demographic profiles predominated. About one half (49.9%) of Denplan patients were present in just over a quarter (25.7%) of the total population of the North West Region. The Lorenz curve demonstrated that Super Profiles at Target Market level had an effectiveness of 37.9% in segmenting the population of the North West Region according to Denplan registration status. The population using this service in the North West Region tend to be from more mature, rural and affluent populations. The Super Profiles classification was moderately successful in segmenting the population of the North West Region according to their Denplan registration status.

  13. Differential gene expression profiling of endometrium during the mid-luteal phase of the estrous cycle between a repeat breeder (RB) and non-RB cows.

    PubMed

    Hayashi, Ken-Go; Hosoe, Misa; Kizaki, Keiichiro; Fujii, Shiori; Kanahara, Hiroko; Takahashi, Toru; Sakumoto, Ryosuke

    2017-03-23

    Repeat breeding directly affects reproductive efficiency in cattle due to an increase in services per conception and calving interval. This study aimed to investigate whether changes in endometrial gene expression profile are involved in repeat breeding in cows. Differential gene expression profiles of the endometrium were investigated during the mid-luteal phase of the estrous cycle between repeat breeder (RB) and non-RB cows using microarray analysis. The caruncular (CAR) and intercaruncular (ICAR) endometrium of both ipsilateral and contralateral uterine horns to the corpus luteum were collected from RB (inseminated at least three times but not pregnant) and non-RB cows on Day 15 of the estrous cycle (4 cows/group). Global gene expression profiles of these endometrial samples were analyzed with a 15 K custom-made oligo-microarray for cattle. Immunohistochemistry was performed to investigate the cellular localization of proteins of three identified transcripts in the endometrium. Microarray analysis revealed that 405 and 397 genes were differentially expressed in the CAR and ICAR of the ipsilateral uterine horn of RB, respectively when compared with non-RB cows. In the contralateral uterine horn, 443 and 257 differentially expressed genes were identified in the CAR and ICAR of RB, respectively when compared with non-RB cows. Gene ontology analysis revealed that genes involved in development and morphogenesis were mainly up-regulated in the CAR of RB cows. In the ICAR of both the ipsilateral and contralateral uterine horns, genes related to the metabolic process were predominantly enriched in the RB cows when compared with non-RB cows. In the analysis of the whole uterus (combining the data above four endometrial compartments), RB cows showed up-regulation of 37 genes including PRSS2, GSTA3 and PIPOX and down-regulation of 39 genes including CHGA, KRT35 and THBS4 when compared with non-RB cows. Immunohistochemistry revealed that CHGA, GSTA3 and PRSS2 proteins were localized in luminal and glandular epithelial cells and stroma of the endometrium. The present study showed that endometrial gene expression profiles are different between RB and non-RB cows. The identified candidate endometrial genes and functions in each endometrial compartment may contribute to bovine reproductive performance.

  14. Latent Class Symptom Profiles of Selective Mutism: Identification and Linkage to Temperamental and Social Constructs.

    PubMed

    Diliberto, Rachele; Kearney, Christopher A

    2017-11-21

    Selective mutism (SM) is a stable, debilitating psychiatric disorder in which a child fails to speak in most public situations. Considerable debate exists as to the typology of this population, with empirically-based studies pointing to possible dimensions of anxiety, oppositionality, and communication problems, among other aspects. Little work has juxtaposed identified symptom profiles with key temperamental and social constructs often implicated in SM. The present study examined a large, diverse, non-clinical, international sample of children aged 6-10 years with SM to empirically identify symptom profiles and to link these profiles to key aspects of temperament (i.e., emotionality, shyness, sociability, activity) and social functioning (i.e., social problems, social competence). Exploratory and confirmatory factor analysis revealed anxiety/distress, oppositionality, and inattention domains. In addition, latent class analysis revealed nuanced profiles labeled as (1) moderately anxious, oppositional, and inattentive, (2) highly anxious, and moderately oppositional and inattentive, and (3) mildly to moderately anxious, and mildly oppositional and inattentive. Class 2 was the most impaired group and was associated with greater emotionality, shyness, and social problems. Class 3 was the least impaired group and was associated with better sociability and social competence and activity. Class 1 was largely between the other classes, demonstrating less shyness and social problems than Class 2. The results help confirm previous findings of anxiety and oppositional profiles among children with SM but that nuanced classes may indicate subtle variations in impairment. The results have implications not only for subtyping this population but also for refining assessment and case conceptualization strategies and pursuing personalized and perhaps less lengthy treatment.

  15. Similar protein expression profiles of ovarian and endometrial high-grade serous carcinomas.

    PubMed

    Hiramatsu, Kosuke; Yoshino, Kiyoshi; Serada, Satoshi; Yoshihara, Kosuke; Hori, Yumiko; Fujimoto, Minoru; Matsuzaki, Shinya; Egawa-Takata, Tomomi; Kobayashi, Eiji; Ueda, Yutaka; Morii, Eiichi; Enomoto, Takayuki; Naka, Tetsuji; Kimura, Tadashi

    2016-03-01

    Ovarian and endometrial high-grade serous carcinomas (HGSCs) have similar clinical and pathological characteristics; however, exhaustive protein expression profiling of these cancers has yet to be reported. We performed protein expression profiling on 14 cases of HGSCs (7 ovarian and 7 endometrial) and 18 endometrioid carcinomas (9 ovarian and 9 endometrial) using iTRAQ-based exhaustive and quantitative protein analysis. We identified 828 tumour-expressed proteins and evaluated the statistical similarity of protein expression profiles between ovarian and endometrial HGSCs using unsupervised hierarchical cluster analysis (P<0.01). Using 45 statistically highly expressed proteins in HGSCs, protein ontology analysis detected two enriched terms and proteins composing each term: IMP2 and MCM2. Immunohistochemical analyses confirmed the higher expression of IMP2 and MCM2 in ovarian and endometrial HGSCs as well as in tubal and peritoneal HGSCs than in endometrioid carcinomas (P<0.01). The knockdown of either IMP2 or MCM2 by siRNA interference significantly decreased the proliferation rate of ovarian HGSC cell line (P<0.01). We demonstrated the statistical similarity of the protein expression profiles of ovarian and endometrial HGSC beyond the organs. We suggest that increased IMP2 and MCM2 expression may underlie some of the rapid HGSC growth observed clinically.

  16. Sweat lipid mediator profiling: a noninvasive approach for cutaneous research[S

    PubMed Central

    Hassoun, Lauren A.; Foolad, Negar; Pedersen, Theresa L.; Sivamani, Raja K.; Newman, John W.

    2017-01-01

    Recent advances in analytical and sweat collection techniques provide new opportunities to identify noninvasive biomarkers for the study of skin inflammation and repair. This study aims to characterize the lipid mediator profile including oxygenated lipids, endocannabinoids, and ceramides/sphingoid bases in sweat and identify differences in these profiles between sweat collected from nonlesional sites on the unflared volar forearm of subjects with and without atopic dermatitis (AD). Adapting routine procedures developed for plasma analysis, over 100 lipid mediators were profiled using LC-MS/MS and 58 lipid mediators were detected in sweat. Lipid mediator concentrations were not affected by sampling or storage conditions. Increases in concentrations of C30–C40 [NS] and [NdS] ceramides, and C18:1 sphingosine, were observed in the sweat of study participants with AD despite no differences being observed in transepidermal water loss between study groups, and this effect was strongest in men (P < 0.05, one-way ANOVA with Tukey’s post hoc HSD). No differences in oxylipins and endocannabinoids were observed between study groups. Sweat mediator profiling may therefore provide a noninvasive diagnostic for AD prior to the presentation of clinical signs. PMID:27875258

  17. Sweat lipid mediator profiling: a noninvasive approach for cutaneous research.

    PubMed

    Agrawal, Karan; Hassoun, Lauren A; Foolad, Negar; Pedersen, Theresa L; Sivamani, Raja K; Newman, John W

    2017-01-01

    Recent advances in analytical and sweat collection techniques provide new opportunities to identify noninvasive biomarkers for the study of skin inflammation and repair. This study aims to characterize the lipid mediator profile including oxygenated lipids, endocannabinoids, and ceramides/sphingoid bases in sweat and identify differences in these profiles between sweat collected from nonlesional sites on the unflared volar forearm of subjects with and without atopic dermatitis (AD). Adapting routine procedures developed for plasma analysis, over 100 lipid mediators were profiled using LC-MS/MS and 58 lipid mediators were detected in sweat. Lipid mediator concentrations were not affected by sampling or storage conditions. Increases in concentrations of C30-C40 [NS] and [NdS] ceramides, and C18:1 sphingosine, were observed in the sweat of study participants with AD despite no differences being observed in transepidermal water loss between study groups, and this effect was strongest in men (P < 0.05, one-way ANOVA with Tukey's post hoc HSD). No differences in oxylipins and endocannabinoids were observed between study groups. Sweat mediator profiling may therefore provide a noninvasive diagnostic for AD prior to the presentation of clinical signs.

  18. Circulating tumor DNA profiling reveals clonal evolution and real-time disease progression in advanced hepatocellular carcinoma.

    PubMed

    Cai, Zhi-Xiong; Chen, Geng; Zeng, Yong-Yi; Dong, Xiu-Qing; Lin, Min-Jie; Huang, Xin-Hui; Zhang, Da; Liu, Xiao-Long; Liu, Jing-Feng

    2017-09-01

    Circulating tumor DNA (ctDNA) provides a potential non-invasive biomarker for cancer diagnosis and prognosis, but whether it could reflect tumor heterogeneity and monitor therapeutic responses in hepatocellular carcinoma (HCC) is unclear. Focusing on 574 cancer genes known to harbor actionable mutations, we identified the mutation repertoire of HCC tissues, and monitored the corresponding ctDNA features in blood samples to evaluate its clinical significance. Analysis of 3 HCC patients' mutation profiles revealed that ctDNA could overcome tumor heterogeneity and provide information of tumor burden and prognosis. Further analysis was conducted on the 4th HCC case with multiple lesion samples and sequential plasma samples. We identified 160 subclonal SNVs in tumor tissues as well as matched peritumor tissues with PBMC as control. 96.9% of this patient's tissue mutations could be also detected in plasma samples. These subclonal SNVs were grouped into 9 clusters according to their trends of cellular prevalence shift in tumor tissues. Two clusters constituted of tumor stem somatic mutations showed circulating levels relating with cancer progression. Analysis of tumor somatic mutations revealed that circulating level of such tumor stem somatic mutations could reflect tumor burden and even predict prognosis earlier than traditional strategies. Furthermore, HCK (p.V174M), identified as a recurrent/metastatic related mutation site, could promote migration and invasion of HCC cells. Taken together, study of mutation profiles in biopsy and plasma samples in HCC patients showed that ctDNA could overcome tumor heterogeneity and real-time track the therapeutic responses in the longitudinal monitoring. © 2017 UICC.

  19. Biosynthesis of the active compounds of Isatis indigotica based on transcriptome sequencing and metabolites profiling

    PubMed Central

    2013-01-01

    Backgroud Isatis indigotica is a widely used herb for the clinical treatment of colds, fever, and influenza in Traditional Chinese Medicine (TCM). Various structural classes of compounds have been identified as effective ingredients. However, little is known at genetics level about these active metabolites. In the present study, we performed de novo transcriptome sequencing for the first time to produce a comprehensive dataset of I. indigotica. Results A database of 36,367 unigenes (average length = 1,115.67 bases) was generated by performing transcriptome sequencing. Based on the gene annotation of the transcriptome, 104 unigenes were identified covering most of the catalytic steps in the general biosynthetic pathways of indole, terpenoid, and phenylpropanoid. Subsequently, the organ-specific expression patterns of the genes involved in these pathways, and their responses to methyl jasmonate (MeJA) induction, were investigated. Metabolites profile of effective phenylpropanoid showed accumulation pattern of secondary metabolites were mostly correlated with the transcription of their biosynthetic genes. According to the analysis of UDP-dependent glycosyltransferases (UGT) family, several flavonoids were indicated to exist in I. indigotica and further identified by metabolic profile using UPLC/Q-TOF. Moreover, applying transcriptome co-expression analysis, nine new, putative UGTs were suggested as flavonol glycosyltransferases and lignan glycosyltransferases. Conclusions This database provides a pool of candidate genes involved in biosynthesis of effective metabolites in I. indigotica. Furthermore, the comprehensive analysis and characterization of the significant pathways are expected to give a better insight regarding the diversity of chemical composition, synthetic characteristics, and the regulatory mechanism which operate in this medical herb. PMID:24308360

  20. Proteomic profiling of early degenerative retina of RCS rats.

    PubMed

    Zhu, Zhi-Hong; Fu, Yan; Weng, Chuan-Huang; Zhao, Cong-Jian; Yin, Zheng-Qin

    2017-01-01

    To identify the underlying cellular and molecular changes in retinitis pigmentosa (RP). Label-free quantification-based proteomics analysis, with its advantages of being more economic and consisting of simpler procedures, has been used with increasing frequency in modern biological research. Dystrophic RCS rats, the first laboratory animal model for the study of RP, possess a similar pathological course as human beings with the diseases. Thus, we employed a comparative proteomics analysis approach for in-depth proteome profiling of retinas from dystrophic RCS rats and non-dystrophic congenic controls through Linear Trap Quadrupole - orbitrap MS/MS, to identify the significant differentially expressed proteins (DEPs). Bioinformatics analyses, including Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway annotation and upstream regulatory analysis, were then performed on these retina proteins. Finally, a Western blotting experiment was carried out to verify the difference in the abundance of transcript factor E2F1. In this study, we identified a total of 2375 protein groups from the retinal protein samples of RCS rats and non-dystrophic congenic controls. Four hundred thirty-four significantly DEPs were selected by Student's t -test. Based on the results of the bioinformatics analysis, we identified mitochondrial dysfunction and transcription factor E2F1 as the key initiation factors in early retinal degenerative process. We showed that the mitochondrial dysfunction and the transcription factor E2F1 substantially contribute to the disease etiology of RP. The results provide a new potential therapeutic approach for this retinal degenerative disease.

  1. Surface Composition of NiPd Alloys

    NASA Technical Reports Server (NTRS)

    Noebe, Ronald D.; Khalil, Joe; Bozzolo, Guillermo; Gray, Hugh R. (Technical Monitor)

    2002-01-01

    Surface segregation in Ni-Pd alloys has been studied using the BFS method for alloys. Not only does the method predict an oscillatory segregation profile but it also indicates that the number of Pd-enriched surface planes can vary as a function of orientation. The segregation profiles were computed as a function of temperature, crystal face, and composition. Pd enrichment of the first layer is observed in (111) and (100) surfaces, and enrichment of the top two layers occurs for (110) surfaces. In all cases, the segregation profile shows oscillations that are actually related to weak ordering tendencies in the bulk. An atom-by-atom analysis was performed to identify the competing mechanisms leading to the observed surface behaviors. Large-scale atomistic simulations were also performed to investigate the temperature dependence of the segregation profiles as well as for analysis of the bulk structures. Finally, the observed surface behaviors are discussed in relation to the bulk phase structure of Ni-Pd alloys, which exhibit a tendency to weakly order.

  2. Customizing chemotherapy for colon cancer: the potential of gene expression profiling.

    PubMed

    Mariadason, John M; Arango, Diego; Augenlicht, Leonard H

    2004-06-01

    The value of gene expression profiling, or microarray analysis, for the classification and prognosis of multiple forms of cancer is now clearly established. For colon cancer, expression profiling can readily discriminate between normal and tumor tissue, and to some extent between tumors of different histopathological stage and prognosis. While a definitive in vivo study demonstrating the potential of this methodology for predicting response to chemotherapy is presently lacking, the ability of microarrays to distinguish other subtleties of colon cancer phenotype, as well as recent in vitro proof-of-principle experiments utilizing colon cancer cell lines, illustrate the potential of this methodology for predicting the probability of response to specific chemotherapeutic agents. This review discusses some of the recent advances in the use of microarray analysis for understanding and distinguishing colon cancer subtypes, and attempts to identify challenges that need to be overcome in order to achieve the goal of using gene expression profiling for customizing chemotherapy in colon cancer.

  3. A combined analysis of genome-wide expression profiling of bipolar disorder in human prefrontal cortex.

    PubMed

    Wang, Jinglu; Qu, Susu; Wang, Weixiao; Guo, Liyuan; Zhang, Kunlin; Chang, Suhua; Wang, Jing

    2016-11-01

    Numbers of gene expression profiling studies of bipolar disorder have been published. Besides different array chips and tissues, variety of the data processes in different cohorts aggravated the inconsistency of results of these genome-wide gene expression profiling studies. By searching the gene expression databases, we obtained six data sets for prefrontal cortex (PFC) of bipolar disorder with raw data and combinable platforms. We used standardized pre-processing and quality control procedures to analyze each data set separately and then combined them into a large gene expression matrix with 101 bipolar disorder subjects and 106 controls. A standard linear mixed-effects model was used to calculate the differentially expressed genes (DEGs). Multiple levels of sensitivity analyses and cross validation with genetic data were conducted. Functional and network analyses were carried out on basis of the DEGs. In the result, we identified 198 unique differentially expressed genes in the PFC of bipolar disorder and control. Among them, 115 DEGs were robust to at least three leave-one-out tests or different pre-processing methods; 51 DEGs were validated with genetic association signals. Pathway enrichment analysis showed these DEGs were related with regulation of neurological system, cell death and apoptosis, and several basic binding processes. Protein-protein interaction network further identified one key hub gene. We have contributed the most comprehensive integrated analysis of bipolar disorder expression profiling studies in PFC to date. The DEGs, especially those with multiple validations, may denote a common signature of bipolar disorder and contribute to the pathogenesis of disease. Copyright © 2016 Elsevier Ltd. All rights reserved.

  4. Metabolomic characterization of rhubarb species by capillary electrophoresis and ultra-high-pressure liquid chromatography.

    PubMed

    Tseng, Yufeng Jane; Kuo, Chun-Ting; Wang, San-Yuan; Liao, Hsiao-Wei; Chen, Guan-Yuan; Ku, Yuan-Ling; Shao, Wei-Cheng; Kuo, Ching-Hua

    2013-10-01

    This study developed CE and ultra-high-pressure LC (UHPLC) methods coupled with UV detectors to characterize the metabolomic profiles of different rhubarb species. The optimal CE conditions used a BGE with 15 mM sodium tetraborate, 15 mM sodium dihydrogen phosphate monohydrate, 30 mM sodium deoxycholate, and 30% ACN v/v at pH 8.3. The optimal UHPLC conditions used a mobile phase composed of 0.05% phosphate buffer and ACN with gradient elution. The gradient profile increased linearly from 10 to 21% ACN within the first 25 min, then increased to 33% ACN for the next 10 min. It took another 5 min to reach the 65% ACN, then for the next 5 min, it stayed unchanged. Sixteen samples of Rheum officinale and Rheum tanguticum collected from various locations were analyzed by CE and UHPLC methods. The metabolite profiles of CE were aligned and baseline corrected before chemometric analysis. Metabolomic signatures of rhubarb species from CE and UHPLC were clustered using principle component analysis and distance-based redundancy analysis; the clusters were not only able to discriminate different species but also different cultivation regions. Similarity measurements were performed by calculating the correlation coefficient of each sample with the authentic samples. Hybrid rhizome was clearly identified through similarity measurement of UHPLC metabolite profile and later confirmed by gene sequencing. The present study demonstrated that CE and UHPLC are efficient and effective tools to identify and authenticate herbs even coupled with simple detectors. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. Toward an operative diagnosis of fussy/picky eating: a latent profile approach in a population-based cohort

    PubMed Central

    2014-01-01

    Background Definitions and assessment methods of fussy/picky eating are heterogeneous and remain unclear. We aimed to identify an eating behavior profile reflecting fussy/picky eating in children and to describe characteristics of fussy eaters. Methods Eating behavior was assessed with the Child Eating Behavior Questionnaire (CEBQ) in 4914 4-year olds in a population-based birth cohort study. Latent Profile Analysis (LPA) was used to identify eating behavior profiles based on CEBQ subscales. Results and discussion We found a “fussy” eating behavior profile (5.6% of children) characterized by high food fussiness, slowness in eating, and satiety responsiveness in combination with low enjoyment of food and food responsiveness. Fussy eaters were more often from families with low household income than non-fussy eaters (42% vs. 31.8% respectively; Χ 2 (1) = 9.97, p < .01). When they were 14 months old, fussy eaters had a lower intake of vegetables (t [3008] = 2.42, p < .05) and fish (t [169.77] = 2.40, p < .05) but higher intake of savory snacks (t [153.69] = -2.03, p < .05) and sweets (t [3008] = -2.30, p < .05) compared to non-fussy eaters. Also, fussy eaters were more likely to be underweight at 4 years of age (19.3%) than non-fussy eaters (12.3%; Χ 2 (1) = 7.71, p < .01). Conclusions A distinct fussy eating behavior profile was identified by LPA, which was related to family and child characteristics, food intake, and BMI. This behavior profile might be used in future research and the development of interventions. PMID:24512388

  6. The risk typology of healthcare access and its association with unmet healthcare needs in Asian Americans.

    PubMed

    Jang, Yuri; Park, Nan Sook; Yoon, Hyunwoo; Huang, Ya-Ching; Rhee, Min-Kyoung; Chiriboga, David A; Kim, Miyong T

    2018-01-01

    Using data from the 2015 Asian American Quality of Life Survey (N = 2,609), latent profile analysis was conducted on general (health insurance, usual place for care and income) and immigrant-specific (nativity, length of stay in the U.S., English proficiency and acculturation) risk factors of healthcare access. Latent profile analysis identified a three-cluster model (low-risk, moderate-risk and high-risk groups). Compared with the low-risk group, the odds of having an unmet healthcare need was 1.52 times greater in the moderate-risk group and 2.24 times greater in the high-risk group. Challenging the myth of model minority, the present sample of Asian Americans demonstrates its vulnerability in access to healthcare. Findings also show the heterogeneity in healthcare access risk profiles. © 2017 John Wiley & Sons Ltd.

  7. Profiles in coping: responses to sexual harassment across persons, organizations, and cultures.

    PubMed

    Cortina, Lilia M; Wasti, S Arzu

    2005-01-01

    This study explicates the complexity of sexual harassment coping behavior among 4 diverse samples of working women: (a) working-class Hispanic Americans, (b) working-class Anglo Americans, (c) professional Turks, and (d) professional Anglo Americans. K-means cluster analysis revealed 3 common harassment coping profiles: (a) detached, (b) avoidant negotiating, and (c) support seeking. The authors then tested an integrated framework of coping profile determinants, involving social power, stressor severity, social support, and culture. Analysis of variance, chi-square, and discriminant function results identified significant determinants at each of the 4 levels of this ecological model. These findings underscore the importance of focusing on whole patterns of experience--and considering influences at the level of the individual employee and multiple levels of the surrounding context--when studying how women cope with workplace sexual harassment.

  8. Wind profiler signal detection improvements

    NASA Technical Reports Server (NTRS)

    Hart, G. F.; Divis, Dale H.

    1992-01-01

    Research is described on potential improvements to the software used with the NASA 49.25 MHz wind profiler located at Kennedy Space Center. In particular, the analysis and results are provided of a study to (1) identify preferred mathematical techniques for the detection of atmospheric signals that provide wind velocities which are obscured by natural and man-made sources, and (2) to analyze one or more preferred techniques to demonstrate proof of the capability to improve the detection of wind velocities.

  9. Predicting new drug indications from network analysis

    NASA Astrophysics Data System (ADS)

    Mohd Ali, Yousoff Effendy; Kwa, Kiam Heong; Ratnavelu, Kurunathan

    This work adapts centrality measures commonly used in social network analysis to identify drugs with better positions in drug-side effect network and drug-indication network for the purpose of drug repositioning. Our basic hypothesis is that drugs having similar phenotypic profiles such as side effects may also share similar therapeutic properties based on related mechanism of action and vice versa. The networks were constructed from Side Effect Resource (SIDER) 4.1 which contains 1430 unique drugs with side effects and 1437 unique drugs with indications. Within the giant components of these networks, drugs were ranked based on their centrality scores whereby 18 prominent drugs from the drug-side effect network and 15 prominent drugs from the drug-indication network were identified. Indications and side effects of prominent drugs were deduced from the profiles of their neighbors in the networks and compared to existing clinical studies while an optimum threshold of similarity among drugs was sought for. The threshold can then be utilized for predicting indications and side effects of all drugs. Similarities of drugs were measured by the extent to which they share phenotypic profiles and neighbors. To improve the likelihood of accurate predictions, only profiles such as side effects of common or very common frequencies were considered. In summary, our work is an attempt to offer an alternative approach to drug repositioning using centrality measures commonly used for analyzing social networks.

  10. Emerging Putative Associations between Non-Coding RNAs and Protein-Coding Genes in Neuropathic Pain: Added Value from Reusing Microarray Data

    PubMed Central

    Raju, Hemalatha B.; Tsinoremas, Nicholas F.; Capobianco, Enrico

    2016-01-01

    Regeneration of injured nerves is likely occurring in the peripheral nervous system, but not in the central nervous system. Although protein-coding gene expression has been assessed during nerve regeneration, little is currently known about the role of non-coding RNAs (ncRNAs). This leaves open questions about the potential effects of ncRNAs at transcriptome level. Due to the limited availability of human neuropathic pain (NP) data, we have identified the most comprehensive time-course gene expression profile referred to sciatic nerve (SN) injury and studied in a rat model using two neuronal tissues, namely dorsal root ganglion (DRG) and SN. We have developed a methodology to identify differentially expressed bioentities starting from microarray probes and repurposing them to annotate ncRNAs, while analyzing the expression profiles of protein-coding genes. The approach is designed to reuse microarray data and perform first profiling and then meta-analysis through three main steps. First, we used contextual analysis to identify what we considered putative or potential protein-coding targets for selected ncRNAs. Relevance was therefore assigned to differential expression of neighbor protein-coding genes, with neighborhood defined by a fixed genomic distance from long or antisense ncRNA loci, and of parental genes associated with pseudogenes. Second, connectivity among putative targets was used to build networks, in turn useful to conduct inference at interactomic scale. Last, network paths were annotated to assess relevance to NP. We found significant differential expression in long-intergenic ncRNAs (32 lincRNAs in SN and 8 in DRG), antisense RNA (31 asRNA in SN and 12 in DRG), and pseudogenes (456 in SN and 56 in DRG). In particular, contextual analysis centered on pseudogenes revealed some targets with known association to neurodegeneration and/or neurogenesis processes. While modules of the olfactory receptors were clearly identified in protein–protein interaction networks, other connectivity paths were identified between proteins already investigated in studies on disorders, such as Parkinson, Down syndrome, Huntington disease, and Alzheimer. Our findings suggest the importance of reusing gene expression data by meta-analysis approaches. PMID:27803687

  11. Emerging Putative Associations between Non-Coding RNAs and Protein-Coding Genes in Neuropathic Pain: Added Value from Reusing Microarray Data.

    PubMed

    Raju, Hemalatha B; Tsinoremas, Nicholas F; Capobianco, Enrico

    2016-01-01

    Regeneration of injured nerves is likely occurring in the peripheral nervous system, but not in the central nervous system. Although protein-coding gene expression has been assessed during nerve regeneration, little is currently known about the role of non-coding RNAs (ncRNAs). This leaves open questions about the potential effects of ncRNAs at transcriptome level. Due to the limited availability of human neuropathic pain (NP) data, we have identified the most comprehensive time-course gene expression profile referred to sciatic nerve (SN) injury and studied in a rat model using two neuronal tissues, namely dorsal root ganglion (DRG) and SN. We have developed a methodology to identify differentially expressed bioentities starting from microarray probes and repurposing them to annotate ncRNAs, while analyzing the expression profiles of protein-coding genes. The approach is designed to reuse microarray data and perform first profiling and then meta-analysis through three main steps. First, we used contextual analysis to identify what we considered putative or potential protein-coding targets for selected ncRNAs. Relevance was therefore assigned to differential expression of neighbor protein-coding genes, with neighborhood defined by a fixed genomic distance from long or antisense ncRNA loci, and of parental genes associated with pseudogenes. Second, connectivity among putative targets was used to build networks, in turn useful to conduct inference at interactomic scale. Last, network paths were annotated to assess relevance to NP. We found significant differential expression in long-intergenic ncRNAs (32 lincRNAs in SN and 8 in DRG), antisense RNA (31 asRNA in SN and 12 in DRG), and pseudogenes (456 in SN and 56 in DRG). In particular, contextual analysis centered on pseudogenes revealed some targets with known association to neurodegeneration and/or neurogenesis processes. While modules of the olfactory receptors were clearly identified in protein-protein interaction networks, other connectivity paths were identified between proteins already investigated in studies on disorders, such as Parkinson, Down syndrome, Huntington disease, and Alzheimer. Our findings suggest the importance of reusing gene expression data by meta-analysis approaches.

  12. Evaluation of volatiles from two subtropical strawberry cultivars using GC-olfactometry, GC-MS odor activity values, and sensory analysis

    USDA-ARS?s Scientific Manuscript database

    Flavor profiles of two Florida strawberry cultivars were determined using GC-olfactometry,GC-MS, odor activity values (OAVs) and sensory analysis. Thirty-six aroma active compounds were detected using GC-O. Thirty-four were identified. The major odor-active compounds in decreasing intensity were: me...

  13. Internalizing and externalizing personality and subjective effects in a sample of adolescent cannabis users.

    PubMed

    García-Sánchez, Sara; Matalí, Josep Lluís; Martín-Fernández, María; Pardo, Marta; Lleras, Maria; Castellano-Tejedor, Carmina; Haro, Josep Maria

    2016-10-06

    Cannabis is the illicit substance most widely used by adolescents. Certain personality traits such as impulsivity and sensation seeking, and the subjective effects experienced after substance use (e.g. euphoria or relaxation) have been identified as some of the main etiological factors of consumption. This study aims to categorize a sample of adolescent cannabis users based on their most dominant personality traits (internalizing and externalizing profile). Then, to make a comparison of both profiles considering a set of variables related to consumption, clinical severity and subjective effects experienced. From a cross-sectional design, 173 adolescents (104 men and 69 women) aged 13 to 18 asking for treatment for cannabis use disorder in an Addictive Behavior Unit (UCAD) from the hospital were recruited. For the assessment, an ad hoc protocol was employed to register consumption, the Millon Adolescent Clinical Inventory (MACI) and the Addiction Research Center Inventory (ARCI) 49-item short form were also administered. Factor analysis suggested a two-profile solution: Introverted, Inhibited, Doleful, Dramatizing (-), Egotistic (-), Self-demeaning and Borderline tendency scales composed the internalizing profile, and Submissive (-), Unruly, Forceful, Conforming (-) and Oppositional scales composed the externalizing profile. The comparative analysis showed that the internalizing profile has higher levels of clinical severity and more subjective effects reported than the externalizing profile. These results suggest the need to design specific intervention strategies for each profile.

  14. When somatization is not the only thing you suffer from: Examining comorbid syndromes using latent profile analysis, parenting practices and adolescent functioning.

    PubMed

    Scharf, Miri; Mayseless, Ofra; Rousseau, Sofie

    2016-10-30

    Understanding somatization presents a challenge to clinicians because it is often associated with other syndromes. We addressed somatization's comorbidity with other internalizing syndromes (anxiety, depression, withdrawal) using latent profile analysis. A representative sample of 3496 Israeli middle and high-school youths reported their internalizing symptoms, perceived parenting practices, psychosocial functioning, and health behaviors. Four profiles, similar across age and gender, were identified: overall-low (65.4%), moderately-high anxiety/depression/withdrawal (24.4%), high somatization (4.8%), and overall-high (5.4%). MANOVAs and follow-up ANOVAs revealed that for the most part the overall-high profile evinced the worst parenting, psychosocial functioning, and health behaviors (smoking and drinking), while the overall-low group evinced the best. For most variables the high somatization and moderately high profiles displayed midway results. However, the moderately-high profile reported higher levels of harsh parenting than the high somatization profile. The high somatization profile reported similar or higher levels of smoking, risk taking, vandalism, and rule violation than the overall-high group. High somatization, either alone or alongside anxiety, depression, and withdrawal, was associated with disruptive and risk-taking behaviors. This link might reflect problems in emotion and anger regulation and become stronger in adolescence because of dysregulation processes characterizing this period. Implications for practice are discussed. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  15. Serum Metabolomic Profiling in Acute Alcoholic Hepatitis Identifies Multiple Dysregulated Pathways

    PubMed Central

    Rachakonda, Vikrant; Gabbert, Charles; Raina, Amit; Bell, Lauren N.; Cooper, Sara; Malik, Shahid; Behari, Jaideep

    2014-01-01

    Background and Objectives While animal studies have implicated derangements of global energy homeostasis in the pathogenesis of acute alcoholic hepatitis (AAH), the relevance of these findings to the development of human AAH remains unclear. Using global, unbiased serum metabolomics analysis, we sought to characterize alterations in metabolic pathways associated with severe AAH and identify potential biomarkers for disease prognosis. Methods This prospective, case-control study design included 25 patients with severe AAH and 25 ambulatory patients with alcoholic cirrhosis. Serum samples were collected within 24 hours of the index clinical encounter. Global, unbiased metabolomics profiling was performed. Patients were followed for 180 days after enrollment to determine survival. Results Levels of 234 biochemicals were altered in subjects with severe AAH. Random-forest analysis, principal component analysis, and integrated hierarchical clustering methods demonstrated that metabolomics profiles separated the two cohorts with 100% accuracy. Severe AAH was associated with enhanced triglyceride lipolysis, impaired mitochondrial fatty acid beta oxidation, and upregulated omega oxidation. Low levels of multiple lysolipids and related metabolites suggested decreased plasma membrane remodeling in severe AAH. While most measured bile acids were increased in severe AAH, low deoxycholate and glycodeoxycholate levels indicated intestinal dysbiosis. Several changes in substrate utilization for energy homeostasis were identified in severe AAH, including increased glucose consumption by the pentose phosphate pathway, altered tricarboxylic acid (TCA) cycle activity, and enhanced peptide catabolism. Finally, altered levels of small molecules related to glutathione metabolism and antioxidant vitamin depletion were observed in patients with severe AAH. Univariable logistic regression revealed 15 metabolites associated with 180-day survival in severe AAH. Conclusion Severe AAH is characterized by a distinct metabolic phenotype spanning multiple pathways. Metabolomics profiling revealed a panel of biomarkers for disease prognosis, and future studies are planned to validate these findings in larger cohorts of patients with severe AAH. PMID:25461442

  16. ¹H NMR-based metabolic profiling of human rectal cancer tissue

    PubMed Central

    2013-01-01

    Background Rectal cancer is one of the most prevalent tumor types. Understanding the metabolic profile of rectal cancer is important for developing therapeutic approaches and molecular diagnosis. Methods Here, we report a metabonomics profiling of tissue samples on a large cohort of human rectal cancer subjects (n = 127) and normal controls (n = 43) using 1H nuclear magnetic resonance (1H NMR) based metabonomics assay, which is a highly sensitive and non-destructive method for the biomarker identification in biological systems. Principal component analysis (PCA), partial least squares discriminant analysis (PLS-DA) and orthogonal projection to latent structure with discriminant analysis (OPLS-DA) were applied to analyze the 1H-NMR profiling data to identify the distinguishing metabolites of rectal cancer. Results Excellent separation was obtained and distinguishing metabolites were observed among the different stages of rectal cancer tissues (stage I = 35; stage II = 37; stage III = 37 and stage IV = 18) and normal controls. A total of 38 differential metabolites were identified, 16 of which were closely correlated with the stage of rectal cancer. The up-regulation of 10 metabolites, including lactate, threonine, acetate, glutathione, uracil, succinate, serine, formate, lysine and tyrosine, were detected in the cancer tissues. On the other hand, 6 metabolites, including myo-inositol, taurine, phosphocreatine, creatine, betaine and dimethylglycine were decreased in cancer tissues. These modified metabolites revealed disturbance of energy, amino acids, ketone body and choline metabolism, which may be correlated with the progression of human rectal cancer. Conclusion Our findings firstly identify the distinguishing metabolites in different stages of rectal cancer tissues, indicating possibility of the attribution of metabolites disturbance to the progression of rectal cancer. The altered metabolites may be as potential biomarkers, which would provide a promising molecular diagnostic approach for clinical diagnosis of human rectal cancer. The role and underlying mechanism of metabolites in rectal cancer progression are worth being further investigated. PMID:24138801

  17. Teaching veterinary professionalism in the Face(book) of change.

    PubMed

    Coe, Jason B; Weijs, Cynthia A; Muise, Amy; Christofides, Emily; Desmarais, Serge

    2011-01-01

    Facebook has been identified as the preferred social networking site among postsecondary students. Repeated findings in the social networking literature have suggested that postsecondary students practice high personal self-disclosure on Facebook and tend not to use privacy settings that would limit public access. This study identified and reviewed Facebook profiles for 805 veterinarians-in-training enrolled at four veterinary colleges across Canada. Of these, 265 (32.9%) were categorized as having low exposure, 286 (35.5%) were categorized as having medium exposure, and 254 (31.6%) were categorized as having high exposure of information. Content analysis on a sub-sample (n=80) of the high-exposure profiles revealed publicly available unprofessional content, including indications of substance use and abuse, obscene comments, and breaches of client confidentiality. Regression analysis revealed that an increasing number of years to graduation and having a publicly visible wall were both positively associated with having a high-exposure profile. Given the rapid uptake of social media in recent years, veterinary educators should be aware of and begin to educate students on the associated risks and repercussions of blurring one's private life and one's emerging professional identity through personal online disclosures.

  18. Time-Resolved Transcriptome Analysis of Bacillus subtilis Responding to Valine, Glutamate, and Glutamine

    PubMed Central

    Ye, Bang-Ce; Zhang, Yan; Yu, Hui; Yu, Wen-Bang; Liu, Bao-Hong; Yin, Bin-Cheng; Yin, Chun-Yun; Li, Yuan-Yuan; Chu, Ju; Zhang, Si-Liang

    2009-01-01

    Microorganisms can restructure their transcriptional output to adapt to environmental conditions by sensing endogenous metabolite pools. In this paper, an Agilent customized microarray representing 4,106 genes was used to study temporal transcript profiles of Bacillus subtilis in response to valine, glutamate and glutamine pulses over 24 h. A total of 673, 835, and 1135 amino-acid-regulated genes were identified having significantly changed expression at one or more time points in response to valine, glutamate, and glutamine, respectively, including genes involved in cell wall, cellular import, metabolism of amino-acids and nucleotides, transcriptional regulation, flagellar motility, chemotaxis, phage proteins, sporulation, and many genes of unknown function. Different amino acid treatments were compared in terms of both the global temporal profiles and the 5-minute quick regulations, and between-experiment differential genes were identified. The highlighted genes were analyzed based on diverse sources of gene functions using a variety of computational tools, including T-profiler analysis, and hierarchical clustering. The results revealed the common and distinct modes of action of these three amino acids, and should help to elucidate the specific signaling mechanism of each amino acid as an effector. PMID:19763274

  19. Subcellular proteome profiles of different latex fractions revealed washed solutions from rubber particles contain crucial enzymes for natural rubber biosynthesis.

    PubMed

    Wang, Dan; Sun, Yong; Chang, Lili; Tong, Zheng; Xie, Quanliang; Jin, Xiang; Zhu, Liping; He, Peng; Li, Hongbin; Wang, Xuchu

    2018-06-30

    Rubber particle (RP) is a specific organelle for natural rubber biosynthesis (NRB) and storage in rubber tree Hevea brasiliensis. NRB is processed by RP membrane-localized proteins, which were traditionally purified by repeated washing. However, we noticed many proteins in the discarded washing solutions (WS) from RP. Here, we compared the proteome profiles of WS, C-serum (CS) and RP by 2-DE, and identified 233 abundant proteins from WS by mass spectrometry. Many spots on 2-DE gels were identified as different protein species. We further performed shotgun analysis of CS, WS and RP and identified 1837, 1799 and 1020 unique proteins, respectively. Together with 2-DE, we finally identified 1825 proteins from WS, 246 were WS-specific. These WS-specific proteins were annotated in Gene Ontology, indicating most abundant pathways are organic substance metabolic process, protein degradation, primary metabolic process, and energy metabolism. Protein-protein interaction analysis revealed these WS-specific proteins are mainly involved in ribosomal metabolism, proteasome system, vacuolar protein sorting and endocytosis. Label free and Western blotting revealed many WS-specific proteins and protein complexes are crucial for NRB initiation. These findings not only deepen our understanding of WS proteome, but also provide new evidences on the roles of RP membrane proteins in NRB. Natural rubber is stored in rubber particle from the rubber tree. Rubber particles were traditionally purified by repeated washing, but many proteins were identified from the washing solutions (WS). We obtained the first visualization proteome profiles with 1825 proteins from WS, including 246 WS-specific ones. These WS proteins contain almost all enzymes for polyisoprene initiation and may play important roles in rubber biosynthesis. Copyright © 2018 Elsevier B.V. All rights reserved.

  20. Removal of novel antiandrogens identified in biological effluents of domestic wastewater by activated carbon.

    PubMed

    Ma, Dehua; Chen, Lujun; Liu, Rui

    2017-10-01

    Environmental antiandrogenic (AA) contaminants in effluents from wastewater treatment plants have the potential for negative impacts on wildlife and human health. The aim of our study was to identify chemical contaminants with likely AA activity in the biological effluents and evaluate the removal of these antiandrogens (AAs) during advanced treatment comprising adsorption onto granular activated carbon (GAC). In this study, profiling of AA contaminants in biological effluents and tertiary effluents was conducted using effect-directed analysis (EDA) including high performance liquid chromatography (HPLC) fractionation, a recombinant yeast screen containing androgen receptor (YAS), in combination with mass spectrometry analyses. Analysis of a wastewater secondary effluent from a membrane bioreactor revealed complex profiles of AA activity comprising 14 HPLC fractions and simpler profiles of GAC effluents with only 2 to 4 moderately polar HPLC fractions depending on GAC treatment conditions. Gas chromatography-mass spectrometry and ultra-high performance liquid chromatography-nanospray mass spectrometry analyses of AA fractions in the secondary effluent resulted in detection of over 10 chemical contaminants, which showed inhibition of YAS activity and were potential AAs. The putative AAs included biocides, food additives, flame retardants, pharmaceuticals and industrial contaminants. To our knowledge, it is the first time that the AA properties of N-ethyl-2-isopropyl-5-methylcyclohexanecarboxamide (WS3), cetirizine, and oxcarbazepine are reported. The EDA used in this study was proven to be a powerful tool to identify novel chemical structures with AA activity in the complex aquatic environment. The adsorption process to GAC of all the identified antiandrogens, except WS3 and triclosan, fit well with the pseudo-second order kinetics models. Adsorption to GAC could further remove most of the AAs identified in the biological effluents with high efficiencies. Copyright © 2017 Elsevier B.V. All rights reserved.

  1. Distinct Evening Fatigue Profiles in Oncology Outpatients Receiving Chemotherapy

    PubMed Central

    Wright, Fay; Cooper, Bruce A.; Conley, Yvette P.; Hammer, Marilyn J.; Chen, Lee-May; Paul, Steven M.; Levine, Jon D.; Miaskowski, Christine; Kober, Kord M.

    2018-01-01

    Background Fatigue is the most common and debilitating symptom experienced by oncology patients during chemotherapy (CTX). Fatigue severity demonstrates a large amount of inter-individual and diurnal variability. Purpose Study purposes were to evaluate for subgroups of patients with distinct evening fatigue profiles and evaluate how these subgroups differed on demographic, clinical, and symptom characteristics. Methods Outpatients with breast, gastrointestinal, gynecological, or lung cancer (n=1332) completed questionnaires six times over two cycles of CTX. Lee Fatigue Scale (LFS) evaluated evening fatigue severity. Latent profile analysis was used to identify distinct evening fatigue profiles. Results Four distinct evening fatigue classes (i.e., Low (14.0%), Moderate (17.2%), High (36.0%), Very High (32.8%)) were identified. Compared to the Low class, patients in the Very High evening fatigue class were: younger, female, had childcare responsibilities, had more years of education, had a lower functional status, had a higher comorbidity burden, and were diagnosed with breast cancer. Patients in the Very High class reported higher levels of depressive symptoms, sleep disturbance, and evening fatigue at enrollment. Conclusions Findings provide new insights into modifiable risk factors for higher levels of evening fatigue. Clinicians can use this information to identify higher risk patients and plan appropriate interventions. PMID:29725554

  2. Dose-response relationships in gene expression profiles in rainbow trout, Oncorhyncus mykiss, exposed to ethynylestradiol.

    PubMed

    Hook, Sharon E; Skillman, Ann D; Small, Jack A; Schultz, Irvin R

    2006-07-01

    Determining how gene expression profiles change with toxicant dose will improve the utility of arrays in identifying biomarkers and modes of toxic action. Isogenic rainbow trout, Oncorhyncus mykiss,were exposed to 10, 50 or 100 ng/L ethynylestradiol (a xeno-estrogen) for 7 days. Following exposure hepatic RNA was extracted. Fluorescently labeled cDNA were generated and hybridized against a commercially available Atlantic Salmon/Trout array (GRASP project, University of Victoria) spotted with 16,000 cDNAs. Transcript expression in treated vs control fish was analyzed via Genespring (Silicon Genetics) to identify genes with altered expression, as well as to determine gene clustering patterns that can be used as "expression signatures". Array results were confirmed via qRT PCR. Our analysis indicates that gene expression profiles varied somewhat with dose. Established biomarkers of exposure to estrogenic chemicals, such as vitellogenin, vitelline envelope proteins, and the estrogen receptor alpha, were induced at every dose. Other genes were dose specific, suggesting that different doses induce distinct physiological responses. These findings demonstrate that cDNA microarrays could be used to identify both toxicant class and relative dose.

  3. Validation of a combined autosomal/Y-chromosomal STR approach for analyzing typical biological stains in sexual-assault cases.

    PubMed

    Purps, Josephine; Geppert, Maria; Nagy, Marion; Roewer, Lutz

    2015-11-01

    DNA testing is an established part of the investigation and prosecution of sexual assault. The primary purpose of DNA evidence is to identify a suspect and/or to demonstrate sexual contact. However, due to highly uneven proportions of female and male DNA in typical stains, routine autosomal analysis often fails to detect the DNA of the assailant. To evaluate the forensic efficiency of the combined application of autosomal and Y-chromosomal short tandem repeat (STR) markers, we present a large retrospective casework study of probative evidence collected in sexual-assault cases. We investigated up to 39 STR markers by testing combinations of the 16-locus NGMSElect kit with both the 23-locus PowerPlex Y23 and the 17-locus Yfiler kit. Using this dual approach we analyzed DNA extracts from 2077 biological stains collected in 287 cases over 30 months. To assess the outcome of the combined approach in comparison to stand-alone autosomal analysis we evaluated informative DNA profiles. Our investigation revealed that Y-STR analysis added up to 21% additional, highly informative (complete, single-source) profiles to the set of reportable autosomal STR profiles for typical stains collected in sexual-assault cases. Detection of multiple male contributors was approximately three times more likely with Y-chromosomal profiling than with autosomal STR profiling. In summary, 1/10 cases would have remained inconclusive (and could have been dismissed) if Y-STR analysis had been omitted from DNA profiling in sexual-assault cases. Copyright © 2015 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.

  4. Isolation of Polysomal RNA for Analyzing Stress-Responsive Genes Regulated at the Translational Level in Plants.

    PubMed

    Li, Yong-Fang; Mahalingam, Ramamurthy; Sunkar, Ramanjulu

    2017-01-01

    Alteration of gene expression is an essential mechanism, which allows plants to respond and adapt to adverse environmental conditions. Transcriptome and proteome analyses in plants exposed to abiotic stresses revealed that protein levels are not correlated with the changes in corresponding mRNAs, indicating regulation at translational level is another major regulator for gene expression. Analysis of translatome, which refers to all mRNAs associated with ribosomes, thus has the potential to bridge the gap between transcriptome and proteome. Polysomal RNA profiling and recently developed ribosome profiling (Ribo-seq) are two main methods for translatome analysis at global level. Here, we describe the classical procedure for polysomal RNA isolation by sucrose gradient ultracentrifugation followed by highthroughput RNA-seq to identify genes regulated at translational level. Polysomal RNA can be further used for a variety of downstream applications including Northern blot analysis, qRT-PCR, RNase protection assay, and microarray-based gene expression profiling.

  5. Biomarkers identified by urinary metabonomics for noninvasive diagnosis of nutritional rickets.

    PubMed

    Wang, Maoqing; Yang, Xue; Ren, Lihong; Li, Songtao; He, Xuan; Wu, Xiaoyan; Liu, Tingting; Lin, Liqun; Li, Ying; Sun, Changhao

    2014-09-05

    Nutritional rickets is a worldwide public health problem; however, the current diagnostic methods retain shortcomings for accurate diagnosis of nutritional rickets. To identify urinary biomarkers associated with nutritional rickets and establish a noninvasive diagnosis method, urinary metabonomics analysis by ultra-performance liquid chromatography/quadrupole time-of-flight tandem mass spectrometry and multivariate statistical analysis were employed to investigate the metabolic alterations associated with nutritional rickets in 200 children with or without nutritional rickets. The pathophysiological changes and pathogenesis of nutritional rickets were illustrated by the identified biomarkers. By urinary metabolic profiling, 31 biomarkers of nutritional rickets were identified and five candidate biomarkers for clinical diagnosis were screened and identified by quantitative analysis and receiver operating curve analysis. Urinary levels of five candidate biomarkers were measured using mass spectrometry or commercial kits. In the validation step, the combination of phosphate and sebacic acid was able to give a noninvasive and accurate diagnostic with high sensitivity (94.0%) and specificity (71.2%). Furthermore, on the basis of the pathway analysis of biomarkers, our urinary metabonomics analysis gives new insight into the pathogenesis and pathophysiology of nutritional rickets.

  6. A metabolomics-based method for studying the effect of yfcC gene in Escherichia coli on metabolism.

    PubMed

    Wang, Xiyue; Xie, Yuping; Gao, Peng; Zhang, Sufang; Tan, Haidong; Yang, Fengxu; Lian, Rongwei; Tian, Jing; Xu, Guowang

    2014-04-15

    Metabolomics is a potent tool to assist in identifying the function of unknown genes through analysis of metabolite changes in the context of varied genetic backgrounds. However, the availability of a universal unbiased profiling analysis is still a big challenge. In this study, we report an optimized metabolic profiling method based on gas chromatography-mass spectrometry for Escherichia coli. It was found that physiological saline at -80°C could ensure satisfied metabolic quenching with less metabolite leakage. A solution of methanol/water (21:79, v/v) was proved to be efficient for intracellular metabolite extraction. This method was applied to investigate the metabolome difference among wild-type E. coli, its yfcC deletion, and overexpression mutants. Statistical and bioinformatic analysis of the metabolic profiling data indicated that the expression of yfcC potentially affected the metabolism of glyoxylate shunt. This finding was further validated by real-time quantitative polymerase chain reactions showing that expression of aceA and aceB, the key genes in glyoxylate shunt, was upregulated by yfcC. This study exemplifies the robustness of the proposed metabolic profiling analysis strategy and its potential roles in investigating unknown gene functions in view of metabolome difference. Copyright © 2014 Elsevier Inc. All rights reserved.

  7. Transcriptional response of peripheral lymphocytes to early fibrosarcoma: a model system for cancer detection based on hybridization signatures.

    PubMed

    Marques, Márcia M C; Junta, Cristina M; Zárate-Blades, Carlos R; Sakamoto-Hojo, Elza Tiemi; Donadi, Eduardo A; Passos, Geraldo A S

    2009-07-01

    Since circulating leukocytes, mainly B and T cells, continuously maintain vigilant and comprehensive immune surveillance, these cells could be used as reporters for signs of infection or other pathologies, including cancer. Activated lymphocyte clones trigger a sensitive transcriptional response, which could be identified by gene expression profiling. To assess this hypothesis, we conducted microarray analysis of the gene expression profile of lymphocytes isolated from immunocompetent BALB/c mice subcutaneously injected with different numbers of tumorigenic B61 fibrosarcoma cells. Flow cytometry demonstrated that the number of circulating T (CD3(+)CD4(+) or CD3(+)CD8(+)) or B (CD19(+)) cells did not change. However, the lymphocytes isolated from tumor cell-injected animals expressed a unique transcriptional profile that was identifiable before the development of a palpable tumor mass. This finding demonstrates that the transcriptional response appears before alterations in the main lymphocyte subsets and that the gene expression profile of peripheral lymphocytes can serve as a sensitive and accurate method for the early detection of cancer.

  8. An Analysis of natural mentoring relationship profiles and associations with mentees’ mental health: considering links via support from important others

    PubMed Central

    Hurd, Noelle M.; Zimmerman, Marc A.

    2015-01-01

    We explored associations between natural mentoring relationship profiles and young adults’ life satisfaction and symptoms of depression via participants’ perceived support from important others accounting for participants’ perceived support and mental health prior to the onset of their natural mentoring relationships. Participants included 396 young adults (57% female; mean age = 30.97, SD = .6), the majority of whom identified as Black or African American (79% Black, 18% White, 3% Biracial). Most participants had completed high school but few participants (13%) had completed degrees from 4-year institutions. We used a latent profile approach to identify natural mentoring relationship profiles and employed structural equation modeling to test our study hypotheses. Slightly over half of study participants (53%) reported the presence of a natural mentor in their lives since the age of 14. Results suggest that natural mentoring relationships characterized by high levels of relational closeness and either extended relationship duration or frequent contact may promote improvements in psychological well-being among mentees over time via greater experiences of social support from important others. PMID:24132713

  9. [The problem of molecular-genetic identification of sweat and grease deposits in the human fingerprints].

    PubMed

    Faleeva, T G; Ivanov, I N; Mishin, E S; Vnukova, N V; Kornienko, I V

    2016-01-01

    The objective of the present experimental molecular-genetic study of DNA contained in of human fingerprints was to establish the relationship between the reference genetic profiles and the genotypes of the individuals leaving their fingerprints on a smooth metal object. The biological material for the purpose of the investigation was sampled at different time intervals. The were taken using a scotch tape and used to obtain the complete genetic profile immediately after the fingerprints had been left as well as within the next 24 hours and one week. It proved impossible to identify the complete genetic profile one month after the fingerprints had been left. The alleles not typical for reference samples were identified within one week after swabbing the material from the metal surface. The results of the sudy can be explained by the decrease of the concentration of the initial DNA-matrix in the samples due to its degradation in the course of time. It is concluded that the parallel genetic analysis is needed if reliable evidence of identity of the profiles of interest or its absence is to be obtained.

  10. Prioritization of anti-malarial hits from nature: chemo-informatic profiling of natural products with in vitro antiplasmodial activities and currently registered anti-malarial drugs.

    PubMed

    Egieyeh, Samuel Ayodele; Syce, James; Malan, Sarel F; Christoffels, Alan

    2016-01-29

    A large number of natural products have shown in vitro antiplasmodial activities. Early identification and prioritization of these natural products with potential for novel mechanism of action, desirable pharmacokinetics and likelihood for development into drugs is advantageous. Chemo-informatic profiling of these natural products were conducted and compared to currently registered anti-malarial drugs (CRAD). Natural products with in vitro antiplasmodial activities (NAA) were compiled from various sources. These natural products were sub-divided into four groups based on inhibitory concentration (IC50). Key molecular descriptors and physicochemical properties were computed for these compounds and analysis of variance used to assess statistical significance amongst the sets of compounds. Molecular similarity analysis, estimation of drug-likeness, in silico pharmacokinetic profiling, and exploration of structure-activity landscape were also carried out on these sets of compounds. A total of 1040 natural products were selected and a total of 13 molecular descriptors were analysed. Significant differences were observed among the sub-groups of NAA and CRAD for at least 11 of the molecular descriptors, including number of hydrogen bond donors and acceptors, molecular weight, polar and hydrophobic surface areas, chiral centres, oxygen and nitrogen atoms, and shape index. The remaining molecular descriptors, including clogP, number of rotatable bonds and number of aromatic rings, did not show any significant difference when comparing the two compound sets. Molecular similarity and chemical space analysis identified natural products that were structurally diverse from CRAD. Prediction of the pharmacokinetic properties and drug-likeness of these natural products identified over 50% with desirable drug-like properties. Nearly 70% of all natural products were identified as potentially promiscuous compounds. Structure-activity landscape analysis highlighted compound pairs that form 'activity cliffs'. In all, prioritization strategies for the NAA were proposed. Chemo-informatic profiling of NAA and CRAD have produced a wealth of information that may guide decisions and facilitate anti-malarial drug development from natural products. Articulation of the information provided within an interactive data-mining environment led to a prioritized list of NAA.

  11. Criminal psychological profiling of serial arson crimes.

    PubMed

    Kocsis, Richard N; Cooksey, Ray W

    2002-12-01

    The practice of criminal psychological profiling is frequently cited as being applicable to serial arson crimes. Despite this claim, there does not appear to be any empirical research that examines serial arson offence behaviors in the context of profiling. This study seeks to develop an empirical model of serial arsonist behaviors that can be systematically associated with probable offender characteristics. Analysis has produced a model of offence behaviors that identify four discrete behavior patterns, all of which share a constellation of common nondiscriminatory behaviors. The inherent behavioral themes of each of these patterns are explored with discussion of their broader implications for our understanding of serial arson and directions for future research.

  12. Genetic Polymorphisms and Phenotypic Profiles of Sulfadiazine-Resistant and Sensitive Toxoplasma gondii Isolates Obtained from Newborns with Congenital Toxoplasmosis in Minas Gerais, Brazil.

    PubMed

    Silva, Letícia Azevedo; Reis-Cunha, João Luís; Bartholomeu, Daniella Castanheira; Vítor, Ricardo Wagner Almeida

    2017-01-01

    Previous Toxoplasma gondii studies revealed that mutations in the dhps (dihydropteroate synthase) gene are associated with resistance to sulfonamides. Although Brazilian strains are genotypically different, very limited data are available regarding the susceptibility of strains obtained from human to sulfonamides. The aim of this study was to evaluate the efficacy of sulfadiazine (SDZ) against Brazilian isolates of T. gondii and verify whether isolates present polymorphisms in the dhps gene. We also investigated whether the virulence-phenotype and/or genotype were associated with the profile of susceptibility to SDZ. Five T. gondii isolates obtained from newborns with congenital toxoplasmosis were used to verify susceptibility. Mice were infected with 104 tachyzoites and orally treated with different doses of SDZ. The mortality curve was evaluated by the Log-rank test. The presence of polymorphisms in the dhps gene was verified using sequencing. A descriptive analysis for 11 Brazilian isolates was used to assess the association between susceptibility, genotype, and virulence-phenotype. Statistical analysis showed that TgCTBr03, 07, 08, and 16 isolates were susceptible to SDZ, whereas TgCTBr11 isolate presented a profile of resistance to SDZ. Nineteen polymorphisms were identified in dhps exons. Seven polymorphisms corresponded to non-synonymous mutations, with four being new mutations, described for the first time in this study. No association was found between the profile of susceptibility and the virulence-phenotype or genotype of the parasite. There is a high variability in the susceptibilities of Brazilian T. gondii strains to SDZ, with evidence of drug resistance. Despite the large number of polymorphisms identified, the profile of susceptibility to SDZ was not associated with any of the dhps variants identified in this study. Other genetic factors, not yet determined, may be associated with the resistance to SDZ; thus, further studies are needed as a basis for a more adequate toxoplasmosis treatment.

  13. Genetic Polymorphisms and Phenotypic Profiles of Sulfadiazine-Resistant and Sensitive Toxoplasma gondii Isolates Obtained from Newborns with Congenital Toxoplasmosis in Minas Gerais, Brazil

    PubMed Central

    Silva, Letícia Azevedo; Reis-Cunha, João Luís; Bartholomeu, Daniella Castanheira; Vítor, Ricardo Wagner Almeida

    2017-01-01

    Background Previous Toxoplasma gondii studies revealed that mutations in the dhps (dihydropteroate synthase) gene are associated with resistance to sulfonamides. Although Brazilian strains are genotypically different, very limited data are available regarding the susceptibility of strains obtained from human to sulfonamides. The aim of this study was to evaluate the efficacy of sulfadiazine (SDZ) against Brazilian isolates of T. gondii and verify whether isolates present polymorphisms in the dhps gene. We also investigated whether the virulence-phenotype and/or genotype were associated with the profile of susceptibility to SDZ. Methods Five T. gondii isolates obtained from newborns with congenital toxoplasmosis were used to verify susceptibility. Mice were infected with 104 tachyzoites and orally treated with different doses of SDZ. The mortality curve was evaluated by the Log-rank test. The presence of polymorphisms in the dhps gene was verified using sequencing. A descriptive analysis for 11 Brazilian isolates was used to assess the association between susceptibility, genotype, and virulence-phenotype. Results Statistical analysis showed that TgCTBr03, 07, 08, and 16 isolates were susceptible to SDZ, whereas TgCTBr11 isolate presented a profile of resistance to SDZ. Nineteen polymorphisms were identified in dhps exons. Seven polymorphisms corresponded to non-synonymous mutations, with four being new mutations, described for the first time in this study. No association was found between the profile of susceptibility and the virulence-phenotype or genotype of the parasite. Conclusions There is a high variability in the susceptibilities of Brazilian T. gondii strains to SDZ, with evidence of drug resistance. Despite the large number of polymorphisms identified, the profile of susceptibility to SDZ was not associated with any of the dhps variants identified in this study. Other genetic factors, not yet determined, may be associated with the resistance to SDZ; thus, further studies are needed as a basis for a more adequate toxoplasmosis treatment. PMID:28118394

  14. Integrated RNA-Seq and sRNA-Seq Analysis Identifies Chilling and Freezing Responsive Key Molecular Players and Pathways in Tea Plant (Camellia sinensis)

    PubMed Central

    Zheng, Chao; Zhao, Lei; Wang, Yu; Shen, Jiazhi; Zhang, Yinfei; Jia, Sisi; Li, Yusheng; Ding, Zhaotang

    2015-01-01

    Tea [Camellia sinensis (L) O. Kuntze, Theaceae] is one of the most popular non-alcoholic beverages worldwide. Cold stress is one of the most severe abiotic stresses that limit tea plants’ growth, survival and geographical distribution. However, the genetic regulatory network and signaling pathways involved in cold stress responses in tea plants remain unearthed. Using RNA-Seq, DGE and sRNA-Seq technologies, we performed an integrative analysis of miRNA and mRNA expression profiling and their regulatory network of tea plants under chilling (4℃) and freezing (-5℃) stress. Differentially expressed (DE) miRNA and mRNA profiles were obtained based on fold change analysis, miRNAs and target mRNAs were found to show both coherent and incoherent relationships in the regulatory network. Furthermore, we compared several key pathways (e.g., ‘Photosynthesis’), GO terms (e.g., ‘response to karrikin’) and transcriptional factors (TFs, e.g., DREB1b/CBF1) which were identified as involved in the early chilling and/or freezing response of tea plants. Intriguingly, we found that karrikins, a new group of plant growth regulators, and β-primeverosidase (BPR), a key enzyme functionally relevant with the formation of tea aroma might play an important role in both early chilling and freezing response of tea plants. Quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR) analysis further confirmed the results from RNA-Seq and sRNA-Seq analysis. This is the first study to simultaneously profile the expression patterns of both miRNAs and mRNAs on a genome-wide scale to elucidate the molecular mechanisms of early responses of tea plants to cold stress. In addition to gaining a deeper insight into the cold resistant characteristics of tea plants, we provide a good case study to analyse mRNA/miRNA expression and profiling of non-model plant species using next-generation sequencing technology. PMID:25901577

  15. Integrated RNA-Seq and sRNA-Seq Analysis Identifies Chilling and Freezing Responsive Key Molecular Players and Pathways in Tea Plant (Camellia sinensis).

    PubMed

    Zheng, Chao; Zhao, Lei; Wang, Yu; Shen, Jiazhi; Zhang, Yinfei; Jia, Sisi; Li, Yusheng; Ding, Zhaotang

    2015-01-01

    Tea [Camellia sinensis (L) O. Kuntze, Theaceae] is one of the most popular non-alcoholic beverages worldwide. Cold stress is one of the most severe abiotic stresses that limit tea plants' growth, survival and geographical distribution. However, the genetic regulatory network and signaling pathways involved in cold stress responses in tea plants remain unearthed. Using RNA-Seq, DGE and sRNA-Seq technologies, we performed an integrative analysis of miRNA and mRNA expression profiling and their regulatory network of tea plants under chilling (4℃) and freezing (-5℃) stress. Differentially expressed (DE) miRNA and mRNA profiles were obtained based on fold change analysis, miRNAs and target mRNAs were found to show both coherent and incoherent relationships in the regulatory network. Furthermore, we compared several key pathways (e.g., 'Photosynthesis'), GO terms (e.g., 'response to karrikin') and transcriptional factors (TFs, e.g., DREB1b/CBF1) which were identified as involved in the early chilling and/or freezing response of tea plants. Intriguingly, we found that karrikins, a new group of plant growth regulators, and β-primeverosidase (BPR), a key enzyme functionally relevant with the formation of tea aroma might play an important role in both early chilling and freezing response of tea plants. Quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR) analysis further confirmed the results from RNA-Seq and sRNA-Seq analysis. This is the first study to simultaneously profile the expression patterns of both miRNAs and mRNAs on a genome-wide scale to elucidate the molecular mechanisms of early responses of tea plants to cold stress. In addition to gaining a deeper insight into the cold resistant characteristics of tea plants, we provide a good case study to analyse mRNA/miRNA expression and profiling of non-model plant species using next-generation sequencing technology.

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

    PubMed

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

    2009-07-31

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

  17. A geochemical study of overbank sediments in an urban area (Madrid, Spain).

    PubMed

    Adánez Sanjuán, Paula; Llamas Borrajo, Juan F; Locutura Rupérez, Juan; García Cortés, Angel

    2014-12-01

    Overbank and stream sediments have been studied in the Community of Madrid. Four vertical profiles have been sampled corresponding to Guadarrama, Jarama, and finally Manzanares River, where two profiles have been studied upstream (El Pardo profile) and downstream (Rivas profile) Madrid city. Sieved samples (<63 µm) were subjected to total (ICP-MS/ICP-OES and INAA) and partial analysis (ICP-MS). AMS radiocarbon dating techniques revealed a young age (170 ± 40 years BP) at 2.40-2.65 m depth for Rivas profile. It has not been possible to detect pristine or pre-industrial overbank sediments, since in the rest of the studied profiles, anthropogenic wastes were found even in the lower levels. Three main sources of sediment have been detected in the area. Granitic and arkosic geology, located in the northern part of Madrid (U, Th, W, K, Na, or rare earth elements); clays located in the southeast of Madrid (Ni, Cr, or V), and finally an anthropogenic source has been identified (Au, Ag, Pb, Zn, or Sb) in Rivas profile. The influence of the anthropogenic activity has been established based on the contents distribution of contaminant elements in the profile. This can be associated to the growth of industrial activities and population in the city of Madrid during the last decades. The comparison of the profiles by a k-means cluster analysis showed some similarities for these samples that could have analogous sources (anthropogenic and geological).

  18. Identifying avian sources of faecal contamination using sterol analysis.

    PubMed

    Devane, Megan L; Wood, David; Chappell, Andrew; Robson, Beth; Webster-Brown, Jenny; Gilpin, Brent J

    2015-10-01

    Discrimination of the source of faecal pollution in water bodies is an important step in the assessment and mitigation of public health risk. One tool for faecal source tracking is the analysis of faecal sterols which are present in faeces of animals in a range of distinctive ratios. Published ratios are able to discriminate between human and herbivore mammal faecal inputs but are of less value for identifying pollution from wildfowl, which can be a common cause of elevated bacterial indicators in rivers and streams. In this study, the sterol profiles of 50 avian-derived faecal specimens (seagulls, ducks and chickens) were examined alongside those of 57 ruminant faeces and previously published sterol profiles of human wastewater, chicken effluent and animal meatwork effluent. Two novel sterol ratios were identified as specific to avian faecal scats, which, when incorporated into a decision tree with human and herbivore mammal indicative ratios, were able to identify sterols from avian-polluted waterways. For samples where the sterol profile was not consistent with herbivore mammal or human pollution, avian pollution is indicated when the ratio of 24-ethylcholestanol/(24-ethylcholestanol + 24-ethylcoprostanol + 24-ethylepicoprostanol) is ≥0.4 (avian ratio 1) and the ratio of cholestanol/(cholestanol + coprostanol + epicoprostanol) is ≥0.5 (avian ratio 2). When avian pollution is indicated, further confirmation by targeted PCR specific markers can be employed if greater confidence in the pollution source is required. A 66% concordance between sterol ratios and current avian PCR markers was achieved when 56 water samples from polluted waterways were analysed.

  19. Genetic overlap between diagnostic subtypes of ischemic stroke.

    PubMed

    Holliday, Elizabeth G; Traylor, Matthew; Malik, Rainer; Bevan, Steve; Falcone, Guido; Hopewell, Jemma C; Cheng, Yu-Ching; Cotlarciuc, Ioana; Bis, Joshua C; Boerwinkle, Eric; Boncoraglio, Giorgio B; Clarke, Robert; Cole, John W; Fornage, Myriam; Furie, Karen L; Ikram, M Arfan; Jannes, Jim; Kittner, Steven J; Lincz, Lisa F; Maguire, Jane M; Meschia, James F; Mosley, Thomas H; Nalls, Mike A; Oldmeadow, Christopher; Parati, Eugenio A; Psaty, Bruce M; Rothwell, Peter M; Seshadri, Sudha; Scott, Rodney J; Sharma, Pankaj; Sudlow, Cathie; Wiggins, Kerri L; Worrall, Bradford B; Rosand, Jonathan; Mitchell, Braxton D; Dichgans, Martin; Markus, Hugh S; Levi, Christopher; Attia, John; Wray, Naomi R

    2015-03-01

    Despite moderate heritability, the phenotypic heterogeneity of ischemic stroke has hampered gene discovery, motivating analyses of diagnostic subtypes with reduced sample sizes. We assessed evidence for a shared genetic basis among the 3 major subtypes: large artery atherosclerosis (LAA), cardioembolism, and small vessel disease (SVD), to inform potential cross-subtype analyses. Analyses used genome-wide summary data for 12 389 ischemic stroke cases (including 2167 LAA, 2405 cardioembolism, and 1854 SVD) and 62 004 controls from the Metastroke consortium. For 4561 cases and 7094 controls, individual-level genotype data were also available. Genetic correlations between subtypes were estimated using linear mixed models and polygenic profile scores. Meta-analysis of a combined LAA-SVD phenotype (4021 cases and 51 976 controls) was performed to identify shared risk alleles. High genetic correlation was identified between LAA and SVD using linear mixed models (rg=0.96, SE=0.47, P=9×10(-4)) and profile scores (rg=0.72; 95% confidence interval, 0.52-0.93). Between LAA and cardioembolism and SVD and cardioembolism, correlation was moderate using linear mixed models but not significantly different from zero for profile scoring. Joint meta-analysis of LAA and SVD identified strong association (P=1×10(-7)) for single nucleotide polymorphisms near the opioid receptor μ1 (OPRM1) gene. Our results suggest that LAA and SVD, which have been hitherto treated as genetically distinct, may share a substantial genetic component. Combined analyses of LAA and SVD may increase power to identify small-effect alleles influencing shared pathophysiological processes. © 2015 American Heart Association, Inc.

  20. 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

  1. Gene expression profiling in whole blood of patients with coronary artery disease

    PubMed Central

    Taurino, Chiara; Miller, William H.; McBride, Martin W.; McClure, John D.; Khanin, Raya; Moreno, María U.; Dymott, Jane A.; Delles, Christian; Dominiczak, Anna F.

    2010-01-01

    Owing to the dynamic nature of the transcriptome, gene expression profiling is a promising tool for discovery of disease-related genes and biological pathways. In the present study, we examined gene expression in whole blood of 12 patients with CAD (coronary artery disease) and 12 healthy control subjects. Furthermore, ten patients with CAD underwent whole-blood gene expression analysis before and after the completion of a cardiac rehabilitation programme following surgical coronary revascularization. mRNA and miRNA (microRNA) were isolated for expression profiling. Gene expression analysis identified 365 differentially expressed genes in patients with CAD compared with healthy controls (175 up- and 190 down-regulated in CAD), and 645 in CAD rehabilitation patients (196 up- and 449 down-regulated post-rehabilitation). Biological pathway analysis identified a number of canonical pathways, including oxidative phosphorylation and mitochondrial function, as being significantly and consistently modulated across the groups. Analysis of miRNA expression revealed a number of differentially expressed miRNAs, including hsa-miR-140-3p (control compared with CAD, P=0.017), hsa-miR-182 (control compared with CAD, P=0.093), hsa-miR-92a and hsa-miR-92b (post- compared with pre-exercise, P<0.01). Global analysis of predicted miRNA targets found significantly reduced expression of genes with target regions compared with those without: hsa-miR-140-3p (P=0.002), hsa-miR-182 (P=0.001), hsa-miR-92a and hsa-miR-92b (P=2.2×10−16). In conclusion, using whole blood as a ‘surrogate tissue’ in patients with CAD, we have identified differentially expressed miRNAs, differentially regulated genes and modulated pathways which warrant further investigation in the setting of cardiovascular function. This approach may represent a novel non-invasive strategy to unravel potentially modifiable pathways and possible therapeutic targets in cardiovascular disease. PMID:20528768

  2. Identification of gene expression profiles and key genes in subchondral bone of osteoarthritis using weighted gene coexpression network analysis.

    PubMed

    Guo, Sheng-Min; Wang, Jian-Xiong; Li, Jin; Xu, Fang-Yuan; Wei, Quan; Wang, Hai-Ming; Huang, Hou-Qiang; Zheng, Si-Lin; Xie, Yu-Jie; Zhang, Chi

    2018-06-15

    Osteoarthritis (OA) significantly influences the quality life of people around the world. It is urgent to find an effective way to understand the genetic etiology of OA. We used weighted gene coexpression network analysis (WGCNA) to explore the key genes involved in the subchondral bone pathological process of OA. Fifty gene expression profiles of GSE51588 were downloaded from the Gene Expression Omnibus database. The OA-associated genes and gene ontologies were acquired from JuniorDoc. Weighted gene coexpression network analysis was used to find disease-related networks based on 21756 gene expression correlation coefficients, hub-genes with the highest connectivity in each module were selected, and the correlation between module eigengene and clinical traits was calculated. The genes in the traits-related gene coexpression modules were subject to functional annotation and pathway enrichment analysis using ClusterProfiler. A total of 73 gene modules were identified, of which, 12 modules were found with high connectivity with clinical traits. Five modules were found with enriched OA-associated genes. Moreover, 310 OA-associated genes were found, and 34 of them were among hub-genes in each module. Consequently, enrichment results indicated some key metabolic pathways, such as extracellular matrix (ECM)-receptor interaction (hsa04512), focal adhesion (hsa04510), the phosphatidylinositol 3'-kinase (PI3K)-Akt signaling pathway (PI3K-AKT) (hsa04151), transforming growth factor beta pathway, and Wnt pathway. We intended to identify some core genes, collagen (COL)6A3, COL6A1, ITGA11, BAMBI, and HCK, which could influence downstream signaling pathways once they were activated. In this study, we identified important genes within key coexpression modules, which associate with a pathological process of subchondral bone in OA. Functional analysis results could provide important information to understand the mechanism of OA. © 2018 Wiley Periodicals, Inc.

  3. Gene Expression Profiling of Multiple Leiomyomata Uteri and Matched Normal Tissue from a Single Patient

    PubMed Central

    Dimitrova, Irina K.; Richer, Jennifer K.; Rudolph, Michael C.; Spoelstra, Nicole S.; Reno, Elaine M.; Medina, Theresa M.; Bradford, Andrew P.

    2009-01-01

    Objective To identify differentially expressed genes between fibroid and adjacent normal myometrium in an identical hormonal and genetic background. Design Array analysis of 3 leiomyomata and matched adjacent normal myometrium in a single patient. Setting University of Colorado Hospital. Patient(s) A single female undergoing medically indicated hysterectomy for symptomatic fibroids. Interventions(s) mRNA isolation and microarray analysis, reverse-transcriptase polymerase chain reaction, western blotting and immunohistochemistry. Main Outcome Measure(s) Changes in mRNA and protein levels in leiomyomata and matched normal myometrium. Result(s) Expression of 197 genes was increased and 619 decreased, significantly by at least 2 fold, in leiomyomata relative to normal myometrium. Expression profiles between tumors were similar and normal myometrial samples showed minimal variation. Changes in, and variation of, expression of selected genes were confirmed in additional normal and leiomyoma samples from multiple patients. Conclusion(s) Analysis of multiple tumors from a single patient confirmed changes in expression of genes described in previous, apparently disparate, studies and identified novel targets. Gene expression profiles in leiomyomata are consistent with increased activation of mitogenic pathways and inhibition of apoptosis. Down-regulation of genes implicated in invasion and metastasis, of cancers, was observed in fibroids. This expression pattern may underlie the benign nature of uterine leiomyomata and may aid in the differential diagnosis of leiomyosarcoma. PMID:18672237

  4. E-Nose and GC-MS Reveal a Difference in the Volatile Profiles of White- and Red-Fleshed Peach Fruit

    PubMed Central

    Xin, Rui; Liu, Xiaohong; Wei, Chunyan; Yang, Chong; Liu, Hongru; Cao, Xiangmei; Wu, Di; Chen, Kunsong

    2018-01-01

    First purchases of fruit are mainly dependent on aspects of appearance such as color. However, repeat buys of fruit are determined by internal quality traits such as flavor-related volatiles. Differences in volatile profiles in white- and red-fleshed peach fruit are not well understood. In the present study, peach cultivars with white- and red-fleshed fruit were subjected to sensory analysis using electronic nose (e-nose) to evaluate overview volatile profiles. Approximately 97.3% of the total variation in peach color-volatiles was explained by the first principle component 1 (PC1) and PC2. After analyzing sensory differences between peach fruit samples, 50 volatile compounds were characterized based on GC-MS. Multivariate analysis such as partial least squares discriminant analysis (PLS-DA) was applied to identify volatile compounds that contribute to difference in white- and red-fleshed peach fruit cultivars. A total of 18 volatiles that could separate peach fruit cultivars with different colors in flesh during ripening were identified based on variable importance in projection (VIP) score. Fruity note latone γ-hexalactone had higher contents in red-fleshed cultivars, while grassy note C6 compounds such as hexanal, 2-hexenal, (E)-2-hexenal, 1-hexanol, and (Z)-2-hexen-1-ol showed great accumulation in white-fleshed peach fruit. PMID:29498705

  5. Longitudinal Patterns of Glycemic Control and Blood Pressure in Pregnant Women with Type 1 Diabetes Mellitus: Phenotypes from Functional Data Analysis.

    PubMed

    Szczesniak, Rhonda D; Li, Dan; Duan, Leo L; Altaye, Mekibib; Miodovnik, Menachem; Khoury, Jane C

    2016-11-01

    Objective  To identify phenotypes of type 1 diabetes control and associations with maternal/neonatal characteristics based on blood pressure (BP), glucose, and insulin curves during gestation, using a novel functional data analysis approach that accounts for sparse longitudinal patterns of medical monitoring during pregnancy. Methods  We performed a retrospective longitudinal cohort study of women with type 1 diabetes whose BP, glucose, and insulin requirements were monitored throughout gestation as part of a program-project grant. Scores from sparse functional principal component analysis (fPCA) were used to classify gestational profiles according to the degree of control for each monitored measure. Phenotypes created using fPCA were compared with respect to maternal and neonatal characteristics and outcome. Results  Most of the gestational profile variation in the monitored measures was explained by the first principal component (82-94%). Profiles clustered into three subgroups of high, moderate, or low heterogeneity, relative to the overall mean response. Phenotypes were associated with baseline characteristics, longitudinal changes in glycohemoglobin A1 and weight, and to pregnancy-related outcomes. Conclusion  Three distinct longitudinal patterns of glucose, insulin, and BP control were found. By identifying these phenotypes, interventions can be targeted for subgroups at highest risk for compromised outcome, to optimize diabetes management during pregnancy. Thieme Medical Publishers 333 Seventh Avenue, New York, NY 10001, USA.

  6. The Brazilian version of the three-factor eating questionnaire-R21: psychometric evaluation and scoring pattern.

    PubMed

    de Medeiros, Anna Cecília Queiroz; Yamamoto, Maria Emilia; Pedrosa, Lucia Fatima Campos; Hutz, Claudio Simon

    2017-03-01

    This study aimed to evaluate the psychometric properties and scoring pattern of the Brazilian version of the three-factor eating questionnaire-r21 (TFEQ-R21). Data were collected from 410 undergraduate students. Confirmatory factor analysis was conducted to examine the factor structure of the TFEQ-R21. Convergent and discriminant validity also was assessed. Cluster analysis was performed to investigate scoring patterns. In assessing the quality setting, the model was considered satisfactory (χ 2 /gl = 2.24, CFI = 0.97, TLI = 0.96, RMSEA = 0.05). The instrument was also considered appropriate in relation to the discriminant and convergent validity. There was a positive correlation between body mass index and the dimensions of cognitive restraint (r s  = 0.449, p < 0.001) and emotional eating (r s  = 0.112, p = 0.023). Using cluster analysis three respondent profiles were identified. The profile "A" was associated with appropriate weight, the "B" was characterized by high scores in cognitive restraint dimension, and the cluster "C" focused individuals who had higher scores on the uncontrolled eating and emotional eating dimensions. The Brazilian version of TFEQ-R21 has adequate psychometric properties, and the identified response profiles offer a promising prospect for its use in clinical practice, in weight loss interventions.

  7. Online identification of the antioxidant constituents of traditional Chinese medicine formula Chaihu-Shu-Gan-San by LC-LTQ-Orbitrap mass spectrometry and microplate spectrophotometer.

    PubMed

    Su, Zhi-Heng; Zou, Guo-An; Preiss, Alfred; Zhang, Hong-Wu; Zou, Zhong-Mei

    2010-11-02

    Chaihu-Shu-Gan-San (CSGS), a traditional Chinese medicine (TCM) formula containing seven herbal medicines, has been used in treatment of gastritis, peptic ulcer, irritable bowel syndrome and depression clinically. However, the chemical constituents in CSGS had not been studied so far. To quickly identify the chemical constituents of CSGS and to understand the chemical profiles related to antioxidant activity of CSGS, liquid chromatography coupled with electrospray ionization hybrid linear trap quadrupole orbitrap (LC-LTQ-Orbitrap) mass spectrometry has been applied for online identification of chemical constituents in complex system, meanwhile, antioxidant profile of CSGS was investigated by the fraction collecting and microplate reading system. As a result, 33 chemical constituents in CSGS were identified. Among them, 13 components could be detected both in positive and in negative ion modes, 20 constituents were determined only in positive ion mode and 2 components were only detected in negative ion mode. Meanwhile, the potential antioxidant profile of CSGS was also characterized by combination of 96-well plate collection of elutes from HPLC analysis and microplate spectrophotometer, in which the scavenging activities of free radical produced by DPPH of each fraction could be directly investigated by the analysis of microplate reader. This study quickly screened the contribution of CSGS fractions to the antioxidant activity and online identified the corresponding active constituents. The results indicated that the combination of LC-MS(n) and 96-well plate assay system established in this paper would be a useful strategy for correlating the chemical profile of TCMs with their bioactivities without isolation and purification. Crown Copyright (c) 2010. Published by Elsevier B.V. All rights reserved.

  8. Territorial energy assessment. Phase I

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

    Not Available

    1981-07-31

    The goal of the project is to provide a current perspective on territorial energy problems, to identify existing energy supply and demand data, and to identify energy resources that might be developed and appropriate technology options. The cost of the technical assessment and economic analysis activities required to support the development of specific energy plans is defined and estimated. Information is summarized for the US Territories, the Pacific Trust Territories, and Puerto Rico. An overview and analysis of the the Pacific Island Entities; profiles of the Pacifc Island Entities; and the Caribbean Island Entities are presented. (MCW)

  9. Daily chronomics of proteomic profile in aging and rotenone-induced Parkinson's disease model in male Wistar rat and its modulation by melatonin.

    PubMed

    Jagota, Anita; Mattam, Ushodaya

    2017-08-01

    Aging is associated with changes in several basic parameters of circadian timing system (CTS) in mammals leading to circadian dysfunction. We had reported earlier that upon aging and in rotenone induced Parkinson's disease (RIPD) rat model there were significant alterations in the core clock genes expression levels and daily pulses. To identify biomarkers of aging and PD chronomics of proteomic day-night profiles in suprachiasmatic nucleus (SCN), pineal and substantia nigra (SN) in 3 month (m), 12, 24 m and RIPD rat model were studied at two time points i.e. Zeitgeber Time (ZT)-6 (mid-day) and ZT-18 (mid-night). Proteome analysis was done by using two dimensional (2-D) electrophoresis and the spots showing robust day-night variations were identified by using MALDI TOF/TOF analysis. In 3 m rats the number of proteins showing day-night variations were relatively more than 12, 24 m and RIPD rat model in SCN and SN. But in pineal there was increase in number of protein spots showing day-night variations in 24 m. Mass spectroscopy of the protein spots showing robust day night variation in aging and RIPD rats were identified. As melatonin, a multitasking molecule, an endogenous synchronizer of rhythm, an antioxidant and an antiaging drug, declines with aging, the effects of melatonin administration on differential alterations in chronomics of 2-D protein profiles in aging and RIPD male Wistar rats were studied. We report here that the melatonin could be playing an important role in modulating the chronomics of 2-D protein profiles. Additionally, various proteins were identified for the first time in this study showing significant day night variation in SCN, pineal and SN may prove useful towards targeting novel treatments for circadian dysfunction, good health and longevity.

  10. Identifying drought response of semi-arid aeolian systems using near-surface luminescence profiles and changepoint analysis, Nebraska Sandhills.

    NASA Astrophysics Data System (ADS)

    Buckland, Catherine; Bailey, Richard; Thomas, David

    2017-04-01

    Two billion people living in drylands are affected by land degradation. Sediment erosion by wind and water removes fertile soil and destabilises landscapes. Vegetation disturbance is a key driver of dryland erosion caused by both natural and human forcings: drought, fire, land use, grazing pressure. A quantified understanding of vegetation cover sensitivities and resultant surface change to forcing factors is needed if the vegetation and landscape response to future climate change and human pressure are to be better predicted. Using quartz luminescence dating and statistical changepoint analysis (Killick & Eckley, 2014) this study demonstrates the ability to identify step-changes in depositional age of near-surface sediments. Lx/Tx luminescence profiles coupled with statistical analysis show the use of near-surface sediments in providing a high-resolution record of recent system response and aeolian system thresholds. This research determines how the environment has recorded and retained sedimentary evidence of drought response and land use disturbances over the last two hundred years across both individual landforms and the wider Nebraska Sandhills. Identifying surface deposition and comparing with records of climate, fire and land use changes allows us to assess the sensitivity and stability of the surface sediment to a range of forcing factors. Killick, R and Eckley, IA. (2014) "changepoint: An R Package for Changepoint Analysis." Journal of Statistical Software, (58) 1-19.

  11. Genome-wide identification and characterisation of F-box family in maize.

    PubMed

    Jia, Fengjuan; Wu, Bingjiang; Li, Hui; Huang, Jinguang; Zheng, Chengchao

    2013-11-01

    F-box-containing proteins, as the key components of the protein degradation machinery, are widely distributed in higher plants and are considered as one of the largest known families of regulatory proteins. The F-box protein family plays a crucial role in plant growth and development and in response to biotic and abiotic stresses. However, systematic analysis of the F-box family in maize (Zea mays) has not been reported yet. In this paper, we identified and characterised the maize F-box genes in a genome-wide scale, including phylogenetic analysis, chromosome distribution, gene structure, promoter analysis and gene expression profiles. A total of 359 F-box genes were identified and divided into 15 subgroups by phylogenetic analysis. The F-box domain was relatively conserved, whereas additional motifs outside the F-box domain may indicate the functional diversification of maize F-box genes. These genes were unevenly distributed in ten maize chromosomes, suggesting that they expanded in the maize genome because of tandem and segmental duplication events. The expression profiles suggested that the maize F-box genes had temporal and spatial expression patterns. Putative cis-acting regulatory DNA elements involved in abiotic stresses were observed in maize F-box gene promoters. The gene expression profiles under abiotic stresses also suggested that some genes participated in stress responsive pathways. Furthermore, ten genes were chosen for quantitative real-time PCR analysis under drought stress and the results were consistent with the microarray data. This study has produced a comparative genomics analysis of the maize ZmFBX gene family that can be used in further studies to uncover their roles in maize growth and development.

  12. Molecular Profiles for Lung Cancer Pathogenesis and Detection in U.S. Veterans

    DTIC Science & Technology

    2012-10-01

    C, Virmani AK,Mele G, Milchgrub S, Girard L, Fondon JW III, Garner HR, McKay B, Latif F, et al . High resolution chromosome 3p allelotyping of human...analyzed the field cancerization profiles in the publicly available and published cohort by Spira et al (9) comprised of 129 proximal airway samples...from the original report by Spira et al . This list was then used to perform a pre-ranked GSEA analysis to identify which of the field

  13. Molecular Profiles for Lung Cancer Pathogenesis and Detection in U.S. Veterans

    DTIC Science & Technology

    2012-10-01

    Milchgrub S, Girard L, Fondon JW III, Garner HR, McKay B, Latif F, et al . High resolution chromosome 3p allelotyping of human lung cancer and...airways in lung cancer patients and high-risk smokers. We, therefore, analyzed the field cancerization profiles from Spira et al 9 comprised of 129...from the original report by Spira et al . This list was then used to perform a pre-ranked GSEA analysis to identify which of the field cancerization

  14. Gene set differential analysis of time course expression profiles via sparse estimation in functional logistic model with application to time-dependent biomarker detection.

    PubMed

    Kayano, Mitsunori; Matsui, Hidetoshi; Yamaguchi, Rui; Imoto, Seiya; Miyano, Satoru

    2016-04-01

    High-throughput time course expression profiles have been available in the last decade due to developments in measurement techniques and devices. Functional data analysis, which treats smoothed curves instead of originally observed discrete data, is effective for the time course expression profiles in terms of dimension reduction, robustness, and applicability to data measured at small and irregularly spaced time points. However, the statistical method of differential analysis for time course expression profiles has not been well established. We propose a functional logistic model based on elastic net regularization (F-Logistic) in order to identify the genes with dynamic alterations in case/control study. We employ a mixed model as a smoothing method to obtain functional data; then F-Logistic is applied to time course profiles measured at small and irregularly spaced time points. We evaluate the performance of F-Logistic in comparison with another functional data approach, i.e. functional ANOVA test (F-ANOVA), by applying the methods to real and synthetic time course data sets. The real data sets consist of the time course gene expression profiles for long-term effects of recombinant interferon β on disease progression in multiple sclerosis. F-Logistic distinguishes dynamic alterations, which cannot be found by competitive approaches such as F-ANOVA, in case/control study based on time course expression profiles. F-Logistic is effective for time-dependent biomarker detection, diagnosis, and therapy. © The Author 2015. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  15. An analysis of current source density profiles activated by local stimulation in the mouse auditory cortex in vitro.

    PubMed

    Yamamura, Daiki; Sano, Ayaka; Tateno, Takashi

    2017-03-15

    To examine local network properties of the mouse auditory cortex in vitro, we recorded extracellular spatiotemporal laminar profiles driven by short electric local stimulation on a planar multielectrode array substrate. The recorded local field potentials were subsequently evaluated using current source density (CSD) analysis to identify sources and sinks. Current sinks are thought to be an indicator of net synaptic current in the small volume of cortex surrounding the recording site. Thus, CSD analysis combined with multielectrode arrays enabled us to compare mean synaptic activity in response to small current stimuli on a layer-by-layer basis. We also used senescence-accelerated mice (SAM), some strains of which show earlier onset of age-related hearing loss, to examine the characteristic spatiotemporal CSD profiles stimulated by electrodes in specific cortical layers. Thus, the CSD patterns were classified into several clusters based on stimulation sites in the cortical layers. We also found some differences in CSD patterns between the two SAM strains in terms of aging according to principle component analysis with dimension reduction. For simultaneous two-site stimulation, we modeled the obtained CSD profiles as a linear superposition of the CSD profiles to individual single-site stimulation. The model analysis indicated the nonlinearity of spatiotemporal integration over stimulus-driven activity in a layer-specific manner. Finally, on the basis of these results, we discuss the auditory cortex local network properties and the effects of aging on these mouse strains. Copyright © 2017 Elsevier B.V. All rights reserved.

  16. Common patterns and disease-related signatures in tuberculosis and sarcoidosis.

    PubMed

    Maertzdorf, Jeroen; Weiner, January; Mollenkopf, Hans-Joachim; Bauer, Torsten; Prasse, Antje; Müller-Quernheim, Joachim; Kaufmann, Stefan H E

    2012-05-15

    In light of the marked global health impact of tuberculosis (TB), strong focus has been on identifying biosignatures. Gene expression profiles in blood cells identified so far are indicative of a persistent activation of the immune system and chronic inflammatory pathology in active TB. Definition of a biosignature with unique specificity for TB demands that identified profiles can differentiate diseases with similar pathology, like sarcoidosis (SARC). Here, we present a detailed comparison between pulmonary TB and SARC, including whole-blood gene expression profiling, microRNA expression, and multiplex serum analytes. Our analysis reveals that previously disclosed gene expression signatures in TB show highly similar patterns in SARC, with a common up-regulation of proinflammatory pathways and IFN signaling and close similarity to TB-related signatures. microRNA expression also presented a highly similar pattern in both diseases, whereas cytokines in the serum of TB patients revealed a slightly elevated proinflammatory pattern compared with SARC and controls. Our results indicate several differences in expression between the two diseases, with increased metabolic activity and significantly higher antimicrobial defense responses in TB. However, matrix metallopeptidase 14 was identified as the most distinctive marker of SARC. Described communalities as well as unique signatures in blood profiles of two distinct inflammatory pulmonary diseases not only have considerable implications for the design of TB biosignatures and future diagnosis, but they also provide insights into biological processes underlying chronic inflammatory disease entities of different etiology.

  17. Identification of Potential Biomarkers for Rhegmatogenous Retinal Detachment Associated with Choroidal Detachment by Vitreous iTRAQ-Based Proteomic Profiling

    PubMed Central

    Wu, Zhifeng; Ding, Nannan; Yu, Mengxi; Wang, Ke; Luo, Shasha; Zou, Wenjun; Zhou, Ying; Yan, Biao; Jiang, Qin

    2016-01-01

    Rhegmatogenous retinal detachment associated with choroidal detachment (RRDCD) is a complicated and serious type of rhegmatogenous retinal detachment (RRD). In this study, we identified differentially expressed proteins in the vitreous humors of RRDCD and RRD using isobaric tags for relative and absolute quantitation (iTRAQ) combined with nano-liquid chromatography-electrospray ion trap-mass spectrometry-mass spectrometry (nano-LC-ESI-MS/MS) and bioinformatic analysis. Our result shows that 103 differentially expressed proteins, including 54 up-regulated and 49 down-regulated proteins were identified in RRDCD. Gene ontology (GO) analysis suggested that most of the differentially expressed proteins were extracellular．The Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis suggested that proteins related to complement and coagulation cascades were significantly enriched. iTRAQ-based proteomic profiling reveals that complement and coagulation cascades and inflammation may play important roles in the pathogenesis of RRDCD. This study may provide novel insights into the pathogenesis of RRDCD and offer potential opportunities for the diagnosis and treatment of RRDCD. PMID:27941623

  18. Characterization of volatile profile from ten different varieties of Chinese jujubes by HS-SPME/GC-MS coupled with E-nose.

    PubMed

    Chen, Qinqin; Song, Jianxin; Bi, Jinfeng; Meng, Xianjun; Wu, Xinye

    2018-03-01

    Volatile profile of ten different varieties of fresh jujubes was characterized by HS-SPME/GC-MS (headspace solid phase micro-extraction combined with gas chromatography-mass spectrometry) and E-nose (electronic nose). GC-MS results showed that a total of 51 aroma compounds were identified in jujubes, hexanoic acid, hexanal, (E)-2-hexenal, (Z)-2-heptenal, benzaldehyde and (E)-2-nonenal were the main aroma components with contributions that over 70%. Differentiation of jujube varieties was conducted by cluster analysis of GC-MS data and principal component analysis & linear discriminant analysis of E-nose data. Both results showed that jujubes could be mainly divided into two groups: group A (JZ, PDDZ, JSXZ and LWZZ) and group B (BZ, YZ, MZ, XZ and DZ). There were significant differences in contents of alcohols, acids and aromatic compounds between group A and B. GC-MS coupled with E-nose could be a fast and accurate method to identify the general flavor difference in different varieties of jujubes. Copyright © 2017 Elsevier Ltd. All rights reserved.

  19. The perception of the relationship between environment and health according to data from Italian Behavioural Risk Factor Surveillance System (PASSI).

    PubMed

    Sampaolo, Letizia; Tommaso, Giulia; Gherardi, Bianca; Carrozzi, Giuliano; Freni Sterrantino, Anna; Ottone, Marta; Goldoni, Carlo Alberto; Bertozzi, Nicoletta; Scaringi, Meri; Bolognesi, Lara; Masocco, Maria; Salmaso, Stefania; Lauriola, Paolo

    2017-01-01

    "OBJECTIVES: to identify groups of people in relation to the perception of environmental risk and to assess the main characteristics using data collected in the environmental module of the surveillance network Italian Behavioral Risk Factor Surveillance System (PASSI). perceptive profiles were identified using a latent class analysis; later they were included as outcome in multinomial logistic regression models to assess the association between environmental risk perception and demographic, health, socio-economic and behavioural variables. the latent class analysis allowed to split the sample in "worried", "indifferent", and "positive" people. The multinomial logistic regression model showed that the "worried" profile typically includes people of Italian nationality, living in highly urbanized areas, with a high level of education, and with economic difficulties; they pay special attention to their own health and fitness, but they have a negative perception of their own psychophysical state. the application of advanced statistical analysis enable to appraise PASSI data in order to characterize the perception of environmental risk, making the planning of interventions related to risk communication possible. ".

  20. #Proana: Pro-Eating Disorder Socialization on Twitter.

    PubMed

    Arseniev-Koehler, Alina; Lee, Hedwig; McCormick, Tyler; Moreno, Megan A

    2016-06-01

    Pro-eating disorder (ED) online movements support engagement with ED lifestyles and are associated with negative health consequences for adolescents with EDs. Twitter is a popular social media site among adolescents that provides a unique setting for Pro-ED content to be publicly exchanged. The purpose of this study was to investigate Pro-ED Twitter profiles' references to EDs and how their social connections (followers) reference EDs. A purposeful sample of 45 Pro-ED profiles was selected from Twitter. Profile information, all tweets, and a random sample of 100 of their followers' profile information were collected for content analysis using the Twitter Application Programming Interface. A codebook based on ED screening guidelines was applied to evaluate ED references. For each Pro-ED profile, proportion of tweets with ED references and proportion of followers with ED references in their own profile were evaluated. In total, our 45 Pro-ED profiles generated 4,245 tweets for analysis. A median of 36.4% of profiles' tweets contained ED references. Pro-ED profiles had a median of 173 followers, and a median of 44.5% of followers had ED references. Pro-ED profiles with more tweets with ED references also tended to have more followers with ED references (β = .37, p < .01). Findings suggest that profiles which self-identify as Pro-ED express disordered eating patterns through tweets and have an audience of followers, many of whom also reference ED in their own profiles. ED socialization on Twitter might provide social support, but in the Pro-ED context this activity might also reinforce an ED identity. Copyright © 2016 The Society for Adolescent Health and Medicine. All rights reserved.

  1. Transcriptome Analysis and Discovery of Genes Involved in Immune Pathways from Coelomocytes of Sea Cucumber (Apostichopus japonicus) after Vibrio splendidus Challenge.

    PubMed

    Gao, Qiong; Liao, Meijie; Wang, Yingeng; Li, Bin; Zhang, Zheng; Rong, Xiaojun; Chen, Guiping; Wang, Lan

    2015-07-17

    Vibrio splendidus is identified as one of the major pathogenic factors for the skin ulceration syndrome in sea cucumber (Apostichopus japonicus), which has vastly limited the development of the sea cucumber culture industry. In order to screen the immune genes involving Vibrio splendidus challenge in sea cucumber and explore the molecular mechanism of this process, the related transcriptome and gene expression profiling of resistant and susceptible biotypes of sea cucumber with Vibrio splendidus challenge were collected for analysis. A total of 319,455,942 trimmed reads were obtained, which were assembled into 186,658 contigs. After that, 89,891 representative contigs (without isoform) were clustered. The analysis of the gene expression profiling identified 358 differentially expression genes (DEGs) in the bacterial-resistant group, and 102 DEGs in the bacterial-susceptible group, compared with that in control group. According to the reported references and annotation information from BLAST, GO and KEGG, 30 putative bacterial-resistant genes and 19 putative bacterial-susceptible genes were identified from DEGs. The qRT-PCR results were consistent with the RNA-Seq results. Furthermore, many DGEs were involved in immune signaling related pathways, such as Endocytosis, Lysosome, MAPK, Chemokine and the ERBB signaling pathway.

  2. Transcriptome Analysis and Discovery of Genes Involved in Immune Pathways from Coelomocytes of Sea Cucumber (Apostichopus japonicus) after Vibrio splendidus Challenge

    PubMed Central

    Gao, Qiong; Liao, Meijie; Wang, Yingeng; Li, Bin; Zhang, Zheng; Rong, Xiaojun; Chen, Guiping; Wang, Lan

    2015-01-01

    Vibrio splendidus is identified as one of the major pathogenic factors for the skin ulceration syndrome in sea cucumber (Apostichopus japonicus), which has vastly limited the development of the sea cucumber culture industry. In order to screen the immune genes involving Vibrio splendidus challenge in sea cucumber and explore the molecular mechanism of this process, the related transcriptome and gene expression profiling of resistant and susceptible biotypes of sea cucumber with Vibrio splendidus challenge were collected for analysis. A total of 319,455,942 trimmed reads were obtained, which were assembled into 186,658 contigs. After that, 89,891 representative contigs (without isoform) were clustered. The analysis of the gene expression profiling identified 358 differentially expression genes (DEGs) in the bacterial-resistant group, and 102 DEGs in the bacterial-susceptible group, compared with that in control group. According to the reported references and annotation information from BLAST, GO and KEGG, 30 putative bacterial-resistant genes and 19 putative bacterial-susceptible genes were identified from DEGs. The qRT-PCR results were consistent with the RNA-Seq results. Furthermore, many DGEs were involved in immune signaling related pathways, such as Endocytosis, Lysosome, MAPK, Chemokine and the ERBB signaling pathway. PMID:26193268

  3. Dynamic motif occupancy (DynaMO) analysis identifies transcription factors and their binding sites driving dynamic biological processes.

    PubMed

    Kuang, Zheng; Ji, Zhicheng; Boeke, Jef D; Ji, Hongkai

    2018-01-09

    Biological processes are usually associated with genome-wide remodeling of transcription driven by transcription factors (TFs). Identifying key TFs and their spatiotemporal binding patterns are indispensable to understanding how dynamic processes are programmed. However, most methods are designed to predict TF binding sites only. We present a computational method, dynamic motif occupancy analysis (DynaMO), to infer important TFs and their spatiotemporal binding activities in dynamic biological processes using chromatin profiling data from multiple biological conditions such as time-course histone modification ChIP-seq data. In the first step, DynaMO predicts TF binding sites with a random forests approach. Next and uniquely, DynaMO infers dynamic TF binding activities at predicted binding sites using their local chromatin profiles from multiple biological conditions. Another landmark of DynaMO is to identify key TFs in a dynamic process using a clustering and enrichment analysis of dynamic TF binding patterns. Application of DynaMO to the yeast ultradian cycle, mouse circadian clock and human neural differentiation exhibits its accuracy and versatility. We anticipate DynaMO will be generally useful for elucidating transcriptional programs in dynamic processes. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  4. Pain sensitivity profiles in patients with advanced knee osteoarthritis

    PubMed Central

    Frey-Law, Laura A.; Bohr, Nicole L.; Sluka, Kathleen A.; Herr, Keela; Clark, Charles R.; Noiseux, Nicolas O.; Callaghan, John J; Zimmerman, M Bridget; Rakel, Barbara A.

    2016-01-01

    The development of patient profiles to subgroup individuals on a variety of variables has gained attention as a potential means to better inform clinical decision-making. Patterns of pain sensitivity response specific to quantitative sensory testing (QST) modality have been demonstrated in healthy subjects. It has not been determined if these patterns persist in a knee osteoarthritis population. In a sample of 218 participants, 19 QST measures along with pain, psychological factors, self-reported function, and quality of life were assessed prior to total knee arthroplasty. Component analysis was used to identify commonalities across the 19 QST assessments to produce standardized pain sensitivity factors. Cluster analysis then grouped individuals that exhibited similar patterns of standardized pain sensitivity component scores. The QST resulted in four pain sensitivity components: heat, punctate, temporal summation, and pressure. Cluster analysis resulted in five pain sensitivity profiles: a “low pressure pain” group, an “average pain” group, and three “high pain” sensitivity groups who were sensitive to different modalities (punctate, heat, and temporal summation). Pain and function differed between pain sensitivity profiles, along with sex distribution; however no differences in OA grade, medication use, or psychological traits were found. Residualizing QST data by age and sex resulted in similar components and pain sensitivity profiles. Further, these profiles are surprisingly similar to those reported in healthy populations suggesting that individual differences in pain sensitivity are a robust finding even in an older population with significant disease. PMID:27152688

  5. A male and female RNA marker to infer sex in forensic analysis.

    PubMed

    van den Berge, M; Sijen, T

    2017-01-01

    In forensics, DNA profiling is used for the identification of the donor of a trace, while messenger RNA (mRNA) profiling can be applied to identify the cellular origin such as body fluids or organ tissues. The presence of male cell material can be readily assessed by the incorporation of Y-chromosomal markers in quantitation or STR profiling systems. However, no forensic marker exists to positively identify female cell material; merely the presence of female DNA is deduced from the absence of a Y peak, or unbalanced X-Y signals at the Amelogenin locus or unbalanced response of the total and Y-specific quantifier. The presence of two X-chromosomes in female cells invokes dosage compensation, which is achieved through inactivation of one of the X-chromosomes in females. Since this process involves specific RNA molecules, identification of female cellular material may be possible through RNA profiling. Additionally, male material may be identified through RNAs expressed from the Y-chromosome. RNAs preferentially expressed in either sex were assessed for their potential to act as sex markers in forensic RNA assays. To confirm sex-specificity, body fluids and organ tissues of multiple donors of either sex were tested. Additionally, sensitivity of the markers and the suitability of positively identifying male-female mixtures were assessed and degraded samples were used to assess performance of the markers in forensic settings. The addition of sex-specific markers is of added informative value in any RNA profiling system and both markers were incorporated into existing RNA assays that either target body fluids or organs. These are the first forensic assays that enable positive identification of female cellular material. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  6. Proteomic analysis associated with coronary artery dilatation caused by Kawasaki disease using serum exosomes.

    PubMed

    Zhang, Li; Wang, Wei; Bai, Jun; Xu, Yu-Fen; Li, Lai-Qing; Hua, Liang; Deng, Li; Jia, Hong-Ling

    2016-05-01

    The aim of this study was to investigate the serum exosome proteome profile of coronary artery dilatation (CAD) caused by Kawasaki disease (KD). Two-dimensional electrophoresis was implemented on proteins of serum exosomes obtained from children with CAD caused by KD and from healthy controls. Differentially expressed proteins were identified by matrix-assisted laser desorption/ionization time-of-flight/time-of-flight mass spectrometry analysis. We identified 38 differentially expressed proteins (13 up-regulated and 25 down-regulated) from serum exosomes of patients with CAD caused by KD compared with healthy controls. Expression levels of three differentially expressed proteins (leucine-rich alpha-2-glycoprotein, sex hormone-binding globulin, and serotransferrin) were validated using western blot analysis. Classification and protein-protein network analysis showed that they are associated with multiple functional groups involved in the acute inflammatory response, defense response, complement activation, humoral immune response, and response to wounding. The majority of the proteins are involved in the inflammation and coagulation cascades. These findings establish a comprehensive proteome profile of CAD caused by KD and increase our knowledge of scientific insight into its mechanisms. Copyright © 2016 Sociedade Portuguesa de Cardiologia. Published by Elsevier España. All rights reserved.

  7. The Development of the Problematic Online Gaming Questionnaire (POGQ)

    PubMed Central

    Demetrovics, Zsolt; Urbán, Róbert; Nagygyörgy, Katalin; Farkas, Judit; Griffiths, Mark D.; Pápay, Orsolya; Kökönyei, Gyöngyi; Felvinczi, Katalin; Oláh, Attila

    2012-01-01

    Background Online gaming has become increasingly popular. However, this has led to concerns that these games might induce serious problems and/or lead to dependence for a minority of players. Aim: The aim of this study was to uncover and operationalize the components of problematic online gaming. Methods A total of 3415 gamers (90% males; mean age 21 years), were recruited through online gaming websites. A combined method of exploratory factor analysis (EFA) and confirmatory factor analysis (CFA) was applied. Latent profile analysis was applied to identify persons at-risk. Results EFA revealed a six-factor structure in the background of problematic online gaming that was also confirmed by a CFA. For the assessment of the identified six dimensions – preoccupation, overuse, immersion, social isolation, interpersonal conflicts, and withdrawal – the 18-item Problematic Online Gaming Questionnaire (POGQ) proved to be exceedingly suitable. Based on the latent profile analysis, 3.4% of the gamer population was considered to be at high risk, while another 15.2% was moderately problematic. Conclusions The POGQ seems to be an adequate measurement tool for the differentiated assessment of gaming related problems on six subscales. PMID:22590541

  8. Divorce is a part of my life... resilience, survival, and vulnerability: young adults' perception of the implications of parental divorce.

    PubMed

    Eldar-Avidan, Dorit; Haj-Yahia, Muhammad M; Greenbaum, Charles W

    2009-01-01

    A qualitative study among 22 young adults (20-25 years old) whose parents divorced during their childhood was conducted in Israel, using semi-structured, in-depth, open-ended interviews. Qualitative data analysis led to identification of three profiles, aiming at a grounded theoretical conceptualization. Three core themes were identified: the centrality of the family; short- and long-term implications of parental divorce and its relations to supportive coping resources; and perspective at young adulthood. Further analysis led to typifying participants by three profiles, which represent the grounded theoretical conceptualizations: resilience, survival, and vulnerability. The most prominent difference among the profiles was the relationships between participants and their parents, and their perception of ongoing parental responsibility. A thorough discussion of the results and their implications for future research, theory development, and practice are presented.

  9. The Cancer Genome Atlas Pan-Cancer Analysis Project

    PubMed Central

    Weinstein, John N.; Collisson, Eric A.; Mills, Gordon B.; Shaw, Kenna M.; Ozenberger, Brad A.; Ellrott, Kyle; Shmulevich, Ilya; Sander, Chris; Stuart, Joshua M.

    2014-01-01

    Cancer can take hundreds of different forms depending on the location, cell of origin and spectrum of genomic alterations that promote oncogenesis and affect therapeutic response. Although many genomic events with direct phenotypic impact have been identified, much of the complex molecular landscape remains incompletely charted for most cancer lineages. For that reason, The Cancer Genome Atlas (TCGA) Research Network has profiled and analyzed large numbers of human tumours to discover molecular aberrations at the DNA, RNA, protein, and epigenetic levels. The resulting rich data provide a major opportunity to develop an integrated picture of commonalities, differences, and emergent themes across tumour lineages. The Pan-Cancer initiative compares the first twelve tumour types profiled by TCGA. Analysis of the molecular aberrations and their functional roles across tumour types will teach us how to extend therapies effective in one cancer type to others with a similar genomic profile. PMID:24071849

  10. The application of Skylab altimetry to marine geoid determination

    NASA Technical Reports Server (NTRS)

    Mourad, A. G.; Gopalapillai, S.; Kuhner, M.; Fubara, D. M. (Principal Investigator)

    1975-01-01

    The author had identified the following significant results. The major results can be divided broadly into two groups. One group is concerned with the effects of errors inherent in the various input data, such as the orbit emphemeris, a priori geoid etc. The other consists of the results of the actual analysis of the data from the Skylab EREP passes 4, 6, 7, and 9. Results from the first group were obtained from the analysis of some preliminary data from EREP pass 9 mode 5. The second group of results consists of a set of recovered bias terms for each of the submodes of observations and a set of nine altimetry geoid profiles corresponding to the various passes and modes. Along with each of these profiles, the a priori geoid, gravity anomaly, and the bathymetric data profiles are also presented for easy comparison.

  11. Comparative Profiling of Primary Colorectal Carcinomas and Liver Metastases Identifies LEF1 as a Prognostic Biomarker

    PubMed Central

    Lin, Albert Y.; Chua, Mei-Sze; Choi, Yoon-La; Yeh, William; Kim, Young H.; Azzi, Raymond; Adams, Gregg A.; Sainani, Kristin; van de Rijn, Matt; So, Samuel K.; Pollack, Jonathan R.

    2011-01-01

    Purpose We sought to identify genes of clinical significance to predict survival and the risk for colorectal liver metastasis (CLM), the most common site of metastasis from colorectal cancer (CRC). Patients and Methods We profiled gene expression in 31 specimens from primary CRC and 32 unmatched specimens of CLM, and performed Significance Analysis of Microarrays (SAM) to identify genes differentially expressed between these two groups. To characterize the clinical relevance of two highly-ranked differentially-expressed genes, we analyzed the expression of secreted phosphoprotein 1 (SPP1 or osteopontin) and lymphoid enhancer factor-1 (LEF1) by immunohistochemistry using a tissue microarray (TMA) representing an independent set of 154 patients with primary CRC. Results Supervised analysis using SAM identified 963 genes with significantly higher expression in CLM compared to primary CRC, with a false discovery rate of <0.5%. TMA analysis showed SPP1 and LEF1 protein overexpression in 60% and 44% of CRC cases, respectively. Subsequent occurrence of CLM was significantly correlated with the overexpression of LEF1 (chi-square p = 0.042), but not SPP1 (p = 0.14). Kaplan Meier analysis revealed significantly worse survival in patients with overexpression of LEF1 (p<0.01), but not SPP1 (p = 0.11). Both univariate and multivariate analyses identified stage (p<0.0001) and LEF1 overexpression (p<0.05) as important prognostic markers, but not tumor grade or SPP1. Conclusion Among genes differentially expressed between CLM and primary CRC, we demonstrate overexpression of LEF1 in primary CRC to be a prognostic factor for poor survival and increased risk for liver metastasis. PMID:21383983

  12. Identification and Functional Analysis of Healing Regulators in Drosophila

    PubMed Central

    Álvarez-Fernández, Carmen; Tamirisa, Srividya; Prada, Federico; Chernomoretz, Ariel; Podhajcer, Osvaldo; Blanco, Enrique; Martín-Blanco, Enrique

    2015-01-01

    Wound healing is an essential homeostatic mechanism that maintains the epithelial barrier integrity after tissue damage. Although we know the overall steps in wound healing, many of the underlying molecular mechanisms remain unclear. Genetically amenable systems, such as wound healing in Drosophila imaginal discs, do not model all aspects of the repair process. However, they do allow the less understood aspects of the healing response to be explored, e.g., which signal(s) are responsible for initiating tissue remodeling? How is sealing of the epithelia achieved? Or, what inhibitory cues cancel the healing machinery upon completion? Answering these and other questions first requires the identification and functional analysis of wound specific genes. A variety of different microarray analyses of murine and humans have identified characteristic profiles of gene expression at the wound site, however, very few functional studies in healing regulation have been carried out. We developed an experimentally controlled method that is healing-permissive and that allows live imaging and biochemical analysis of cultured imaginal discs. We performed comparative genome-wide profiling between Drosophila imaginal cells actively involved in healing versus their non-engaged siblings. Sets of potential wound-specific genes were subsequently identified. Importantly, besides identifying and categorizing new genes, we functionally tested many of their gene products by genetic interference and overexpression in healing assays. This non-saturated analysis defines a relevant set of genes whose changes in expression level are functionally significant for proper tissue repair. Amongst these we identified the TCP1 chaperonin complex as a key regulator of the actin cytoskeleton essential for the wound healing response. There is promise that our newly identified wound-healing genes will guide future work in the more complex mammalian wound healing response. PMID:25647511

  13. Secondary metabolite profiling of Curcuma species grown at different locations using GC/TOF and UPLC/Q-TOF MS.

    PubMed

    Lee, Jueun; Jung, Youngae; Shin, Jeoung-Hwa; Kim, Ho Kyoung; Moon, Byeong Cheol; Ryu, Do Hyun; Hwang, Geum-Sook

    2014-07-04

    Curcuma, a genus of rhizomatous herbaceous species, has been used as a spice, traditional medicine, and natural dye. In this study, the metabolite profile of Curcuma extracts was determined using gas chromatography-time of flight mass spectrometry (GC/TOF MS) and ultrahigh-performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC/Q-TOF MS) to characterize differences between Curcuma aromatica and Curcuma longa grown on the Jeju-do or Jin-do islands, South Korea. Previous studies have performed primary metabolite profiling of Curcuma species grown in different regions using NMR-based metabolomics. This study focused on profiling of secondary metabolites from the hexane extract of Curcuma species. Principal component analysis (PCA) and partial least-squares discriminant analysis (PLS-DA) plots showed significant differences between the C. aromatica and C. longa metabolite profiles, whereas geographical location had little effect. A t-test was performed to identify statistically significant metabolites, such as terpenoids. Additionally, targeted profiling using UPLC/Q-TOF MS showed that the concentration of curcuminoids differed depending on the plant origin. Based on these results, a combination of GC- and LC-MS allowed us to analyze curcuminoids and terpenoids, the typical bioactive compounds of Curcuma, which can be used to discriminate Curcuma samples according to species or geographical origin.

  14. Analysis of hepatic transcript profile and plasma lipid profile in early lactating dairy cows fed grape seed and grape marc meal extract.

    PubMed

    Gessner, Denise K; Winkler, Anne; Koch, Christian; Dusel, Georg; Liebisch, Gerhard; Ringseis, Robert; Eder, Klaus

    2017-03-23

    It was recently reported that dairy cows fed a polyphenol-rich grape seed and grape marc meal extract (GSGME) during the transition period had an increased milk yield, but the underlying reasons remained unclear. As polyphenols exert a broad spectrum of metabolic effects, we hypothesized that feeding of GSGME influences metabolic pathways in the liver which could account for the positive effects of GSGME in dairy cows. In order to identify these pathways, we performed genome-wide transcript profiling in the liver and lipid profiling in plasma of dairy cows fed GSGME during the transition period at 1 week postpartum. Transcriptomic analysis of the liver revealed 207 differentially expressed transcripts, from which 156 were up- and 51 were down-regulated, between cows fed GSGME and control cows. Gene set enrichment analysis of the 155 up-regulated mRNAs showed that the most enriched gene ontology (GO) biological process terms were dealing with cell cycle regulation and the most enriched Kyoto Encyclopedia of Genes and Genomes pathways were p53 signaling and cell cycle. Functional analysis of the 43 down-regulated mRNAs revealed that a great part of these genes are involved in endoplasmic reticulum (ER) stress-induced unfolded protein response (UPR) and inflammatory processes. Accordingly, protein folding, response to unfolded protein, unfolded protein binding, chemokine activity and heat shock protein binding were identified as one of the most enriched GO biological process and molecular function terms assigned to the down-regulated genes. In line with the transcriptomics data the plasma concentrations of the acute phase proteins serum amyloid A (SAA) and haptoglobin were reduced in cows fed GSGME compared to control cows. Lipidomic analysis of plasma revealed no differences in the concentrations of individual species of major and minor lipid classes between cows fed GSGME and control cows. Analysis of hepatic transcript profile in cows fed GSGME during the transition period at 1 week postpartum indicates that polyphenol-rich feed components are able to inhibit ER stress-induced UPR and inflammatory processes, both of which are considered to contribute to liver-associated diseases and to impair milk performance in dairy cows, in the liver of dairy cows during early lactation.

  15. Carpentry. Ohio's Competency Analysis Profile.

    ERIC Educational Resources Information Center

    Ohio State Univ., Columbus. Vocational Instructional Materials Lab.

    This comprehensive and verified employer competency list was developed from a modified DACUM (Developing a Curriculum) process involving business, industry, labor, and community agency representatives from Ohio. This competency list contains 14 units (with or without subunits), competencies, and competency builders that identify the occupational,…

  16. Project for the analysis of technology transfer

    NASA Technical Reports Server (NTRS)

    Kottenstette, J. P.; Freeman, J. E.; Staskin, E. R.

    1971-01-01

    The special task of preparing technology transfer profiles during the first six months of 1971 produced two major results: refining a new method for identifying and describing technology transfer activities, and generating practical insights into a number of issues associated with transfer programs.

  17. Cosmetology. Ohio's Competency Analysis Profile.

    ERIC Educational Resources Information Center

    Ohio State Univ., Columbus. Vocational Instructional Materials Lab.

    This comprehensive and verified employer competency list was developed from a modified DACUM (Developing a Curriculum) process involving business, industry, labor, and community agency representatives from Ohio. This competency list contains 17 units (with or without subunits), competencies, and competency builders that identify the occupational,…

  18. Profile Analysis of Psychological Symptoms Associated With Misophonia: A Community Sample.

    PubMed

    McKay, Dean; Kim, Se-Kang; Mancusi, Lauren; Storch, Eric A; Spankovich, Christopher

    2018-03-01

    Misophonia is characterized by extreme aversive reactions to certain classes of sounds. It has recently been recognized as a condition associated with significant disability. Research has begun to evaluate psychopathological correlates of misophonia. This study sought to identify profiles of psychopathology that characterize misophonia in a large community sample. A total of N = 628 adult participants completed a battery of measures assessing anxiety and anxiety sensitivity, depression, stress responses, anger, dissociative experiences, obsessive-compulsive symptoms and beliefs, distress tolerance, bodily perceptions, as well as misophonia severity. Profile Analysis via Multidimensional Scaling (PAMS) was employed to evaluate profiles associated with elevated misophonia and those without symptoms. Three profiles were extracted. The first two accounted for 70% total variance and did not show distinctions between groups. The third profile accounted for 11% total variance, and showed that misophonia is associated with lower obsessive-compulsive symptoms for neutralizing, obsessions generally, and washing compared to those not endorsing misophonia, and higher levels of obsessive-compulsive symptoms associated with ordering and harm avoidance. This third profile extracted also showed significant differences between those with and without misophonia on the scale assessing physical concerns (that is, sensitivity to interoceptive sensations) as assessed with the ASI-3. Further research is called for involving diagnostic interviewing and experimental methods to clarify these putative mechanisms associated with misophonia. Copyright © 2017. Published by Elsevier Ltd.

  19. [UPLC characteristic chromatographic profile of Poria].

    PubMed

    Zhang, Qi; Wang, Zhenzhong; Xiao, Wei; Zhang, Liangqi; Bi, Kaishun; Jia, Ying

    2012-04-01

    To establish a UPLC characteristic chromatographic profile analysis method to quickly assess Poria quality and provide basis fro controlling Poria quality. The UPLC characteristic chromatographic profiles of fifteen batches of Poria were determined by ACQUITY UPLC, with HSS T3 Column (2.1 mm x 100 mm, 1.8 microm) eluted with the mobile phases of water containing 0.05% phosphoric acid and acetonitrile in gradient mode. The detection wavelength was set at 243 nm. The common mode of the UPLC characteristic chromatographic profile was set up. There were 20 common peaks, seven of which were identified, and the similar degrees of the fifteen samples to the common mode were between 0.787 and 0.974. The method was so time-saving that it can be used for the quality control of Poria.

  20. Concurrent validity of Zimbardo Time Perspective Inventory profiles: A secondary analysis of data from the United Kingdom.

    PubMed

    Worrell, Frank C; McKay, Michael T; Andretta, James R

    2015-07-01

    This paper examined the association between membership in profiles based on a shortened form of the Zimbardo Time Perspective Inventory (ZTPI-S; McKay, Andretta, McGee, & Worrell, 2014) and other temporal and psychosocial variables. Participants consisted of 1620 adolescents attending high school in Northern Ireland. ZTPI-S scores had correlations with other temporal and psychosocial variables that were similar to those reported for ZTPI scores in previous studies. Four ZTPI-S profiles were identified-Balanced, Past Negative, Present Hedonistic, and Future-and results indicated that these profiles had theoretically meaningful relationships with self-esteem, self-efficacy, aggression, parental attachment, consideration of future consequences, and future temporal focus. Unlike studies of college students where the Balanced profile was related to more adaptive functioning, the Future profile was related to more adaptive functioning. Future studies are needed to establish the generalizability of these profiles and to determine if there are developmental differences in which profiles are more adaptive. Copyright © 2015 The Foundation for Professionals in Services for Adolescents. All rights reserved.

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