Encouraging Students with Different Profiles of Perceptions to Pursue Science by Choosing Appropriate Teaching Methods for Each Age Group

NASA Astrophysics Data System (ADS)

Potvin, Patrice; Hasni, Abdelkrim

2017-06-01

This research aimed at identifying student profiles of perceptions by means of a clustering method using a validated questionnaire. These profiles describe students' attraction to science and technology (S&T) studies and careers as a variable driven by school S&T self-concept and interest in school S&T. In addition to three rather predictable student profiles (confident enthusiast, average ambitious, and pessimistic dropout), the fourth fairly well-populated profile called confident indifferent was produced. Our second and third research questions allowed us to describe each profile in terms of the instructional methods to which their population was exposed (including the degree to which they were actively involved) and the instructional methods to which they would like more exposure. An analysis of the evolution of the profiles' population over time is also presented. The results suggest that pedagogical variety and active involvement in the decision to pursue S&T are important. The perception of the utility and importance of S&T both in and out of school may also play an important role in these decisions. Minor pedagogical preferences were also found in certain age groups.

Contribution to a Taxonomic Revision of the Sicilian Helichrysum Taxa by PCA Analysis of Their Essential-Oil Compositions.

PubMed

Maggio, Antonella; Bruno, Maurizio; Guarino, Riccardo; Senatore, Felice; Ilardi, Vincenzo

2016-02-01

The chemical profile of the essential oils in ten populations of the genus Helichrysum Mill. (Asteraceae), collected in the loci classici of the nomenclatural types of the taxa endemic to Sicily, were analyzed. Our results confirm that the analysis of secondary metabolites can be used to fingerprint wild populations of Helichrysum, the chemical profiles being coherent with the systematic arrangement of the investigated populations in three main clusters, referring to the aggregates of H. stoechas, H. rupestre, and H. italicum, all belonging to the section Stoechadina. The correct nomenclatural designation of the investigated populations is discussed and the following two new combinations are proposed: Helichrysum preslianum subsp. compactum (Guss.) Maggio, Bruno, Guarino, Senatore & Ilardi and Helichrysum panormitanum subsp. latifolium Maggio, Bruno, Guarino, Senatore & Ilardi. Copyright © 2016 Verlag Helvetica Chimica Acta AG, Zürich.

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.

Population Analysis of Disabled Children by Departments in France

NASA Astrophysics Data System (ADS)

Meidatuzzahra, Diah; Kuswanto, Heri; Pech, Nicolas; Etchegaray, Amélie

2017-06-01

In this study, a statistical analysis is performed by model the variations of the disabled about 0-19 years old population among French departments. The aim is to classify the departments according to their profile determinants (socioeconomic and behavioural profiles). The analysis is focused on two types of methods: principal component analysis (PCA) and multiple correspondences factorial analysis (MCA) to review which one is the best methods for interpretation of the correlation between the determinants of disability (independent variable). The PCA is the best method for interpretation of the correlation between the determinants of disability (independent variable). The PCA reduces 14 determinants of disability to 4 axes, keeps 80% of total information, and classifies them into 7 classes. The MCA reduces the determinants to 3 axes, retains only 30% of information, and classifies them into 4 classes.

Convergence to a pulsating travelling wave for an epidemic reaction-diffusion system with non-diffusive susceptible population.

PubMed

Ducrot, Arnaud; Giletti, Thomas

2014-09-01

In this work we study the asymptotic behaviour of the Kermack-McKendrick reaction-diffusion system in a periodic environment with non-diffusive susceptible population. This problem was proposed by Kallen et al. as a model for the spatial spread for epidemics, where it can be reasonable to assume that the susceptible population is motionless. For arbitrary dimensional space we prove that large classes of solutions of such a system have an asymptotic spreading speed in large time, and that the infected population has some pulse-like asymptotic shape. The analysis of the one-dimensional problem is more developed, as we are able to uncover a much more accurate description of the profile of solutions. Indeed, we will see that, for some initially compactly supported infected population, the profile of the solution converges to some pulsating travelling wave with minimal speed, that is to some entire solution moving at a constant positive speed and whose profile's shape is periodic in time.

Current genetic methodologies in the identification of disaster victims and in forensic analysis.

PubMed

Ziętkiewicz, Ewa; Witt, Magdalena; Daca, Patrycja; Zebracka-Gala, Jadwiga; Goniewicz, Mariusz; Jarząb, Barbara; Witt, Michał

2012-02-01

This review presents the basic problems and currently available molecular techniques used for genetic profiling in disaster victim identification (DVI). The environmental conditions of a mass disaster often result in severe fragmentation, decomposition and intermixing of the remains of victims. In such cases, traditional identification based on the anthropological and physical characteristics of the victims is frequently inconclusive. This is the reason why DNA profiling became the gold standard for victim identification in mass-casualty incidents (MCIs) or any forensic cases where human remains are highly fragmented and/or degraded beyond recognition. The review provides general information about the sources of genetic material for DNA profiling, the genetic markers routinely used during genetic profiling (STR markers, mtDNA and single-nucleotide polymorphisms [SNP]) and the basic statistical approaches used in DNA-based disaster victim identification. Automated technological platforms that allow the simultaneous analysis of a multitude of genetic markers used in genetic identification (oligonucleotide microarray techniques and next-generation sequencing) are also presented. Forensic and population databases containing information on human variability, routinely used for statistical analyses, are discussed. The final part of this review is focused on recent developments, which offer particularly promising tools for forensic applications (mRNA analysis, transcriptome variation in individuals/populations and genetic profiling of specific cells separated from mixtures).

Determining clinical benefits of drug-eluting coronary stents according to the population risk profile: a meta-regression from 31 randomized trials.

PubMed

Moreno, Raul; Martin-Reyes, Roberto; Jimenez-Valero, Santiago; Sanchez-Recalde, Angel; Galeote, Guillermo; Calvo, Luis; Plaza, Ignacio; Lopez-Sendon, Jose-Luis

2011-04-01

The use of drug-eluting stents (DES) in unfavourable patients has been associated with higher rates of clinical complications and stent thrombosis, and because of that concerns about the use of DES in high-risk settings have been raised. This study sought to demonstrate that the clinical benefit of DES increases as the risk profile of the patients increases. A meta-regression analysis from 31 randomized trials that compared DES and bare-metal stents, including overall 12,035 patients, was performed. The relationship between the clinical benefit of using DES (number of patients to treat [NNT] to prevent one episode of target lesion revascularization [TLR]), and the risk profile of the population (rate of TLR in patients allocated to bare-metal stents) in each trial was evaluated. The clinical benefit of DES increased as the risk profile of each study population increased: NNT for TLR=31.1-1.2 (TLR for bare-metal stents); p<0.001. The use of DES was safe regardless of the risk profile of each study population, since the effect of DES in mortality, myocardial infarction, and stent thrombosis, was not adversely affected by the risk profile of each study population (95% confidence interval for β value 0.09 to 0.11, -0.12 to 0.19, and -0.03 to-0.15 for mortality, myocardial infarction, and stent thrombosis, respectively). The clinical benefit of DES increases as the risk profile of the patients increases, without affecting safety. Copyright © 2009 Elsevier Ireland Ltd. All rights reserved.

Statistical and population genetics issues of two Hungarian datasets from the aspect of DNA evidence interpretation.

PubMed

Szabolcsi, Zoltán; Farkas, Zsuzsa; Borbély, Andrea; Bárány, Gusztáv; Varga, Dániel; Heinrich, Attila; Völgyi, Antónia; Pamjav, Horolma

2015-11-01

When the DNA profile from a crime-scene matches that of a suspect, the weight of DNA evidence depends on the unbiased estimation of the match probability of the profiles. For this reason, it is required to establish and expand the databases that reflect the actual allele frequencies in the population applied. 21,473 complete DNA profiles from Databank samples were used to establish the allele frequency database to represent the population of Hungarian suspects. We used fifteen STR loci (PowerPlex ESI16) including five, new ESS loci. The aim was to calculate the statistical, forensic efficiency parameters for the Databank samples and compare the newly detected data to the earlier report. The population substructure caused by relatedness may influence the frequency of profiles estimated. As our Databank profiles were considered non-random samples, possible relationships between the suspects can be assumed. Therefore, population inbreeding effect was estimated using the FIS calculation. The overall inbreeding parameter was found to be 0.0106. Furthermore, we tested the impact of the two allele frequency datasets on 101 randomly chosen STR profiles, including full and partial profiles. The 95% confidence interval estimates for the profile frequencies (pM) resulted in a tighter range when we used the new dataset compared to the previously published ones. We found that the FIS had less effect on frequency values in the 21,473 samples than the application of minimum allele frequency. No genetic substructure was detected by STRUCTURE analysis. Due to the low level of inbreeding effect and the high number of samples, the new dataset provides unbiased and precise estimates of LR for statistical interpretation of forensic casework and allows us to use lower allele frequencies. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

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

Transcriptional profiling at whole population and single cell levels reveals somatosensory neuron molecular diversity

PubMed Central

Chiu, Isaac M; Barrett, Lee B; Williams, Erika K; Strochlic, David E; Lee, Seungkyu; Weyer, Andy D; Lou, Shan; Bryman, Gregory S; Roberson, David P; Ghasemlou, Nader; Piccoli, Cara; Ahat, Ezgi; Wang, Victor; Cobos, Enrique J; Stucky, Cheryl L; Ma, Qiufu; Liberles, Stephen D; Woolf, Clifford J

2014-01-01

The somatosensory nervous system is critical for the organism's ability to respond to mechanical, thermal, and nociceptive stimuli. Somatosensory neurons are functionally and anatomically diverse but their molecular profiles are not well-defined. Here, we used transcriptional profiling to analyze the detailed molecular signatures of dorsal root ganglion (DRG) sensory neurons. We used two mouse reporter lines and surface IB4 labeling to purify three major non-overlapping classes of neurons: 1) IB4+SNS-Cre/TdTomato+, 2) IB4−SNS-Cre/TdTomato+, and 3) Parv-Cre/TdTomato+ cells, encompassing the majority of nociceptive, pruriceptive, and proprioceptive neurons. These neurons displayed distinct expression patterns of ion channels, transcription factors, and GPCRs. Highly parallel qRT-PCR analysis of 334 single neurons selected by membership of the three populations demonstrated further diversity, with unbiased clustering analysis identifying six distinct subgroups. These data significantly increase our knowledge of the molecular identities of known DRG populations and uncover potentially novel subsets, revealing the complexity and diversity of those neurons underlying somatosensation. DOI: http://dx.doi.org/10.7554/eLife.04660.001 PMID:25525749

PROFILES OF GREAT LAKES CRITICAL POLLUTANTS: A SENTINEL ANALYSIS OF HUMAN BLOOD AND URINE

EPA Science Inventory

To determine the contaminants that should be studied further in the subsequent population-based study, a profile of Great Lakes (GL) sport fish contaminant residues were studied in human blood and urine specimens from 32 sport fish consumers from three Great Lakes: Lake Michigan ...

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…

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,…

Influence of arterial hypertension, type 2 diabetes and cardiovascular risk factors on ALS outcome: a population-based study.

PubMed

Moglia, Cristina; Calvo, Andrea; Canosa, Antonio; Bertuzzo, Davide; Cugnasco, Paolo; Solero, Luca; Grassano, Maurizio; Bersano, Enrica; Cammarosano, Stefania; Manera, Umberto; Pisano, Fabrizio; Mazzini, Letizia; Dalla Vecchia, Laura A; Mora, Gabriele; Chiò, Adriano

2017-11-01

To assess the prognostic influence of pre-morbid type 2 diabetes mellitus, arterial hypertension and cardiovascular (CV) risk profile on ALS phenotype and outcome in a population-based cohort of Italian patients. A total of 650 ALS patients from the Piemonte/Valle d'Aosta Register for ALS, incident in the 2007-2011 period, were recruited. Information about premorbid presence of type 2 diabetes mellitus, arterial hypertension was collected at the time of diagnosis. Patients' CV risk profile was calculated according to the Joint British Societies' guidelines on prevention of cardiovascular disease in clinical practice (JBS2). At the univariate analysis, the presence of pre-morbid arterial hypertension was associated with a higher age at onset of ALS and a shorter survival, and patients with a high CV risk profile had a worse prognosis than those with a low CV risk profile. The Cox multivariable analysis did not confirm such findings. Type 2 diabetes mellitus did not modify either the phenotype or the prognosis of ALS patients. This study performed on a large population-based cohort of ALS patients has demonstrated that arterial hypertension, type 2 diabetes and CV risk factors, calculated using the Framingham equation, do not influence ALS phenotype and prognosis.

Choice of population database for forensic DNA profile analysis.

PubMed

Steele, Christopher D; Balding, David J

2014-12-01

When evaluating the weight of evidence (WoE) for an individual to be a contributor to a DNA sample, an allele frequency database is required. The allele frequencies are needed to inform about genotype probabilities for unknown contributors of DNA to the sample. Typically databases are available from several populations, and a common practice is to evaluate the WoE using each available database for each unknown contributor. Often the most conservative WoE (most favourable to the defence) is the one reported to the court. However the number of human populations that could be considered is essentially unlimited and the number of contributors to a sample can be large, making it impractical to perform every possible WoE calculation, particularly for complex crime scene profiles. We propose instead the use of only the database that best matches the ancestry of the queried contributor, together with a substantial FST adjustment. To investigate the degree of conservativeness of this approach, we performed extensive simulations of one- and two-contributor crime scene profiles, in the latter case with, and without, the profile of the second contributor available for the analysis. The genotypes were simulated using five population databases, which were also available for the analysis, and evaluations of WoE using our heuristic rule were compared with several alternative calculations using different databases. Using FST=0.03, we found that our heuristic gave WoE more favourable to the defence than alternative calculations in well over 99% of the comparisons we considered; on average the difference in WoE was just under 0.2 bans (orders of magnitude) per locus. The degree of conservativeness of the heuristic rule can be adjusted through the FST value. We propose the use of this heuristic for DNA profile WoE calculations, due to its ease of implementation, and efficient use of the evidence while allowing a flexible degree of conservativeness. Copyright © 2014. Published by Elsevier Ireland Ltd.

Genotypes of pathogenic Leptospira spp isolated from rodents in Argentina

PubMed Central

Loffler, Sylvia Grune; Pavan, Maria Elisa; Vanasco, Bibiana; Samartino, Luis; Suarez, Olga; Auteri, Carmelo; Romero, Graciela; Brihuega, Bibiana

2014-01-01

Leptospirosis is the most widespread zoonosis in the world and significant efforts have been made to determine and classify pathogenic Leptospira strains. This zoonosis is maintained in nature through chronic renal infections of carrier animals, with rodents and other small mammals serving as the most important reservoirs. Additionally, domestic animals, such as livestock and dogs, are significant sources of human infection. In this study, a multiple-locus variable-number tandem repeat analysis (MLVA) was applied to genotype 22 pathogenic Leptospira strains isolated from urban and periurban rodent populations from different regions of Argentina. Three MLVA profiles were identified in strains belonging to the species Leptospira interrogans (serovars Icterohaemorrhagiae and Canicola); one profile was observed in serovar Icterohaemorrhagiae and two MLVA profiles were observed in isolates of serovars Canicola and Portlandvere. All strains belonging to Leptospira borgpetersenii serovar Castellonis exhibited the same MLVA profile. Four different genotypes were isolated from urban populations of rodents, including both mice and rats and two different genotypes were isolated from periurban populations. PMID:24676656

Essential-oil composition of the needles collected from natural populations of Macedonian pine (Pinus peuce Griseb.) from the Scardo-Pindic mountain system.

PubMed

Nikolić, Biljana; Ristić, Mihailo; Bojović, Srdjan; Matevski, Vlado; Krivošej, Zoran; Marin, Petar D

2014-06-01

The needle-terpene profiles of two natural Pinus peuce populations from the Scardo-Pindic mountain system (Mt. Ošljak and Mt. Pelister) were analyzed. Among the 90 detected compounds, 87 were identified. The dominant constituents were α-pinene (45.5%), germacrene D (11.1%), β-pinene (10.8%), and camphene (10.3%). The following eight additional components were found to be present in medium-to-high amounts (0.5-10%): bornyl acetate (5.0%), β-phellandrene (3.4%), β-caryophyllene (2.9%), β-myrcene (0.9%), germacrene D-4-ol (0.9%), tricyclene (0.7%), (E)-hex-2-enal (0.7%), and bicyclogermacrene (0.6%). Although the general needle-terpene profiles of the populations from Mt. Ošljak and Mt. Pelister were found to be similar to those of the populations from Zeletin, Sjekirica, and Mokra Gora (Dinaric Alps), principle component analysis (PCA) of eight terpenes (α-pinene, β-myrcene, α-terpinolene, bornyl acetate, α-terpinyl acetate, β-caryophyllene, trans-β-farnesene, and germacrene D) in 139 tree samples suggested a divergence between the two population groups, i.e., the samples from the Scardo-Pindic mountain system and those from the Dinaric Alps. Genetic analysis of the β-pinene content demonstrated a partial divergence between the two geographical groups. The profiles of both population groups differed from those published for populations from the Balkan-Rhodope mountains system (literature results), which were characterized by high contents of bornyl acetate and citronellol (Greek populations) or δ-car-3-ene (Bulgarian populations). Copyright © 2014 Verlag Helvetica Chimica Acta AG, Zürich.

Fatty Acid Diversity is Not Associated with Neutral Genetic Diversity in Native Populations of the Biodiesel Plant Jatropha curcas L.

PubMed

Martínez-Díaz, Yesenia; González-Rodríguez, Antonio; Rico-Ponce, Héctor Rómulo; Rocha-Ramírez, Víctor; Ovando-Medina, Isidro; Espinosa-García, Francisco J

2017-01-01

Jatropha curcas L. (Euphorbiaceae) is a shrub native to Mexico and Central America, which produces seeds with a high oil content that can be converted to biodiesel. The genetic diversity of this plant has been widely studied, but it is not known whether the diversity of the seed oil chemical composition correlates with neutral genetic diversity. The total seed oil content, the diversity of profiles of fatty acids and phorbol esters were quantified, also, the genetic diversity obtained from simple sequence repeats was analyzed in native populations of J. curcas in Mexico. Using the fatty acids profiles, a discriminant analysis recognized three groups of individuals according to geographical origin. Bayesian assignment analysis revealed two genetic groups, while the genetic structure of the populations could not be explained by isolation-by-distance. Genetic and fatty acid profile data were not correlated based on Mantel test. Also, phorbol ester content and genetic diversity were not associated. Multiple linear regression analysis showed that total oil content was associated with altitude and seasonality of temperature. The content of unsaturated fatty acids was associated with altitude. Therefore, the cultivation planning of J. curcas should take into account chemical variation related to environmental factors. © 2017 Wiley-VHCA AG, Zurich, Switzerland.

Microsatellite analysis of Fasciola spp. in Egypt.

PubMed

Dar, Yasser; Amer, Said; Courtioux, Bertrand; Dreyfuss, Gilles

2011-12-01

Recently, the topic of diversity in Fasciola population in Egypt is controversial. The present study was performed to study the genetic diversity of isolated flukes based on microsatellites markers. Fasciola worms were collected from different hosts and geographical locations in Egypt. Control samples of Fasciola hepatica from France as well as Fasciola gigantica from Cameroon were included in the study. Collected flukes were identified morphologically and subjected for analysis using four microsatellite markers. Results of microsatellite profile (FM1 and FM2) proved that both species of Fasciola are distributed in Egypt irrespective of geographical location and host. Nevertheless, the microsatellite profile of some analyzed loci (FM2 and FM3) proved that Egyptian flukes showed more alleles compared to the reference ones. Differences of microsatellite profile in Egyptian isolates than that of corresponding reference samples indicate the remarkable diversity of these isolates. The present results highlighted the utility of microsatellite profile to discriminate between Fasciola species and to elucidate the diversity within the species. To our knowledge, this is the first time to study microsatellite polymorphism in Fasciola populations in Egypt.

The Isolation of Pure Populations of Neurons by Laser Capture Microdissection: Methods and Application in Neuroscience.

PubMed

Morris, Renée; Mehta, Prachi

2018-01-01

In mammals, the central nervous system (CNS) is constituted of various cellular elements, posing a challenge to isolating specific cell types to investigate their expression profile. As a result, tissue homogenization is not amenable to analyses of motor neurons profiling as these represent less than 10% of the total spinal cord cell population. One way to tackle the problem of tissue heterogeneity and obtain meaningful genomic, proteomic, and transcriptomic profiling is to use laser capture microdissection technology (LCM). In this chapter, we describe protocols for the capture of isolated populations of motor neurons from spinal cord tissue sections and for downstream transcriptomic analysis of motor neurons with RT-PCR. We have also included a protocol for the immunological confirmation that the captured neurons are indeed motor neurons. Although focused on spinal cord motor neurons, these protocols can be easily optimized for the isolation of any CNS neurons.

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.

Old worries and new anxieties: behavioral symptoms and mild cognitive impairment in a population study.

PubMed

Andreescu, Carmen; Teverovsky, Esther; Fu, Bo; Hughes, Tiffany F; Chang, Chung-Chou H; Ganguli, Mary

2014-03-01

To disentangle the complex associations of depression and anxiety with mild cognitive impairment (MCI) at the population level. We examined subgroups of anxiety symptoms and depression symptom profiles in relation to MCI, which we defined using both cognitive and functional approaches. We used an epidemiologic, cross-sectional study with an age-stratified, random, population-based sample of 1,982 individuals aged 65 years and over. Three definitions of MCI were used: 1) a purely cognitive classification into amnestic and nonamnestic MCI, 2) a combined cognitive-functional definition by International Working Group (IWG) criteria, and 3) a purely functional definition by the Clinical Dementia Rating (CDR) of 0.5. Three depression profiles were identified by factor analysis of the modified Center for Epidemiological Studies-Depression Scale: core mood, self-esteem/interpersonal, and apathy/neurovegetative profiles. Three anxiety groups, chronic mild worry, chronic severe anxiety, and recent-onset anxiety, were based on screening questions. Recent-onset anxiety was associated with MCI by nonamnestic and IWG criteria, chronic severe anxiety was associated with MCI by all definitions, and chronic mild worry was associated with none. Of the depression profiles, the core mood profile was associated with CDR-defined MCI, the apathy/neurovegetative profile was associated with MCI by amnestic, IWG, and CDR definitions, and the self-esteem/interpersonal profile was associated with none. In this population-based sample, subgroups with different anxiety and depression profiles had different relationships with cognitive and functional definitions of MCI. Anxiety, depression, and MCI are all multidimensional entities, interacting in complex ways that may shed light on underlying neural mechanisms. Copyright © 2014 American Association for Geriatric Psychiatry. Published by Elsevier Inc. All rights reserved.

Patterns of stigma toward schizophrenia among the general population: a latent profile analysis.

PubMed

Loch, Alexandre A; Wang, Yuan-Pang; Guarniero, Francisco B; Lawson, Fabio L; Hengartner, Michael P; Rössler, Wulf; Gattaz, Wagner F

2014-09-01

Our purpose was to assess stigma toward schizophrenia in a representative sample of the Brazilian general population. The sample consisted of 1015 individuals interviewed by telephone. A vignette describing someone with schizophrenia was read, and four stigma aspects regarding this hypothetical individual were assessed: stereotypes, restrictions, perceived prejudice and social distance. Latent profile analysis searched for stigma profiles among the sample. Multinomial logistic regression was used to find correlates of each class. Four stigma profiles were found; 'no stigma' individuals (n = 251) mostly displayed positive opinions. 'Labelers' (n = 222) scored high on social distance; they more often had familial contact with mental illness and more often labeled the vignette's disorder as schizophrenia. 'Discriminators', the group with the majority of individuals (n = 302), showed high levels of stigmatizing beliefs in all dimensions; discriminators were significantly older. 'Unobtrusive stigma' individuals (n = 240) seemed to demonstrate uncertainty or low commitment since they mostly answered items with the middle/impartial option. Some findings from the international literature were replicated; however, familial contact increased stigma, possibly denoting a locally modulated determinant. Hereby, our study also adds important cross-cultural data by showing that stigma toward schizophrenia is high in a Latin-American setting. We highlight the importance of analyzing the general population as a heterogeneous group, aiming to better elaborate anti-stigma campaigns. © The Author(s) 2013.

Women in American Society: A Historical and Demographic Profile. Population Profiles, Unit No. 15.

ERIC Educational Resources Information Center

Reilly, Mary Ellen; Bouvier, Leon F.

An historical and contemporary analysis of the role of women in American society is presented. Specifically, the report considers women's involvement in the labor force. During the colonial period, most women worked in the home, producing cloth, clothing, shoes, and food. With the development of the textile industry, women obtained jobs in…

Sun exposure profile in the French population. Results of the EDIFICE Melanoma survey.

PubMed

Sassolas, B; Grange, F; Touboul, C; Lebbe, C; Saiag, P; Mortier, L; Lhomel, C; Robert, C

2015-02-01

The incidence of melanoma is increasing worldwide, causing significant economic burden at community and individual levels. Ultraviolet radiation, from natural sunlight or artificial sources, is the main environmental, modifiable risk factor for melanoma. The present analysis assesses the profile of sun exposure in the French population as well as the level of awareness about ultraviolet risk and protection. The survey was conducted via telephone interviews in September and October 2011. In total, 1502 respondents were questioned about their own sun exposure with the question "do you ever, even occasionally, spend time in the sun, during leisure-time, vacation or your professional occupation?" They were also asked about sun protection measures used: protective clothing, a hat or sunscreen. More than three respondents out of four (78%) declared exposing themselves to the sun, with an average of 113 days per year. Of these, 38% did not use appropriate sun protection measures. We identified the following characteristics of individuals declaring high sun exposure: chiefly men under the age of 40, higher socio-professional levels, and adults with no children. Individuals who make a poor use of protective measures are mostly men and of low educational levels. Individuals declaring low sun exposure were chiefly: women, individuals over the age of 60, and those with no professional activity. The high sun protection population comprises mostly: women, higher socio-professional levels, with no specific age-group profile. Analysis of the EDIFICE Melanoma survey provides information about the attitudes of the French population towards sun exposure. The most frequent contexts of sun exposure and the associated socio-demographic characteristics of the population with at-risk attitudes regarding sun exposure are identified. This deeper insight into the profile of at-risk populations will allow interventions to be more accurately targeted, thus potentially improving public health benefits. © 2015 European Academy of Dermatology and Venereology.

Discourse, Health and Well-being of Military Populations through the Social Media Lens

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

Pavalanathan, Umashanthi; Datla, Vivek V.; Volkova, Svitlana

Social media can provide a resource for characterizing communities and small populations through activities and content shared online. For instance, studying the language use in social media within military populations may provide insights into their health and wellbeing. In this paper, we address three research questions: (1) How do military populations use social media? (2) What do military users discuss in social media? And (3) Do military users talk about health and well-being differently than civilians? Military Twitter users were identified through keywords in the profile description of users who posted geo-tagged tweets at military installations. The data was anonymizedmore » for the analysis. User profiles that belong to military population were compared to the nonmilitary population. Our results indicate that military users talk more about events in their military life, whereas nonmilitary users talk more about school, work, and leisure activities. We also found that the online content generated by both populations is significantly different, including health-related language and communication behavior.« less

Motivational profiles of medical students: association with study effort, academic performance and exhaustion.

PubMed

Kusurkar, Rashmi A; Croiset, Gerda; Galindo-Garré, Francisca; Ten Cate, Olle

2013-06-19

Students enter the medical study with internally generated motives like genuine interest (intrinsic motivation) and/or externally generated motives like parental pressure or desire for status or prestige (controlled motivation). According to Self-determination theory (SDT), students could differ in their study effort, academic performance and adjustment to the study depending on the endorsement of intrinsic motivation versus controlled motivation. The objectives of this study were to generate motivational profiles of medical students using combinations of high or low intrinsic and controlled motivation and test whether different motivational profiles are associated with different study outcomes. Participating students (N = 844) from University Medical Center Utrecht, the Netherlands, were classified to different subgroups through K-means cluster analysis using intrinsic and controlled motivation scores. Cluster membership was used as an independent variable to assess differences in study strategies, self-study hours, academic performance and exhaustion from study. Four clusters were obtained: High Intrinsic High Controlled (HIHC), Low Intrinsic High Controlled (LIHC), High Intrinsic Low Controlled (HILC), and Low Intrinsic Low Controlled (LILC). HIHC profile, including the students who are interest + status motivated, constituted 25.2% of the population (N = 213). HILC profile, including interest-motivated students, constituted 26.1% of the population (N = 220). LIHC profile, including status-motivated students, constituted 31.8% of the population (N = 268). LILC profile, including students who have a low-motivation and are neither interest nor status motivated, constituted 16.9% of the population (N = 143). Interest-motivated students (HILC) had significantly more deep study strategy (p < 0.001) and self-study hours (p < 0.05), higher GPAs (p < 0.001) and lower exhaustion (p < 0.001) than status-motivated (LIHC) and low-motivation (LILC) students. The interest-motivated profile of medical students (HILC) is associated with good study hours, deep study strategy, good academic performance and low exhaustion from study. The interest + status motivated profile (HIHC) was also found to be associated with a good learning profile, except that students with this profile showed higher surface strategy. Low-motivation (LILC) and status-motivated profiles (LIHC) were associated with the least desirable learning behaviours.

Cuticular hydrocarbon profiles differentiate tropical fire ant populations (Solenopsis geminata, Hymenoptera: Formicidae)

USDA-ARS?s Scientific Manuscript database

The cuticular hydrocarbons (CHCs) from hexane rinses of workers from two Florida populations (dark and red forms) of the tropical fire ant, Solenopsis geminata, were separated by silica gel chromatography and identified by GC-MS analysis. Both the dark form and the red form produce similar CHCs with...

Correlation-based network analysis of metabolite and enzyme profiles reveals a role of citrate biosynthesis in modulating N and C metabolism in zea mays

USDA-ARS?s Scientific Manuscript database

To investigate the natural variability of leaf metabolism and enzymatic activity in a maize inbred population, statistical and network analyses were employed on metabolite and enzyme profiles. The test of coefficient of variation showed that sugars and amino acids displayed opposite trends in their ...

Physical activity and sleep profiles in Finnish men and women.

PubMed

Wennman, Heini; Kronholm, Erkki; Partonen, Timo; Tolvanen, Asko; Peltonen, Markku; Vasankari, Tommi; Borodulin, Katja

2014-01-27

Physical activity (PA) and sleep are related to cardiovascular diseases (CVD) and their risk factors. The interrelationship between these behaviors has been studied, but there remain questions regarding the association of different types of PA, such as occupational, commuting, and leisure time to sleep, including quality, duration and sufficiency. It is also unclear to what extent sleep affects peoples' PA levels and patterns. Our aim is to investigate the interrelationship between PA and sleep behaviors in the Finnish population, including employment status and gender. The study comprised population based data from the FINRISK 2012 Study. A stratified, random sample of 10,000 Finns, 25 to 74 years-old, were sent a questionnaire and an invitation to a health examination. The participation rate was 64% (n = 6,414). Latent class analysis was used to search for different underlying profiles of PA and sleep behavior in men and women, respectively. Models with one through five latent profiles were fitted to the data. Based on fit indicators, a four-class model for men and women, respectively, was decided to be the best fitted model. Four different profiles of PA and sleep were found in both men and women. The most common profile of men comprised 45% of the total participants, and in women, 47%. These profiles were distinguished by probabilities for high leisure time PA and sleep, subjectively rated as sufficient, as well as sleep duration of 7-7.9 hours. The least common profiles represented 5% (men) and 11% (women) of the population, and were characterized by probabilities for physical inactivity, short sleep, and evening type for women and morning type for men. There was also one profile in both genders characterized by likelihood for both high occupational PA and subjectively experienced insufficient sleep. The use of latent class analysis in investigating the interrelationship between PA and sleep is a novel perspective. The method provides information on the clustering of behaviors in people and the profiles found suggest an accumulative nature of leisure time PA, and better sleep. Our data also suggest that high levels of occupational PA are associated with shorter and poorer sleep.

FBI's DNA analysis program

NASA Astrophysics Data System (ADS)

Brown, John R.

1994-03-01

Forensic DNA profiling technology is a significant law enforcement tool due to its superior discriminating power. Applying the principles of population genetics to the DNA profile obtained in violent crime investigations results in low frequency of occurrence estimates for the DNA profile. These estimates often range from a frequency of occurrence of 1 in 50 unrelated individuals to 1 in a million unrelated individuals or even smaller. It is this power to discriminate among individuals in the population that has propelled forensic DNA technology to the forefront of forensic testing in violent crime cases. Not only is the technology extremely powerful in including or excluding a criminal suspect as the perpetrator, but it also gives rise to the potential of identifying criminal suspects in cases where the investigators of unknown suspect cases have exhausted all other available leads.

Angular photogrammetric analysis of the soft-tissue facial profile of Indian adults.

PubMed

Pandian, K Saravana; Krishnan, Sindhuja; Kumar, S Aravind

2018-01-01

Soft-tissue analysis has become an important component of orthodontic diagnosis and treatment planning. Photographic evaluation of an orthodontic patient is a very close representation of the appearance of the person. The previously established norms for soft-tissue analysis will vary for different ethnic groups. Thus, there is a need to develop soft-tissue facial profile norms pertaining to Indian ethnic groups. The aim of this study is to establish the angular photogrammetric standards of soft-tissue facial profile for Indian males and females and also to compare sexual dimorphism present between them. The lateral profile photographs of 300 random participants (150 males and 150 females) between ages 18 and 25 years were taken and analyzed using FACAD tracing software. Inclusion criteria were angles Class I molar occlusion with acceptable crowding and proclination, normal growth and development with well-aligned dental arches, and full complements of permanent teeth irrespective of third molar status. This study was conducted in Indian population, and samples were taken from various cities across India. Descriptive statistical analysis was carried out, and sexual dimorphism was evaluated by Student's t-test between males and females. The results of the present study showed statistically significant (P < 0.05) gender difference in 5 parameters out of 12 parameters in Indian population. In the present study, soft-tissue facial measurements were established by means of photogrammetric analysis to facilitate orthodontists to carry out more quantitative evaluation and make disciplined decisions. The mean values obtained can be used for comparison with records of participants with the same characteristics by following this photogrammetric technique.

Inpatient Profile of Patients with Major Depression in Portuguese National Health System Hospitals, in 2008 and 2013: Variation in a Time of Economic Crisis.

PubMed

Rodrigues, Daniel Francisco Santos; Nunes, Carla

2018-02-01

The economic crisis has placed Portugal in a situation of budgetary constraints with repercussions on mental health, since 2009. This study analyses the association between economic crisis and the inpatient profile of major depression in the working-age population in Portuguese National Health System hospitals. This was an observational, descriptive and cross-sectional study. An individual analysis of hospitalisation and an ecological analysis at district level, were performed before 2008 and during the crisis (2013). Data on the hospitalisation episodes, working-age population and psychiatric inpatient beds were analysed. An increase in hospitalisation rates for major depression were observed, and across country, high spatial variations were perceived: districts with lower rates of urbanisation and population density had higher hospitalisation rates for major depression. Hospitalisation rates were positively influenced by the available inpatient beds. The results for 2013 were more critical (higher hospitalisation rates, less beds). Further research is needed to understand all patterns, considering other individual and contextual information.

Cardiometabolic risk clustering in spinal cord injury: results of exploratory factor analysis.

PubMed

Libin, Alexander; Tinsley, Emily A; Nash, Mark S; Mendez, Armando J; Burns, Patricia; Elrod, Matt; Hamm, Larry F; Groah, Suzanne L

2013-01-01

Evidence suggests an elevated prevalence of cardiometabolic risks among persons with spinal cord injury (SCI); however, the unique clustering of risk factors in this population has not been fully explored. The purpose of this study was to describe unique clustering of cardiometabolic risk factors differentiated by level of injury. One hundred twenty-one subjects (mean 37 ± 12 years; range, 18-73) with chronic C5 to T12 motor complete SCI were studied. Assessments included medical histories, anthropometrics and blood pressure, and fasting serum lipids, glucose, insulin, and hemoglobin A1c (HbA1c). The most common cardiometabolic risk factors were overweight/obesity, high levels of low-density lipoprotein (LDL-C), and low levels of high-density lipoprotein (HDL-C). Risk clustering was found in 76.9% of the population. Exploratory principal component factor analysis using varimax rotation revealed a 3-factor model in persons with paraplegia (65.4% variance) and a 4-factor solution in persons with tetraplegia (73.3% variance). The differences between groups were emphasized by the varied composition of the extracted factors: Lipid Profile A (total cholesterol [TC] and LDL-C), Body Mass-Hypertension Profile (body mass index [BMI], systolic blood pressure [SBP], and fasting insulin [FI]); Glycemic Profile (fasting glucose and HbA1c), and Lipid Profile B (TG and HDL-C). BMI and SBP formed a separate factor only in persons with tetraplegia. Although the majority of the population with SCI has risk clustering, the composition of the risk clusters may be dependent on level of injury, based on a factor analysis group comparison. This is clinically plausible and relevant as tetraplegics tend to be hypo- to normotensive and more sedentary, resulting in lower HDL-C and a greater propensity toward impaired carbohydrate metabolism.

Psychological features of North Korean female refugees on the MMPI-2: latent profile analysis.

PubMed

Kim, Seong-Hyeon; Kim, Hee Kyung; Lee, Narae

2013-12-01

This study examined the heterogeneity in the Minnesota Multiphasic Personality Inventory-2nd Edition (MMPI-2; Butcher, Dahlstrom, Graham, Tellegen, & Kaemmer, 1989) profiles of North Korean female refugee population (N = 2,163) using latent profile analysis (LPA). The North Korean female refugee sample arrived at Hanawon, South Korea's resettlement center for North Korean refugees in 2008 and 2009 and took the MMPI-2 as part of an initial psychological screen. The analysis, which included the T scores of the 6 validity scales and the 10 standard clinical scales, identified 4 classes with distinctive psychological features: Class 1 (nonclinical), Class 2 (demoralized), Class 3 (somatized), and Class 4 (detached). The 4 covariates entered into the model (age, education, affiliation with a religion, and the number of forced repatriations) impacted the likelihood of belonging to certain classes. As hypothesized, older age, fewer years of education, and more incidents of forced repatriation predicted higher proneness to psychopathology. However, contrary to our expectation, having a religious faith did not emerge as a salient protective factor. The current LPA results revealed distinct heterogeneous subgroups that previous research on the MMPI and MMPI-2 profiles of refugee populations overlooked with the assumption of a homogeneous sample. Clinical implications for the treatment of North Korean female refugees and the limitations of the study are discussed. (c) 2013 APA, all rights reserved.

Likelihood ratio and posterior odds in forensic genetics: Two sides of the same coin.

PubMed

Caliebe, Amke; Walsh, Susan; Liu, Fan; Kayser, Manfred; Krawczak, Michael

2017-05-01

It has become widely accepted in forensics that, owing to a lack of sensible priors, the evidential value of matching DNA profiles in trace donor identification or kinship analysis is most sensibly communicated in the form of a likelihood ratio (LR). This restraint does not abate the fact that the posterior odds (PO) would be the preferred basis for returning a verdict. A completely different situation holds for Forensic DNA Phenotyping (FDP), which is aimed at predicting externally visible characteristics (EVCs) of a trace donor from DNA left behind at the crime scene. FDP is intended to provide leads to the police investigation helping them to find unknown trace donors that are unidentifiable by DNA profiling. The statistical models underlying FDP typically yield posterior odds (PO) for an individual possessing a certain EVC. This apparent discrepancy has led to confusion as to when LR or PO is the appropriate outcome of forensic DNA analysis to be communicated to the investigating authorities. We thus set out to clarify the distinction between LR and PO in the context of forensic DNA profiling and FDP from a statistical point of view. In so doing, we also addressed the influence of population affiliation on LR and PO. In contrast to the well-known population dependency of the LR in DNA profiling, the PO as obtained in FDP may be widely population-independent. The actual degree of independence, however, is a matter of (i) how much of the causality of the respective EVC is captured by the genetic markers used for FDP and (ii) by the extent to which non-genetic such as environmental causal factors of the same EVC are distributed equally throughout populations. The fact that an LR should be communicated in cases of DNA profiling whereas the PO are suitable for FDP does not conflict with theory, but rather reflects the immanent differences between these two forensic applications of DNA information. Copyright © 2017 Elsevier B.V. All rights reserved.

Addressing environmental justice under the National Environment Policy Act at Sandia National Laboratories/New Mexico

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

Cohen, T.M.; Bleakly, D.R.

1997-04-01

Under Executive Order 12898, Federal Actions to Address Environmental Justice in Minority Populations and Low-Income Populations, the Department of Energy (DOE) and Sandia National Laboratories New Mexico (SNL) are required to identify and address, as appropriate, disproportionately high, adverse human health or environmental effects of their activities on minority and low-income populations. The National Environmental Policy Act (NEPA) also requires that environmental justice issues be identified and addressed. This presents a challenge for SNL because it is located in a culturally diverse area. Successfully addressing potential impacts is contingent upon accurately identifying them through objective analysis of demographic information. However,more » an effective public participation process, which is necessarily subjective, is also needed to understand the subtle nuances of diverse populations that can contribute to a potential impact, yet are not always accounted for in a strict demographic profile. Typically, there is little or no coordination between these two disparate processes. This report proposes a five-step method for reconciling these processes and uses a hypothetical case study to illustrate the method. A demographic analysis and community profile of the population within 50 miles of SNL were developed to support the environmental justice analysis process and enhance SNL`s NEPA and public involvement programs. This report focuses on developing a methodology for identifying potentially impacted populations. Environmental justice issues related to worker exposures associated with SNL activities will be addressed in a separate report.« less

Population and performance analyses of four major populations with Illumina's FGx Forensic Genomics System.

PubMed

Churchill, Jennifer D; Novroski, Nicole M M; King, Jonathan L; Seah, Lay Hong; Budowle, Bruce

2017-09-01

The MiSeq FGx Forensic Genomics System (Illumina) enables amplification and massively parallel sequencing of 59 STRs, 94 identity informative SNPs, 54 ancestry informative SNPs, and 24 phenotypic informative SNPs. Allele frequency and population statistics data were generated for the 172 SNP loci included in this panel on four major population groups (Chinese, African Americans, US Caucasians, and Southwest Hispanics). Single-locus and combined random match probability values were generated for the identity informative SNPs. The average combined STR and identity informative SNP random match probabilities (assuming independence) across all four populations were 1.75E-67 and 2.30E-71 with length-based and sequence-based STR alleles, respectively. Ancestry and phenotype predictions were obtained using the ForenSeq™ Universal Analysis System (UAS; Illumina) based on the ancestry informative and phenotype informative SNP profiles generated for each sample. Additionally, performance metrics, including profile completeness, read depth, relative locus performance, and allele coverage ratios, were evaluated and detailed for the 725 samples included in this study. While some genetic markers included in this panel performed notably better than others, performance across populations was generally consistent. The performance and population data included in this study support that accurate and reliable profiles were generated and provide valuable background information for laboratories considering internal validation studies and implementation. Copyright © 2017 Elsevier B.V. All rights reserved.

DNA methylation patterns of behavior-related gene promoter regions dissect the gray wolf from domestic dog breeds.

PubMed

Banlaki, Zsofia; Cimarelli, Giulia; Viranyi, Zsofia; Kubinyi, Eniko; Sasvari-Szekely, Maria; Ronai, Zsolt

2017-06-01

A growing body of evidence highlights the relationship between epigenetics, especially DNA methylation, and population divergence as well as speciation. However, little is known about how general the phenomenon of epigenetics-wise separation of different populations is, or whether population assignment is, possible based on solely epigenetic marks. In the present study, we compared DNA methylation profiles between four different canine populations: three domestic dog breeds and their ancestor the gray wolf. Altogether, 79 CpG sites constituting the 65 so-called CpG units located in the promoter regions of genes affecting behavioral and temperamental traits (COMT, HTR1A, MAOA, OXTR, SLC6A4, TPH1, WFS1)-regions putatively targeted during domestication and breed selection. Methylation status of buccal cells was assessed using EpiTYPER technology. Significant inter-population methylation differences were found in 52.3% of all CpG units investigated. DNA methylation profile-based hierarchical cluster analysis indicated an unambiguous segregation of wolf from domestic dog. In addition, one of the three dog breeds (Golden Retriever) investigated also formed a separate, autonomous group. The findings support that population segregation is interrelated with shifts in DNA methylation patterns, at least in putative selection target regions, and also imply that epigenetic profiles could provide a sufficient basis for population assignment of individuals.

Global transcriptome profiling reveals molecular mechanisms of metal tolerance in a chronically exposed wild population of brown trout.

PubMed

Uren Webster, T M; Bury, N; van Aerle, R; Santos, E M

2013-08-06

Worldwide, a number of viable populations of fish are found in environments heavily contaminated with metals, including brown trout (Salmo trutta) inhabiting the River Hayle in South-West of England. This population is chronically exposed to a water-borne mixture of metals, including copper and zinc, at concentrations lethal to naïve fish. We aimed to investigate the molecular mechanisms employed by the River Hayle brown trout to tolerate high metal concentrations. To achieve this, we combined tissue metal analysis with whole-transcriptome profiling using RNA-seq on an Illumina platform. Metal concentrations in the Hayle trout, compared to fish from a relatively unimpacted river, were significantly increased in the gills, liver and kidney (63-, 34- and 19-fold respectively), but not the gut. This confirms that these fish can tolerate considerable metal accumulation, highlighting the importance of these tissues in metal uptake (gill), storage and detoxification (liver, kidney). We sequenced, assembled and annotated the brown trout transcriptome using a de novo approach. Subsequent gene expression analysis identified 998 differentially expressed transcripts and functional analysis revealed that metal- and ion-homeostasis pathways are likely to be the most important mechanisms contributing to the metal tolerance exhibited by this population.

Global Transcriptome Profiling Reveals Molecular Mechanisms of Metal Tolerance in a Chronically Exposed Wild Population of Brown Trout

PubMed Central

2013-01-01

Worldwide, a number of viable populations of fish are found in environments heavily contaminated with metals, including brown trout (Salmo trutta) inhabiting the River Hayle in South-West of England. This population is chronically exposed to a water-borne mixture of metals, including copper and zinc, at concentrations lethal to naïve fish. We aimed to investigate the molecular mechanisms employed by the River Hayle brown trout to tolerate high metal concentrations. To achieve this, we combined tissue metal analysis with whole-transcriptome profiling using RNA-seq on an Illumina platform. Metal concentrations in the Hayle trout, compared to fish from a relatively unimpacted river, were significantly increased in the gills, liver and kidney (63-, 34- and 19-fold respectively), but not the gut. This confirms that these fish can tolerate considerable metal accumulation, highlighting the importance of these tissues in metal uptake (gill), storage and detoxification (liver, kidney). We sequenced, assembled and annotated the brown trout transcriptome using a de novo approach. Subsequent gene expression analysis identified 998 differentially expressed transcripts and functional analysis revealed that metal- and ion-homeostasis pathways are likely to be the most important mechanisms contributing to the metal tolerance exhibited by this population. PMID:23834071

Genome-wide expression profiling of in vivo-derived bloodstream parasite stages and dynamic analysis of mRNA alterations during synchronous differentiation in Trypanosoma brucei

PubMed Central

Kabani, Sarah; Fenn, Katelyn; Ross, Alan; Ivens, Al; Smith, Terry K; Ghazal, Peter; Matthews, Keith

2009-01-01

Background Trypanosomes undergo extensive developmental changes during their complex life cycle. Crucial among these is the transition between slender and stumpy bloodstream forms and, thereafter, the differentiation from stumpy to tsetse-midgut procyclic forms. These developmental events are highly regulated, temporally reproducible and accompanied by expression changes mediated almost exclusively at the post-transcriptional level. Results In this study we have examined, by whole-genome microarray analysis, the mRNA abundance of genes in slender and stumpy forms of T.brucei AnTat1.1 cells, and also during their synchronous differentiation to procyclic forms. In total, five biological replicates representing the differentiation of matched parasite populations derived from five individual mouse infections were assayed, with RNAs being derived at key biological time points during the time course of their synchronous differentiation to procyclic forms. Importantly, the biological context of these mRNA profiles was established by assaying the coincident cellular events in each population (surface antigen exchange, morphological restructuring, cell cycle re-entry), thereby linking the observed gene expression changes to the well-established framework of trypanosome differentiation. Conclusion Using stringent statistical analysis and validation of the derived profiles against experimentally-predicted gene expression and phenotypic changes, we have established the profile of regulated gene expression during these important life-cycle transitions. The highly synchronous nature of differentiation between stumpy and procyclic forms also means that these studies of mRNA profiles are directly relevant to the changes in mRNA abundance within individual cells during this well-characterised developmental transition. PMID:19747379

Ant and Mite Diversity Drives Toxin Variation in the Little Devil Poison Frog.

PubMed

McGugan, Jenna R; Byrd, Gary D; Roland, Alexandre B; Caty, Stephanie N; Kabir, Nisha; Tapia, Elicio E; Trauger, Sunia A; Coloma, Luis A; O'Connell, Lauren A

2016-06-01

Poison frogs sequester chemical defenses from arthropod prey, although the details of how arthropod diversity contributes to variation in poison frog toxins remains unclear. We characterized skin alkaloid profiles in the Little Devil poison frog, Oophaga sylvatica (Dendrobatidae), across three populations in northwestern Ecuador. Using gas chromatography/mass spectrometry, we identified histrionicotoxins, 3,5- and 5,8-disubstituted indolizidines, decahydroquinolines, and lehmizidines as the primary alkaloid toxins in these O. sylvatica populations. Frog skin alkaloid composition varied along a geographical gradient following population distribution in a principal component analysis. We also characterized diversity in arthropods isolated from frog stomach contents and confirmed that O. sylvatica specialize on ants and mites. To test the hypothesis that poison frog toxin variability reflects species and chemical diversity in arthropod prey, we (1) used sequencing of cytochrome oxidase 1 to identify individual prey specimens, and (2) used liquid chromatography/mass spectrometry to chemically profile consumed ants and mites. We identified 45 ants and 9 mites in frog stomachs, including several undescribed species. We also showed that chemical profiles of consumed ants and mites cluster by frog population, suggesting different frog populations have access to chemically distinct prey. Finally, by comparing chemical profiles of frog skin and isolated prey items, we traced the arthropod source of four poison frog alkaloids, including 3,5- and 5,8-disubstituted indolizidines and a lehmizidine alkaloid. Together, the data show that toxin variability in O. sylvatica reflects chemical diversity in arthropod prey.

The epidiemiologic profile of HCV infected Hispanic patients from the southern area of Puerto Rico since 2005.

PubMed

Colón-Ruiz, David; Rosado Carrión, Bárbara; Bredy, Rafael

2012-01-01

Seroprevalence studies in adults done in San Juan and Puerto Rico have showed 6.3% and 2.2% of the population respectively, are positive for antibodies to Hepatitis C Virus (anti-HCV). It is been suggested that Hispanics have a lower sustained virological response to current therapy. The epidemiologic profile, the response to treatment and the risk factors to the poor response to treatment of HCV patients have not been studied in the southern area of Puerto Rico. This is a cross-sectional analysis of data from 46 medical records from January 2005 to March 2011. We search for sociodemographic variables, comorbidities, the HCV genotype, the human immunodeficiency virus profile, history of alcoholism and the patients who were treated with peginterferon alpha 2b and ribavirin, and their response to treatment. Our HCV infected population is male predominant (63%), and the most common route of transmission were intravenous drug abuse (37%) and blood transfusions (33%). Only 37% reported alcoholism. The most common comorbidities found in our population were hypertension (35%), diabetes mellitus (20%), hypothyroidism (7%) and dyslipidemia (7%). Most common genotype found in our population was type 1 (61%). From the 46 patients, 10 patients were treated, being genotype 1 the most common. Overall, our population showed an epidemiological profile similar to other Hispanic groups in the literature, which should motivate us to continue exploring these associations, in an effort to improve the management of these patients.

Variability of the needle essential oils of Pinus peuce from different populations in Montenegro and Serbia.

PubMed

Nikolić, Biljana; Ristić, Mihailo; Bojović, Srdjan; Marin, Petar D

2008-07-01

The essential-oil composition of Pinus peuce Griseb. is reported at the population level. Macedonian pine is endemic high-mountain Balkan pine relict of an anthropogenically reduced area, with large morphological diversity and insufficiently clear taxonomic position. In the pine-needle terpene profile of two populations from Montenegro and one from Serbia, 78 compounds were detected, 56 of which are identified (Table 3). The dominant constituents were alpha-pinene (36.5%) and germacrene D (11.4%). The following 20 additional components were found to be present in medium-to-high amounts (0.5-10%): camphene (8.5%), bornyl acetate (6.8%), beta-pinene (6.8%), beta-caryophyllene (5.2%), beta-phellandrene (4.7%), terpinen-4-ol acetate (1.6%), (E)-hex-2-enal (1.5%), alpha-muurolene (1.2%), beta-gurjunene (1.1%), beta-myrcene (1.0%), alpha-terpinyl acetate (0.9%), alpha-phellandrene (0.8%), delta-cadinene (0.8%), alpha-humulene (0.8%), sabinene (0.7%), aromadendrene (0.6%), alpha-thujene (0.6%), gamma-muurolene (0.6%), gamma-cadinene (0.6%), alpha-terpinolene (0.5%), and one unknown component (0.5%). The similarity of the populations and the within-population variability were visualized by principle-component analysis (PCA) and genetic analysis of selected terpenes in 90 tree samples. Our study suggests a closer connection between populations II and III compared to population I. Based on the profile of the main terpene components, the studied populations are more similar to populations from Kosovo and Greece than to the population from Mt. Mokra (Montenegro) and the population in France.

PanFunPro: Bacterial Pan-Genome Analysis Based on the Functional Profiles (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

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

Lukjancenko, Oksana

2012-06-01

Julien Tremblay from DOE JGI presents "Evaluation of Multiplexed 16S rRNA Microbial Population Surveys Using Illumina MiSeq Platorm" at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

PanFunPro: Bacterial Pan-Genome Analysis Based on the Functional Profiles (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

ScienceCinema

Lukjancenko, Oksana

2018-01-10

Julien Tremblay from DOE JGI presents "Evaluation of Multiplexed 16S rRNA Microbial Population Surveys Using Illumina MiSeq Platorm" at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

ampliMethProfiler: a pipeline for the analysis of CpG methylation profiles of targeted deep bisulfite sequenced amplicons.

PubMed

Scala, Giovanni; Affinito, Ornella; Palumbo, Domenico; Florio, Ermanno; Monticelli, Antonella; Miele, Gennaro; Chiariotti, Lorenzo; Cocozza, Sergio

2016-11-25

CpG sites in an individual molecule may exist in a binary state (methylated or unmethylated) and each individual DNA molecule, containing a certain number of CpGs, is a combination of these states defining an epihaplotype. Classic quantification based approaches to study DNA methylation are intrinsically unable to fully represent the complexity of the underlying methylation substrate. Epihaplotype based approaches, on the other hand, allow methylation profiles of cell populations to be studied at the single molecule level. For such investigations, next-generation sequencing techniques can be used, both for quantitative and for epihaplotype analysis. Currently available tools for methylation analysis lack output formats that explicitly report CpG methylation profiles at the single molecule level and that have suited statistical tools for their interpretation. Here we present ampliMethProfiler, a python-based pipeline for the extraction and statistical epihaplotype analysis of amplicons from targeted deep bisulfite sequencing of multiple DNA regions. ampliMethProfiler tool provides an easy and user friendly way to extract and analyze the epihaplotype composition of reads from targeted bisulfite sequencing experiments. ampliMethProfiler is written in python language and requires a local installation of BLAST and (optionally) QIIME tools. It can be run on Linux and OS X platforms. The software is open source and freely available at http://amplimethprofiler.sourceforge.net .

Single-cell gene expression analysis reveals diversity among human spermatogonia.

PubMed

Neuhaus, N; Yoon, J; Terwort, N; Kliesch, S; Seggewiss, J; Huge, A; Voss, R; Schlatt, S; Grindberg, R V; Schöler, H R

2017-02-10

Is the molecular profile of human spermatogonia homogeneous or heterogeneous when analysed at the single-cell level? Heterogeneous expression profiles may be a key characteristic of human spermatogonia, supporting the existence of a heterogeneous stem cell population. Despite the fact that many studies have sought to identify specific markers for human spermatogonia, the molecular fingerprint of these cells remains hitherto unknown. Testicular tissues from patients with spermatogonial arrest (arrest, n = 1) and with qualitatively normal spermatogenesis (normal, n = 7) were selected from a pool of 179 consecutively obtained biopsies. Gene expression analyses of cell populations and single-cells (n = 105) were performed. Two OCT4-positive individual cells were selected for global transcriptional capture using shallow RNA-seq. Finally, expression of four candidate markers was assessed by immunohistochemistry. Histological analysis and blood hormone measurements for LH, FSH and testosterone were performed prior to testicular sample selection. Following enzymatic digestion of testicular tissues, differential plating and subsequent micromanipulation of individual cells was employed to enrich and isolate human spermatogonia, respectively. Endpoint analyses were qPCR analysis of cell populations and individual cells, shallow RNA-seq and immunohistochemical analyses. Unexpectedly, single-cell expression data from the arrest patient (20 cells) showed heterogeneous expression profiles. Also, from patients with normal spermatogenesis, heterogeneous expression patterns of undifferentiated (OCT4, UTF1 and MAGE A4) and differentiated marker genes (BOLL and PRM2) were obtained within each spermatogonia cluster (13 clusters with 85 cells). Shallow RNA-seq analysis of individual human spermatogonia was validated, and a spermatogonia-specific heterogeneous protein expression of selected candidate markers (DDX5, TSPY1, EEF1A1 and NGN3) was demonstrated. The heterogeneity of human spermatogonia at the RNA and protein levels is a snapshot. To further assess the functional meaning of this heterogeneity and the dynamics of stem cell populations, approaches need to be developed to facilitate the repeated analysis of individual cells. Our data suggest that heterogeneous expression profiles may be a key characteristic of human spermatogonia, supporting the model of a heterogeneous stem cell population. Future studies will assess the dynamics of spermatogonial populations in fertile and infertile patients. RNA-seq data is published in the GEO database: GSE91063. This work was supported by the Max Planck Society and the Deutsche Forschungsgemeinschaft DFG-Research Unit FOR 1041 Germ Cell Potential (grant numbers SCHO 340/7-1, SCHL394/11-2). The authors declare that there is no conflict of interest. © The Author 2017. Published by Oxford University Press on behalf of the European Society of Human Reproduction and Embryology. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Clinical utility of gene expression profiling data for clinical decision-making regarding adjuvant therapy in early stage, node-negative breast cancer: a case report.

PubMed

Schuster, Steven R; Pockaj, Barbara A; Bothe, Mary R; David, Paru S; Northfelt, Donald W

2012-09-10

Breast cancer is the most common malignancy among women in the United States with the second highest incidence of cancer-related death following lung cancer. The decision-making process regarding adjuvant therapy is a time intensive dialogue between the patient and her oncologist. There are multiple tools that help individualize the treatment options for a patient. Population-based analysis with Adjuvant! Online and genomic profiling with Oncotype DX are two commonly used tools in patients with early stage, node-negative breast cancer. This case report illustrates a situation in which the population-based prognostic and predictive information differed dramatically from that obtained from genomic profiling and affected the patient's decision. In light of this case, we discuss the benefits and limitations of these tools.

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

Reference ranges for urinary concentrations and ratios of endogenous steroids, which can be used as markers for steroid misuse, in a Caucasian population of athletes.

PubMed

Van Renterghem, Pieter; Van Eenoo, Peter; Geyer, Hans; Schänzer, Wilhelm; Delbeke, Frans T

2010-02-01

The detection of misuse with naturally occurring steroids is a great challenge for doping control laboratories. Intake of natural anabolic steroids alters the steroid profile. Thus, screening for exogenous use of these steroids can be established by monitoring a range of endogenous steroids, which constitute the steroid profile, and evaluate their concentrations and ratios against reference ranges. Elevated values of the steroid profile constitute an atypical finding after which a confirmatory IRMS procedure is needed to unequivocally establish the exogenous origin of a natural steroid. However, the large inter-individual differences in urinary steroid concentrations and the recent availability of a whole range of natural steroids (e.g. dehydroepiandrosterone and androstenedione) which each exert a different effect on the monitored parameters in doping control complicate the interpretation of the current steroid profile. The screening of an extended steroid profile can provide additional parameters to support the atypical findings and can give specific information upon the steroids which have been administered. The natural concentrations of 29 endogenous steroids and 11 ratios in a predominantly Caucasian population of athletes were determined. The upper reference values at 97.5%, 99% and 99.9% levels were assessed for male (n=2027) and female (n=1004) populations. Monitoring minor metabolites and evaluation of concentration ratios with respect to their natural abundances could improve the interpretation of the steroid profile in doping analysis. Copyright 2009 Elsevier Inc. All rights reserved.

A Comparison of Rule-based Analysis with Regression Methods in Understanding the Risk Factors for Study Withdrawal in a Pediatric Study.

PubMed

Haghighi, Mona; Johnson, Suzanne Bennett; Qian, Xiaoning; Lynch, Kristian F; Vehik, Kendra; Huang, Shuai

2016-08-26

Regression models are extensively used in many epidemiological studies to understand the linkage between specific outcomes of interest and their risk factors. However, regression models in general examine the average effects of the risk factors and ignore subgroups with different risk profiles. As a result, interventions are often geared towards the average member of the population, without consideration of the special health needs of different subgroups within the population. This paper demonstrates the value of using rule-based analysis methods that can identify subgroups with heterogeneous risk profiles in a population without imposing assumptions on the subgroups or method. The rules define the risk pattern of subsets of individuals by not only considering the interactions between the risk factors but also their ranges. We compared the rule-based analysis results with the results from a logistic regression model in The Environmental Determinants of Diabetes in the Young (TEDDY) study. Both methods detected a similar suite of risk factors, but the rule-based analysis was superior at detecting multiple interactions between the risk factors that characterize the subgroups. A further investigation of the particular characteristics of each subgroup may detect the special health needs of the subgroup and lead to tailored interventions.

Molecular Profiling of Liquid Biopsy Samples for Precision Medicine.

PubMed

Campos, Camila D M; Jackson, Joshua M; Witek, Małgorzata A; Soper, Steven A

In the context of oncology, liquid biopsies consist of harvesting cancer biomarkers, such as circulating tumor cells, tumor-derived cell-free DNA, and extracellular vesicles, from bodily fluids. These biomarkers provide a source of clinically actionable molecular information that can enable precision medicine. Herein, we review technologies for the molecular profiling of liquid biopsy markers with special emphasis on the analysis of low abundant markers from mixed populations.

A Person-Centered Personality Approach to Heterogeneity in Attention-Deficit/Hyperactivity Disorder (ADHD)

PubMed Central

Martel, Michelle M.; Goth-Owens, Timothy; Martinez-Torteya, Cecilia; Nigg, Joel T.

2010-01-01

Person-centered personality approaches are an underutilized means of illuminating clinical heterogeneity of Attention-Deficit/Hyperactivity Disorder (ADHD). In this study, latent profile analysis was conducted with personality traits to identify homogeneous profiles within the ADHD population. Participants were 548 children ages six to 18 years (302 with ADHD). Personality traits were measured via parent report on the California Q-Sort. Latent profile analysis was conducted on the Big Five Factors. A six profile solution best fit the data. Resulting groups were characterized as “disagreeable,” “introverted,” “poor control,” “well-adjusted,” “extraverted,” and “perfectionistic.” External validation of this model using ADHD diagnosis, subtypes, and comorbid psychopathology suggested that children with ADHD could be parsed into four groups: 1) an introverted group with high rates of the ADHD-inattentive type, 2) a group characterized by poor control, with high rates of ADHD-combined type (ADHD-C) and comorbid disruptive behavior disorders, 3) an extraverted group, with ADHD-C and few associated comorbid disorders, and 4) possibly, a very rare “perfectionistic” group, exhibiting obsessive traits. A person-centered personality approach may be one promising way to capture homogeneous subgroups within the ADHD population. PMID:20141255

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.

Motivational profiles of medical students: Association with study effort, academic performance and exhaustion

PubMed Central

2013-01-01

Background Students enter the medical study with internally generated motives like genuine interest (intrinsic motivation) and/or externally generated motives like parental pressure or desire for status or prestige (controlled motivation). According to Self-determination theory (SDT), students could differ in their study effort, academic performance and adjustment to the study depending on the endorsement of intrinsic motivation versus controlled motivation. The objectives of this study were to generate motivational profiles of medical students using combinations of high or low intrinsic and controlled motivation and test whether different motivational profiles are associated with different study outcomes. Methods Participating students (N = 844) from University Medical Center Utrecht, the Netherlands, were classified to different subgroups through K-means cluster analysis using intrinsic and controlled motivation scores. Cluster membership was used as an independent variable to assess differences in study strategies, self-study hours, academic performance and exhaustion from study. Results Four clusters were obtained: High Intrinsic High Controlled (HIHC), Low Intrinsic High Controlled (LIHC), High Intrinsic Low Controlled (HILC), and Low Intrinsic Low Controlled (LILC). HIHC profile, including the students who are interest + status motivated, constituted 25.2% of the population (N = 213). HILC profile, including interest-motivated students, constituted 26.1% of the population (N = 220). LIHC profile, including status-motivated students, constituted 31.8% of the population (N = 268). LILC profile, including students who have a low-motivation and are neither interest nor status motivated, constituted 16.9% of the population (N = 143). Interest-motivated students (HILC) had significantly more deep study strategy (p < 0.001) and self-study hours (p < 0.05), higher GPAs (p < 0.001) and lower exhaustion (p < 0.001) than status-motivated (LIHC) and low-motivation (LILC) students. Conclusions The interest-motivated profile of medical students (HILC) is associated with good study hours, deep study strategy, good academic performance and low exhaustion from study. The interest + status motivated profile (HIHC) was also found to be associated with a good learning profile, except that students with this profile showed higher surface strategy. Low-motivation (LILC) and status-motivated profiles (LIHC) were associated with the least desirable learning behaviours. PMID:23782767

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.

Estimation of caffeine intake from analysis of caffeine metabolites in wastewater.

PubMed

Gracia-Lor, Emma; Rousis, Nikolaos I; Zuccato, Ettore; Bade, Richard; Baz-Lomba, Jose Antonio; Castrignanò, Erika; Causanilles, Ana; Hernández, Félix; Kasprzyk-Hordern, Barbara; Kinyua, Juliet; McCall, Ann-Kathrin; van Nuijs, Alexander L N; Plósz, Benedek G; Ramin, Pedram; Ryu, Yeonsuk; Santos, Miguel M; Thomas, Kevin; de Voogt, Pim; Yang, Zhugen; Castiglioni, Sara

2017-12-31

Caffeine metabolites in wastewater were investigated as potential biomarkers for assessing caffeine intake in a population. The main human urinary metabolites of caffeine were measured in the urban wastewater of ten European cities and the metabolic profiles in wastewater were compared with the human urinary excretion profile. A good match was found for 1,7-dimethyluric acid, an exclusive caffeine metabolite, suggesting that might be a suitable biomarker in wastewater for assessing population-level caffeine consumption. A correction factor was developed considering the percentage of excretion of this metabolite in humans, according to published pharmacokinetic studies. Daily caffeine intake estimated from wastewater analysis was compared with the average daily intake calculated from the average amount of coffee consumed by country per capita. Good agreement was found in some cities but further information is needed to standardize this approach. Wastewater analysis proved useful to providing additional local information on caffeine use. Copyright © 2017 Elsevier B.V. All rights reserved.

Syndemic Risk Classes and Substance Use Problems among Adults in High-Risk Urban Areas: A Latent Class Analysis.

PubMed

Cleland, Charles M; Lanza, Stephanie T; Vasilenko, Sara A; Gwadz, Marya

2017-01-01

Substance use problems tend to co-occur with risk factors that are especially prevalent in urban communities with high rates of poverty. The present study draws on Syndemics Theory to understand profiles of risk and resilience and their associations with substance use problems in a population at risk for adverse outcomes. African-American/Black and Hispanic heterosexual adults ( N  = 2,853) were recruited by respondent-driven sampling from an urban area with elevated poverty rates, and completed a structured assessment battery covering sociodemographics, syndemic factors (that is, multiple, co-occurring risk factors), and substance use. More than one-third of participants (36%) met criteria for either an alcohol or a drug problem in the past year. Latent class analysis identified profiles of risk and resilience, separately for women and men, which were associated with the probability of a substance use problem. Almost a third of women (27%) and 38% of men had lower risk profiles-patterns of resilience not apparent in other types of analyses. Profiles with more risk and fewer resilience factors were associated with an increased probability of substance use problems, but profiles with fewer risk and more resilience factors had rates of substance use problems that were very similar to the general adult population. Relative to the lowest risk profile, profiles with the most risk and fewest resilience factors were associated with increased odds of a substance use problem for both women [adjusted odds ratio (aOR) = 8.50; 95% CI: 3.85-18.74] and men (aOR = 11.68; 95% CI: 6.91-19.74). Addressing syndemic factors in substance use treatment and prevention may yield improved outcomes.

OBSERVATIONS AND SIMULATIONS OF THE Na i D{sub 1} LINE PROFILES IN AN M-CLASS SOLAR FLARE

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

Kuridze, D.; Mathioudakis, M.; Jess, D. B.

2016-12-01

We study the temporal evolution of the Na i D{sub 1} line profiles in the M3.9 flare SOL2014-06-11T21:03 UT, using observations at high spectral resolution obtained with the Interferometric Bidimensional Spectrometer instrument on the Dunn Solar Telescope combined with radiative hydrodynamic simulations. Our results show a significant increase in the intensities of the line core and wings during the flare. The analysis of the line profiles from the flare ribbons reveals that the Na i D{sub 1} line has a central reversal with excess emission in the blue wing (blue asymmetry). We combine RADYN and RH simulations to synthesize Na imore » D{sub 1} line profiles of the flaring atmosphere and find good agreement with the observations. Heating with a beam of electrons modifies the radiation field in the flaring atmosphere and excites electrons from the ground state 3s {sup 2}S to the first excited state 3p {sup 2}P, which in turn modifies the relative population of the two states. The change in temperature and the population density of the energy states make the sodium line profile revert from absorption into emission. Furthermore, the rapid changes in temperature break the pressure balance between the different layers of the lower atmosphere, generating upflow/downflow patterns. Analysis of the simulated spectra reveals that the asymmetries of the Na i D{sub 1} flare profile are produced by the velocity gradients in the lower solar atmosphere.« less

Predicting Community College and University Student Success: A Test of the Triadic Reciprocal Model for Two Populations

ERIC Educational Resources Information Center

Heller, Monica L.; Cassady, Jerrell C.

2017-01-01

The current study explored the differential influences that behavioral learning strategies (i.e., cognitive-metacognitive, resource management), motivational profiles, and academic anxiety appraisals have on college-level learners in two unique learning contexts. Using multivariate analysis of variance and discriminant analysis, the study first…

Divergence in male sexual odor signal and genetics across populations of the red mason bee, Osmia bicornis, in Europe.

PubMed

Conrad, Taina; Paxton, Robert J; Assum, Günter; Ayasse, Manfred

2018-01-01

In some insect species, females may base their choice for a suitable mate on male odor. In the red mason bee, Osmia bicornis, female choice is based on a male's odor bouquet as well as its thorax vibrations, and its relatedness to the female, a putative form of optimal outbreeding. Interestingly, O. bicornis can be found as two distinct color morphs in Europe, which are thought to represent subspecies and between which we hypothesize that female discrimination may be particularly marked. Here we investigated (i) if these two colors morphs do indeed represent distinct, reproductively differentiated populations, (ii) how odor bouquets of male O. bicornis vary within and between populations, and (iii) whether variation in male odor correlates with genetic distance, which might represent a cue by which females could optimally outbreed. Using GC and GC-MS analysis of male odors and microsatellite analysis of males and females from 9 populations, we show that, in Denmark, an area of subspecies sympatry, the two color morphs at any one site do not differ, either in odor bouquet or in population genetic differentiation. Yet populations across Europe are distinct in their odor profile as well as being genetically differentiated. Odor differences do not, however, mirror genetic differentiation between populations. We hypothesize that populations from Germany, England and Denmark may be under sexual selection through female choice for local odor profiles, which are not related to color morph though which could ultimately lead to population divergence and speciation.

Evolution in Cloud Population Statistics of the MJO: From AMIE Field Observations to Global-Cloud Permitting Models Final Report

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

Kollias, Pavlos

This is a multi-institutional, collaborative project using a three-tier modeling approach to bridge field observations and global cloud-permitting models, with emphases on cloud population structural evolution through various large-scale environments. Our contribution was in data analysis for the generation of high value cloud and precipitation products and derive cloud statistics for model validation. There are two areas in data analysis that we contributed: the development of a synergistic cloud and precipitation cloud classification that identify different cloud (e.g. shallow cumulus, cirrus) and precipitation types (shallow, deep, convective, stratiform) using profiling ARM observations and the development of a quantitative precipitation ratemore » retrieval algorithm using profiling ARM observations. Similar efforts have been developed in the past for precipitation (weather radars), but not for the millimeter-wavelength (cloud) radar deployed at the ARM sites.« less

Population genetic analysis of Enterocytozoon bieneusi in humans.

PubMed

Li, Wei; Cama, Vitaliano; Feng, Yaoyu; Gilman, Robert H; Bern, Caryn; Zhang, Xichen; Xiao, Lihua

2012-01-01

Genotyping based on sequence analysis of the ribosomal internal transcribed spacer has revealed significant genetic diversity in Enterocytozoonbieneusi. Thus far, the population genetics of E. bieneusi and its significance in the epidemiology of microsporidiosis have not been examined. In this study, a multilocus sequence typing of E. bieneusi in AIDS patients in Lima, Peru was conducted, using 72 specimens previously genotyped as A, D, IV, EbpC, WL11, Peru7, Peru8, Peru10 and Peru11 at the internal transcribed spacer locus. Altogether, 39 multilocus genotypes were identified among the 72 specimens. The observation of strong intragenic linkage disequilibria and limited genetic recombination among markers were indicative of an overall clonal population structure of E. bieneusi. Measures of pair-wise intergenic linkage disequilibria and a standardised index of association (IAS) based on allelic profile data further supported this conclusion. Both sequence-based and allelic profile-based phylogenetic analyses showed the presence of two genetically isolated groups in the study population, one (group 1) containing isolates of the anthroponotic internal transcribed spacer genotype A, and the other (group 2) containing isolates of multiple internal transcribed spacer genotypes (mainly genotypes D and IV) with zoonotic potential. The measurement of linkage disequilibria and recombination indicated group 2 had a clonal population structure, whereas group 1 had an epidemic population structure. The formation of the two sub-populations was confirmed by STRUCTURE and Wright's fixation index (FST) analyses. The data highlight the power of MLST in understanding the epidemiology of E. bieneusi. Published by Elsevier Ltd.

A Comparison of Educational Differences on Physical Health, Mortality, and Healthy Life Expectancy in Japan and the United States.

PubMed

Chiu, Chi-Tsun; Hayward, Mark; Saito, Yasuhiko

2016-10-01

This study examined the educational gradient of health and mortality between two long-lived populations: Japan and the United States. This analysis is based on the Nihon University Japanese Longitudinal Study of Aging and the Health and Retirement Study to compare educational gradients in multiple aspects of population health-life expectancy with/without disability, functional limitations, or chronic diseases, using prevalence-based Sullivan life tables. Our results show that education coefficients from physical health and mortality models are similar for both Japan and American populations, and older Japanese have better mortality and health profiles. Japan's compulsory national health service system since April 1961 and living arrangements with adult children may play an important role for its superior health profile compared with that of the United States. © The Author(s) 2016.

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

Effects of clustered transmission on epidemic growth Comment on "Mathematical models to characterize early epidemic growth: A review" by Gerardo Chowell et al.

NASA Astrophysics Data System (ADS)

Merler, Stefano

2016-09-01

Characterizing the early growth profile of an epidemic outbreak is key for predicting the likely trajectory of the number of cases and for designing adequate control measures. Epidemic profiles characterized by exponential growth have been widely observed in the past and a grounding theoretical framework for the analysis of infectious disease dynamics was provided by the pioneering work of Kermack and McKendrick [1]. In particular, exponential growth stems from the assumption that pathogens spread in homogeneous mixing populations; that is, individuals of the population mix uniformly and randomly with each other. However, this assumption was readily recognized as highly questionable [2], and sub-exponential profiles of epidemic growth have been observed in a number of epidemic outbreaks, including HIV/AIDS, foot-and-mouth disease, measles and, more recently, Ebola [3,4].

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.

Identification of kin structure among Guam rail founders: a comparison of pedigrees and DNA profiles

USGS Publications Warehouse

Haig, Susan M.; Ballou, J.D.; Casna, N.J.

1994-01-01

Kin structure among founders can have a significant effect on subsequent population structure. Here we use the correlation between DNA profile similarity and relatedness calculated from pedigrees to test hypotheses regarding kin structure among founders to the captive Guam rail (Rallus owstoni) population. Five different pedigrees were generated under the following hypotheses: (i) founders are unrelated; (ii) founders are unrelated except for same-nest chicks; (iii) founders from the same major site are siblings; (iv) founders from the same local site are siblings; and (v) founders are related as defined by a UPGMA cluster analysis of DNA similarity data. Relatedness values from pedigrees 1, 2 and 5 had the highest correlation with DNA similarity but the correlation between relatedness and similarity were not significantly different among pedigrees. Pedigree 5 resulted in the highest correlation overall when using only relatedness values that changed as a result of different founder hypotheses. Thus, founders were assigned relatedness based on pedigree 5 because it had the highest correlations with DNA similarity, was the most conservative approach, and incorporated all field data. The analyses indicated that estimating relatedness using DNA profiles remains problematic, therefore we compared mean kinship, a measure of genetic importance, with mean DNA profile similarity to determine if genetic importance among individuals could be determined via use of DNA profiles alone. The significant correlation suggests this method may provide more information about population structure than was previously thought. Thus, DNA profiles can provide a reasonable explanation for founder relatedness and mean DNA profile similarity may be helpful in determining relative genetic importance of individuals when detailed pedigrees are absent.

Cardiometabolic Risk Clustering in Spinal Cord Injury: Results of Exploratory Factor Analysis

PubMed Central

2013-01-01

Background: Evidence suggests an elevated prevalence of cardiometabolic risks among persons with spinal cord injury (SCI); however, the unique clustering of risk factors in this population has not been fully explored. Objective: The purpose of this study was to describe unique clustering of cardiometabolic risk factors differentiated by level of injury. Methods: One hundred twenty-one subjects (mean 37 ± 12 years; range, 18–73) with chronic C5 to T12 motor complete SCI were studied. Assessments included medical histories, anthropometrics and blood pressure, and fasting serum lipids, glucose, insulin, and hemoglobin A1c (HbA1c). Results: The most common cardiometabolic risk factors were overweight/obesity, high levels of low-density lipoprotein (LDL-C), and low levels of high-density lipoprotein (HDL-C). Risk clustering was found in 76.9% of the population. Exploratory principal component factor analysis using varimax rotation revealed a 3–factor model in persons with paraplegia (65.4% variance) and a 4–factor solution in persons with tetraplegia (73.3% variance). The differences between groups were emphasized by the varied composition of the extracted factors: Lipid Profile A (total cholesterol [TC] and LDL-C), Body Mass-Hypertension Profile (body mass index [BMI], systolic blood pressure [SBP], and fasting insulin [FI]); Glycemic Profile (fasting glucose and HbA1c), and Lipid Profile B (TG and HDL-C). BMI and SBP formed a separate factor only in persons with tetraplegia. Conclusions: Although the majority of the population with SCI has risk clustering, the composition of the risk clusters may be dependent on level of injury, based on a factor analysis group comparison. This is clinically plausible and relevant as tetraplegics tend to be hypo- to normotensive and more sedentary, resulting in lower HDL-C and a greater propensity toward impaired carbohydrate metabolism. PMID:23960702

Isolation of mouse pancreatic alpha, beta, duct and acinar populations with cell surface markers.

PubMed

Dorrell, Craig; Grompe, Maria T; Pan, Fong Cheng; Zhong, Yongping; Canaday, Pamela S; Shultz, Leonard D; Greiner, Dale L; Wright, Chris V; Streeter, Philip R; Grompe, Markus

2011-06-06

Tools permitting the isolation of live pancreatic cell subsets for culture and/or molecular analysis are limited. To address this, we developed a collection of monoclonal antibodies with selective surface labeling of endocrine and exocrine pancreatic cell types. Cell type labeling specificity and cell surface reactivity were validated on mouse pancreatic sections and by gene expression analysis of cells isolated using FACS. Five antibodies which marked populations of particular interest were used to isolate and study viable populations of purified pancreatic ducts, acinar cells, and subsets of acinar cells from whole pancreatic tissue or of alpha or beta cells from isolated mouse islets. Gene expression analysis showed the presence of known endocrine markers in alpha and beta cell populations and revealed that TTR and DPPIV are primarily expressed in alpha cells whereas DGKB and GPM6A have a beta cell specific expression profile. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

Unveiling bifidobacterial biogeography across the mammalian branch of the tree of life.

PubMed

Milani, Christian; Mangifesta, Marta; Mancabelli, Leonardo; Lugli, Gabriele A; James, Kieran; Duranti, Sabrina; Turroni, Francesca; Ferrario, Chiara; Ossiprandi, Maria C; van Sinderen, Douwe; Ventura, Marco

2017-12-01

Internally transcribed spacer (ITS) rRNA profiling is a novel tool for detailed analysis of microbial populations at low taxonomic ranks. Here we exploited this approach to explore species-level biogeography of the Bifidobacterium genus across 291 adult mammals. These include humans and 13 other primates, domesticated animals, such as dogs, cats, cows, sheep, goats, horses and pigs, and 46 additional species. The collected profiles revealed the presence of 89 putative novel bifidobacterial taxa in addition to 45 previously described species. Remarkably, in contrast to what is currently known for many gut commensals, we did not observe host-specialization among bifidobacterial species but rather their widespread distribution across mammals. Moreover, ITS rRNA profiling of wild relatives of domesticated dogs, rabbits and pigs clearly indicates that domestication and close contact with humans have impacted on the composition of the fecal bifidobacterial population. These data were complemented by analysis of bifidobacterial communities in milk of eight mammalian families, showing that bifidobacteria represent prototypical early gut microbiota members which are inherited by newborns from their lactating mother. Thus this study highlights the role of bifidobacteria as pioneering gut colonizers of a wide range of mammals.

FUNCTIONAL SUBCLONE PROFILING FOR PREDICTION OF TREATMENT-INDUCED INTRA-TUMOR POPULATION SHIFTS AND DISCOVERY OF RATIONAL DRUG COMBINATIONS IN HUMAN GLIOBLASTOMA

PubMed Central

Reinartz, Roman; Wang, Shanshan; Kebir, Sied; Silver, Daniel J.; Wieland, Anja; Zheng, Tong; Küpper, Marius; Rauschenbach, Laurèl; Fimmers, Rolf; Shepherd, Timothy M.; Trageser, Daniel; Till, Andreas; Schäfer, Niklas; Glas, Martin; Hillmer, Axel M.; Cichon, Sven; Smith, Amy A.; Pietsch, Torsten; Liu, Ying; Reynolds, Brent A.; Yachnis, Anthony; Pincus, David W.; Simon, Matthias; Brüstle, Oliver; Steindler, Dennis A.; Scheffler, Björn

2016-01-01

Purpose Investigation of clonal heterogeneity may be key to understanding mechanisms of therapeutic failure in human cancer. However, little is known on the consequences of therapeutic intervention on the clonal composition of solid tumors. Experimental Design Here, we used 33 single cell-derived subclones generated from five clinical glioblastoma specimens for exploring intra- and inter-individual spectra of drug resistance profiles in vitro. In a personalized setting, we explored whether differences in pharmacological sensitivity among subclones could be employed to predict drug-dependent changes to the clonal composition of tumors. Results Subclones from individual tumors exhibited a remarkable heterogeneity of drug resistance to a library of potential anti-glioblastoma compounds. A more comprehensive intra-tumoral analysis revealed that stable genetic and phenotypic characteristics of co-existing subclones could be correlated with distinct drug sensitivity profiles. The data obtained from differential drug response analysis could be employed to predict clonal population shifts within the naïve parental tumor in vitro and in orthotopic xenografts. Furthermore, the value of pharmacological profiles could be shown for establishing rational strategies for individualized secondary lines of treatment. Conclusions Our data provide a previously unrecognized strategy for revealing functional consequences of intra-tumor heterogeneity by enabling predictive modeling of treatment-related subclone dynamics in human glioblastoma. PMID:27521447

Cytokines, hepatic cell profiling and cell interactions during bone marrow cell therapy for liver fibrosis in cholestatic mice

PubMed Central

Pinheiro, Daphne; Leirós, Luana; Dáu, Juliana Barbosa Torreão; Stumbo, Ana Carolina; Thole, Alessandra Alves; Cortez, Erika Afonso Costa; Mandarim-de-Lacerda, Carlos Alberto; de Carvalho, Lais

2017-01-01

Bone marrow cells (BMC) migrate to the injured liver after transplantation, contributing to regeneration through multiple pathways, but mechanisms involved are unclear. This work aimed to study BMC migration, characterize cytokine profile, cell populations and proliferation in mice with liver fibrosis transplanted with GFP+ BMC. Confocal microscopy analysis showed GFP+ BMC near regions expressing HGF and SDF-1 in the fibrotic liver. Impaired liver cell proliferation in fibrotic groups was restored after BMC transplantation. Regarding total cell populations, there was a significant reduction in CD68+ cells and increased Ly6G+ cells in transplanted fibrotic group. BMC contributed to the total populations of CD144, CD11b and Ly6G cells in the fibrotic liver, related to an increment of anti-fibrotic cytokines (IL-10, IL-13, IFN-γ and HGF) and reduction of pro-inflammatory cytokines (IL-17A and IL-6). Therefore, HGF and SDF-1 may represent important chemoattractants for transplanted BMC in the injured liver, where these cells can give rise to populations of extrahepatic macrophages, neutrophils and endothelial progenitor cells that can interact synergistically with other liver cells towards the modulation of an anti-fibrotic cytokine profile promoting the onset of liver regeneration. PMID:29176797

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.

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.

Bayesian Forecasting Tool to Predict the Need for Antidote in Acute Acetaminophen Overdose.

PubMed

Desrochers, Julie; Wojciechowski, Jessica; Klein-Schwartz, Wendy; Gobburu, Jogarao V S; Gopalakrishnan, Mathangi

2017-08-01

Acetaminophen (APAP) overdose is the leading cause of acute liver injury in the United States. Patients with elevated plasma acetaminophen concentrations (PACs) require hepatoprotective treatment with N-acetylcysteine (NAC). These patients have been primarily risk-stratified using the Rumack-Matthew nomogram. Previous studies of acute APAP overdoses found that the nomogram failed to accurately predict the need for the antidote. The objectives of this study were to develop a population pharmacokinetic (PK) model for APAP following acute overdose and evaluate the utility of population PK model-based Bayesian forecasting in NAC administration decisions. Limited APAP concentrations from a retrospective cohort of acute overdosed subjects from the Maryland Poison Center were used to develop the population PK model and to investigate the effect of type of APAP products and other prognostic factors. The externally validated population PK model was used a prior for Bayesian forecasting to predict the individual PK profile when one or two observed PACs were available. The utility of Bayesian forecasted APAP concentration-time profiles inferred from one (first) or two (first and second) PAC observations were also tested in their ability to predict the observed NAC decisions. A one-compartment model with first-order absorption and elimination adequately described the data with single activated charcoal and APAP products as significant covariates on absorption and bioavailability. The Bayesian forecasted individual concentration-time profiles had acceptable bias (6.2% and 9.8%) and accuracy (40.5% and 41.9%) when either one or two PACs were considered, respectively. The sensitivity and negative predictive value of the Bayesian forecasted NAC decisions using one PAC were 84% and 92.6%, respectively. The population PK analysis provided a platform for acceptably predicting an individual's concentration-time profile following acute APAP overdose with at least one PAC, and the individual's covariate profile, and can potentially be used for making early NAC administration decisions. © 2017 Pharmacotherapy Publications, Inc.

Subphenotypes of mild-to-moderate COPD by factor and cluster analysis of pulmonary function, CT imaging and breathomics in a population-based survey.

PubMed

Fens, Niki; van Rossum, Annelot G J; Zanen, Pieter; van Ginneken, Bram; van Klaveren, Rob J; Zwinderman, Aeilko H; Sterk, Peter J

2013-06-01

Classification of COPD is currently based on the presence and severity of airways obstruction. However, this may not fully reflect the phenotypic heterogeneity of COPD in the (ex-) smoking community. We hypothesized that factor analysis followed by cluster analysis of functional, clinical, radiological and exhaled breath metabolomic features identifies subphenotypes of COPD in a community-based population of heavy (ex-) smokers. Adults between 50-75 years with a smoking history of at least 15 pack-years derived from a random population-based survey as part of the NELSON study underwent detailed assessment of pulmonary function, chest CT scanning, questionnaires and exhaled breath molecular profiling using an electronic nose. Factor and cluster analyses were performed on the subgroup of subjects fulfilling the GOLD criteria for COPD (post-BD FEV1/FVC < 0.70). Three hundred subjects were recruited, of which 157 fulfilled the criteria for COPD and were included in the factor and cluster analysis. Four clusters were identified: cluster 1 (n = 35; 22%): mild COPD, limited symptoms and good quality of life. Cluster 2 (n = 48; 31%): low lung function, combined emphysema and chronic bronchitis and a distinct breath molecular profile. Cluster 3 (n = 60; 38%): emphysema predominant COPD with preserved lung function. Cluster 4 (n = 14; 9%): highly symptomatic COPD with mildly impaired lung function. In a leave-one-out validation analysis an accuracy of 97.4% was reached. This unbiased taxonomy for mild to moderate COPD reinforces clusters found in previous studies and thereby allows better phenotyping of COPD in the general (ex-) smoking population.

Population Profile of the United States 1984-85.

ERIC Educational Resources Information Center

Current Population Reports, 1987

1987-01-01

This population profile summarizes the wide range of demographic and socio-economic data collected from the Current Population Survey during 1984 and 1985. The report contains information on the following areas: National Population Trends; National Population Projections; Fertility; State Population Trends; The Metropolitan/Nonmetropolitan…

Profile of Undergraduates in U.S. Postsecondary Education Institutions, 2003-04: With a Special Analysis of Community College Students. Statistical Analysis Report. NCES 2006-184

ERIC Educational Resources Information Center

Horn, Laura; Nevill, Stephanie; Griffith, James

2006-01-01

This report is the fifth in a series of reports that provide a statistical snapshot of the undergraduate population. The reports accompany the newly released data from the National Postsecondary Student Aid Study (NPSAS), and each one includes a focused analysis on a particular topic. This report focuses on community college students, who…

Using machine learning to identify air pollution exposure profiles associated with early cognitive skills among U.S. children.

PubMed

Stingone, Jeanette A; Pandey, Om P; Claudio, Luz; Pandey, Gaurav

2017-11-01

Data-driven machine learning methods present an opportunity to simultaneously assess the impact of multiple air pollutants on health outcomes. The goal of this study was to apply a two-stage, data-driven approach to identify associations between air pollutant exposure profiles and children's cognitive skills. Data from 6900 children enrolled in the Early Childhood Longitudinal Study, Birth Cohort, a national study of children born in 2001 and followed through kindergarten, were linked to estimated concentrations of 104 ambient air toxics in the 2002 National Air Toxics Assessment using ZIP code of residence at age 9 months. In the first-stage, 100 regression trees were learned to identify ambient air pollutant exposure profiles most closely associated with scores on a standardized mathematics test administered to children in kindergarten. In the second-stage, the exposure profiles frequently predicting lower math scores were included within linear regression models and adjusted for confounders in order to estimate the magnitude of their effect on math scores. This approach was applied to the full population, and then to the populations living in urban and highly-populated urban areas. Our first-stage results in the full population suggested children with low trichloroethylene exposure had significantly lower math scores. This association was not observed for children living in urban communities, suggesting that confounding related to urbanicity needs to be considered within the first-stage. When restricting our analysis to populations living in urban and highly-populated urban areas, high isophorone levels were found to predict lower math scores. Within adjusted regression models of children in highly-populated urban areas, the estimated effect of higher isophorone exposure on math scores was -1.19 points (95% CI -1.94, -0.44). Similar results were observed for the overall population of urban children. This data-driven, two-stage approach can be applied to other populations, exposures and outcomes to generate hypotheses within high-dimensional exposure data. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Chemotaxonomic significance of the terpene composition in natural populations of Pinus nigra J.F.Arnold from Serbia.

PubMed

Sarac, Zorica; Bojović, Srdjan; Nikolić, Biljana; Tešević, Vele; Ethorđević, Iris; Marin, Petar D

2013-08-01

The essential-oil variability in seven native populations belonging to different infraspecific taxa of Pinus nigra (ssp. nigra, var. gocensis, ssp. pallasiana, and var. banatica) growing wild in Serbia was analyzed. In the needles of 195 trees from seven populations, 58 essential-oil components were identified. The major components were α-pinene (43.6%) and germacrene D (29.8%), comprising together 73.4% of the total oil composition. Based on the average chemical profile of the main terpene components (with contents >5%), the studied populations were found to be the most similar to populations from central Italy and Greece (ssp. nigra). Cluster analysis showed the division of the populations into three principal groups: the first group consisted of Populations I, II, III, IV, and V (considered as ssp. nigra group), the second of Population VI (ssp. pallasiana group), and the third of Population VII, which had the most distinct oil composition (ssp. banatica group). The taxonomic implications of the essential-oil profiles of the investigated taxa of this very complex species are discussed. Copyright © 2013 Verlag Helvetica Chimica Acta AG, Zürich.

External validation of a forest inventory and analysis volume equation and comparisons with estimates from multiple stem-profile models

Treesearch

Christopher M. Oswalt; Adam M. Saunders

2009-01-01

Sound estimation procedures are desideratum for generating credible population estimates to evaluate the status and trends in resource conditions. As such, volume estimation is an integral component of the U.S. Department of Agriculture, Forest Service, Forest Inventory and Analysis (FIA) program's reporting. In effect, reliable volume estimation procedures are...

Discrimination among populations of sockeye salmon fry with Fourier analysis of otolith banding patterns formed during incubation

USGS Publications Warehouse

Finn, James E.; Burger, Carl V.; Holland-Bartels, Leslie E.

1997-01-01

We used otolith banding patterns formed during incubation to discriminate among hatchery- and wild-incubated fry of sockeye salmon Oncorhynchus nerka from Tustumena Lake, Alaska. Fourier analysis of otolith luminance profiles was used to describe banding patterns: the amplitudes of individual Fourier harmonics were discriminant variables. Correct classification of otoliths to either hatchery or wild origin was 83.1% (cross-validation) and 72.7% (test data) with the use of quadratic discriminant function analysts on 10 Fourier amplitudes. Overall classification rates among the six test groups (one hatchery and five wild groups) were 46.5% (cross-validation) and 39.3% (test data) with the use of linear discriminant function analysis on 16 Fourier amplitudes. Although classification rates for wild-incubated fry from any one site never exceeded 67% (cross-validation) or 60% (test data), location-specific information was evident for all groups because the probability of classifying an individual to its true incubation location was significantly greater than chance. Results indicate phenotypic differences in otolith microstructure among incubation sites separated by less than 10 km. Analysis of otolith luminance profiles is a potentially useful technique for discriminating among and between various populations of hatchery and wild fish.

Suicidality and profiles of childhood adversities, conflict related trauma and psychopathology in the Northern Ireland population.

PubMed

McLafferty, Margaret; Armour, Cherie; O'Neill, Siobhan; Murphy, Sam; Ferry, Finola; Bunting, Brendan

2016-08-01

Over 30 years of conflict in Northern Ireland (NI) has impacted on the population's mental health. However, childhood adversities may add to the psychological impact of conflict. The aims of the study were to assess co-occurrence across childhood adversities, conflict related traumas, and psychological health, then explore demographic variations between identified classes, and examine the impact of class membership on suicidal ideation and behaviour. Data was obtained from the Northern Ireland Study of Health and Stress, a representative epidemiological study which used the CIDI to assess psychopathology and related risk factors in the NI population (N=4340, part 2 n=1986; response rate 64%). Latent Class Analysis uncovered 4 discrete profiles; a conflict class (n=191; 9.6%), a multi-risk class endorsing elevated levels of childhood adversities, conflict related traumas and psychopathology (n=85; 4.3%), a psychopathology class (n=290; 14.6%), and a low risk class (n=1420; 71.5%). Multinomial logistic regression analysis revealed that individuals who grew up during the worst years of the Troubles were more likely to have experienced multiple traumas and psychopathology. Individuals in the multi-risk class were more than fifteen times more likely to endorse suicidal ideation and behaviour. The main limitations are that the study may not be fully representative of the NI population due to the exclusion criteria applied and also the possible misclassification of conflict related events. The findings indicate that treatment providers should be cognisant that those with wide ranging adversity profiles are those also likely to be reporting psychological distress and suicidality. Copyright © 2016 Elsevier B.V. All rights reserved.

Dietary patterns in the French adult population: a study from the second French national cross-sectional dietary survey (INCA2) (2006-2007).

PubMed

Gazan, R; Béchaux, C; Crépet, A; Sirot, V; Drouillet-Pinard, P; Dubuisson, C; Havard, S

2016-07-01

Identification and characterisation of dietary patterns are needed to define public health policies to promote better food behaviours. The aim of this study was to identify the major dietary patterns in the French adult population and to determine their main demographic, socio-economic, nutritional and environmental characteristics. Dietary patterns were defined from food consumption data collected in the second French national cross-sectional dietary survey (2006-2007). Non-negative-matrix factorisation method, followed by a cluster analysis, was implemented to derive the dietary patterns. Logistic regressions were then used to determine their main demographic and socio-economic characteristics. Finally, nutritional profiles and contaminant exposure levels of dietary patterns were compared using ANOVA. Seven dietary patterns, with specific food consumption behaviours, were identified: 'Small eater', 'Health conscious', 'Mediterranean', 'Sweet and processed', 'Traditional', 'Snacker' and 'Basic consumer'. For instance, the Health-conscious pattern was characterised by a high consumption of low-fat and light products. Individuals belonging to this pattern were likely to be older and to have a better nutritional profile than the overall population, but were more exposed to many contaminants. Conversely, individuals of Snacker pattern were likely to be younger, consumed more highly processed foods, had a nutrient-poor profile but were exposed to a limited number of food contaminants. The study identified main dietary patterns in the French adult population with distinct food behaviours and specific demographic, socio-economic, nutritional and environmental features. Paradoxically, for better dietary patterns, potential health risks cannot be ruled out. Therefore, this study demonstrated the need to conduct a risk-benefit analysis to define efficient public health policies regarding diet.

Plasma Free Amino Acid Profiles Predict Four-Year Risk of Developing Diabetes, Metabolic Syndrome, Dyslipidemia, and Hypertension in Japanese Population

PubMed Central

Yamakado, Minoru; Nagao, Kenji; Imaizumi, Akira; Tani, Mizuki; Toda, Akiko; Tanaka, Takayuki; Jinzu, Hiroko; Miyano, Hiroshi; Yamamoto, Hiroshi; Daimon, Takashi; Horimoto, Katsuhisa; Ishizaka, Yuko

2015-01-01

Plasma free amino acid (PFAA) profile is highlighted in its association with visceral obesity and hyperinsulinemia, and future diabetes. Indeed PFAA profiling potentially can evaluate individuals’ future risks of developing lifestyle-related diseases, in addition to diabetes. However, few studies have been performed especially in Asian populations, about the optimal combination of PFAAs for evaluating health risks. We quantified PFAA levels in 3,701 Japanese subjects, and determined visceral fat area (VFA) and two-hour post-challenge insulin (Ins120 min) values in 865 and 1,160 subjects, respectively. Then, models between PFAA levels and the VFA or Ins120 min values were constructed by multiple linear regression analysis with variable selection. Finally, a cohort study of 2,984 subjects to examine capabilities of the obtained models for predicting four-year risk of developing new-onset lifestyle-related diseases was conducted. The correlation coefficients of the obtained PFAA models against VFA or Ins120 min were higher than single PFAA level. Our models work well for future risk prediction. Even after adjusting for commonly accepted multiple risk factors, these models can predict future development of diabetes, metabolic syndrome, and dyslipidemia. PFAA profiles confer independent and differing contributions to increasing the lifestyle-related disease risks in addition to the currently known factors in a general Japanese population. PMID:26156880

Mutation-profile-based methods for understanding selection forces in cancer somatic mutations: a comparative analysis.

PubMed

Zhou, Zhan; Zou, Yangyun; Liu, Gangbiao; Zhou, Jingqi; Wu, Jingcheng; Zhao, Shimin; Su, Zhixi; Gu, Xun

2017-08-29

Human genes exhibit different effects on fitness in cancer and normal cells. Here, we present an evolutionary approach to measure the selection pressure on human genes, using the well-known ratio of the nonsynonymous to synonymous substitution rate in both cancer genomes ( C N / C S ) and normal populations ( p N / p S ). A new mutation-profile-based method that adopts sample-specific mutation rate profiles instead of conventional substitution models was developed. We found that cancer-specific selection pressure is quite different from the selection pressure at the species and population levels. Both the relaxation of purifying selection on passenger mutations and the positive selection of driver mutations may contribute to the increased C N / C S values of human genes in cancer genomes compared with the p N / p S values in human populations. The C N / C S values also contribute to the improved classification of cancer genes and a better understanding of the onco-functionalization of cancer genes during oncogenesis. The use of our computational pipeline to identify cancer-specific positively and negatively selected genes may provide useful information for understanding the evolution of cancers and identifying possible targets for therapeutic intervention.

Y chromosome STR typing in crime casework.

PubMed

Roewer, Lutz

2009-01-01

Since the beginning of the nineties the field of forensic Y chromosome analysis has been successfully developed to become commonplace in laboratories working in crime casework all over the world. The ability to identify male-specific DNA renders highly variable Y-chromosomal polymorphisms, the STR sequences, an invaluable addition to the standard panel of autosomal loci used in forensic genetics. The male-specificity makes the Y chromosome especially useful in cases of male/female cell admixture, namely in sexual assault cases. On the other hand, the haploidy and patrilineal inheritance complicates the interpretation of a Y-STR match, because male relatives share for several generations an identical Y-STR profile. Since paternal relatives tend to live in the geographic and cultural territory of their ancestors, the Y chromosome analysis has a potential to make inferences on the population of origin of a given DNA profile. This review addresses the fields of application of Y chromosome haplotyping, the interpretation of results, databasing efforts and population genetics aspects.

Nose profile morphology and accuracy study of nose profile estimation method in Scottish subadult and Indonesian adult populations.

PubMed

Sarilita, Erli; Rynn, Christopher; Mossey, Peter A; Black, Sue; Oscandar, Fahmi

2018-05-01

This study investigated nose profile morphology and its relationship to the skull in Scottish subadult and Indonesian adult populations, with the aim of improving the accuracy of forensic craniofacial reconstruction. Samples of 86 lateral head cephalograms from Dundee Dental School (mean age, 11.8 years) and 335 lateral head cephalograms from the Universitas Padjadjaran Dental Hospital, Bandung, Indonesia (mean age 24.2 years), were measured. The method of nose profile estimation based on skull morphology previously proposed by Rynn and colleagues in 2010 (FSMP 6:20-34) was tested in this study. Following this method, three nasal aperture-related craniometrics and six nose profile dimensions were measured from the cephalograms. To assess the accuracy of the method, six nose profile dimensions were estimated from the three craniometric parameters using the published method and then compared to the actual nose profile dimensions.In the Scottish subadult population, no sexual dimorphism was evident in the measured dimensions. In contrast, sexual dimorphism of the Indonesian adult population was evident in all craniometric and nose profile dimensions; notably, males exhibited statistically significant larger values than females. The published method by Rynn and colleagues (FSMP 6:20-34, 2010) performed better in the Scottish subadult population (mean difference of maximum, 2.35 mm) compared to the Indonesian adult population (mean difference of maximum, 5.42 mm in males and 4.89 mm in females).In addition, regression formulae were derived to estimate nose profile dimensions based on the craniometric measurements for the Indonesian adult population. The published method is not sufficiently accurate for use on the Indonesian population, so the derived method should be used. The accuracy of the published method by Rynn and colleagues (FSMP 6:20-34, 2010) was sufficiently reliable to be applied in Scottish subadult population.

Variations on a theme: diversification of cuticular hydrocarbons in a clade of cactophilic Drosophila

PubMed Central

2011-01-01

Background We characterized variation and chemical composition of epicuticular hydrocarbons (CHCs) in the seven species of the Drosophila buzzatii cluster with gas chromatography/mass spectrometry. Despite the critical role of CHCs in providing resistance to desiccation and involvement in communication, such as courtship behavior, mating, and aggregation, few studies have investigated how CHC profiles evolve within and between species in a phylogenetic context. We analyzed quantitative differences in CHC profiles in populations of the D. buzzatii species cluster in order to assess the concordance of CHC differentiation with species divergence. Results Thirty-six CHC components were scored in single fly extracts with carbon chain lengths ranging from C29 to C39, including methyl-branched alkanes, n-alkenes, and alkadienes. Multivariate analysis of variance revealed that CHC amounts were significantly different among all species and canonical discriminant function (CDF) analysis resolved all species into distinct, non-overlapping groups. Significant intraspecific variation was found in different populations of D. serido suggesting that this taxon is comprised of at least two species. We summarized CHC variation using CDF analysis and mapped the first five CHC canonical variates (CVs) onto an independently derived period (per) gene + chromosome inversion + mtDNA COI gene for each sex. We found that the COI sequences were not phylogenetically informative due to introgression between some species, so only per + inversion data were used. Positive phylogenetic signal was observed mainly for CV1 when parsimony methods and the test for serial independence (TFSI) were used. These results changed when no outgroup species were included in the analysis and phylogenetic signal was then observed for female CV3 and/or CV4 and male CV4 and CV5. Finally, removal of divergent populations of D. serido significantly increased the amount of phylogenetic signal as up to four out of five CVs then displayed positive phylogenetic signal. Conclusions CHCs were conserved among species while quantitative differences in CHC profiles between populations and species were statistically significant. Most CHCs were species-, population-, and sex-specific. Mapping CHCs onto an independently derived phylogeny revealed that a significant portion of CHC variation was explained by species' systematic affinities indicating phylogenetic conservatism in the evolution of these hydrocarbon arrays, presumptive waterproofing compounds and courtship signals as in many other drosophilid species. PMID:21699713

Global Population Profile: 2002. International Population Reports

ERIC Educational Resources Information Center

Christenson, Matthew; McDevitt, Thomas; Stanecki, Karen

2004-01-01

Global Population Profile: 2002 summarizes the most important trends in global population at the dawn of the 21st century. The presentation is organized around four themes: (1) Global Population; (2) Growth, Global Population; (3) Composition, Contraceptive Prevalence in the Developing World; and (4) the AIDS Pandemic in the 21st Century. This…

Metric and morphological assessment of facial features: a study on three European populations.

PubMed

Ritz-Timme, S; Gabriel, P; Tutkuviene, J; Poppa, P; Obertová, Z; Gibelli, D; De Angelis, D; Ratnayake, M; Rizgeliene, R; Barkus, A; Cattaneo, C

2011-04-15

Identification from video surveillance systems is becoming more and more frequent in the forensic practice. In this field, different techniques have been improved such as height estimation and gait analysis. However, the most natural approach for identifying a person in everyday life is based on facial characteristics. Scientifically, faces can be described using morphological and metric assessment of facial features. The morphological approach is largely affected by the subjective opinion of the observer, which can be mitigated by the application of descriptive atlases. In addition, this approach requires one to investigate which are the most common and rare facial characteristics in different populations. For the metric approach further studies are necessary in order to point out possible metric differences within and between different populations. The acquisition of statistically adequate population data may provide useful information for the reconstruction of biological profiles of unidentified individuals, particularly concerning ethnic affiliation, and possibly also for personal identification. This study presents the results of the morphological and metric assessment of the head and face of 900 male subjects between 20 and 31 years from Italy, Germany and Lithuania. The evaluation of the morphological traits was performed using the DMV atlas with 43 pre-defined facial characteristics. The frequencies of the types of facial features were calculated for each population in order to establish the rarest characteristics which may be used for the purpose of a biological profile and consequently for personal identification. Metric analysis performed in vivo included 24 absolute measurements and 24 indices of the head and face, including body height and body weight. The comparison of the frequencies of morphological facial features showed many similarities between the samples from Germany, Italy and Lithuania. However, several characteristics were rare or significantly more or less common in one population compared to the other two. On the other hand, all measurements and indices, except for labial width and intercanthal-mouth index showed significant differences between the three populations. As far as comparisons with other samples are concerned, the three European Caucasian samples differed from North American Caucasian, African and Asian groups as concerns the frequency of the morphological traits and the mean values of the metric analysis. The metric and morphological data collected from three European populations may be useful for forensic purposes in the construction of biological profiles and in screening for personal identification. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

A Longitudinal Empirical Investigation of the Pathways Model of Problem Gambling.

PubMed

Allami, Youssef; Vitaro, Frank; Brendgen, Mara; Carbonneau, René; Lacourse, Éric; Tremblay, Richard E

2017-12-01

The pathways model of problem gambling suggests the existence of three developmental pathways to problem gambling, each differentiated by a set of predisposing biopsychosocial characteristics: behaviorally conditioned (BC), emotionally vulnerable (EV), and biologically vulnerable (BV) gamblers. This study examined the empirical validity of the Pathways Model among adolescents followed up to early adulthood. A prospective-longitudinal design was used, thus overcoming limitations of past studies that used concurrent or retrospective designs. Two samples were used: (1) a population sample of French-speaking adolescents (N = 1033) living in low socio-economic status (SES) neighborhoods from the Greater Region of Montreal (Quebec, Canada), and (2) a population sample of adolescents (N = 3017), representative of French-speaking students in Quebec. Only participants with at-risk or problem gambling by mid-adolescence or early adulthood were included in the main analysis (n = 180). Latent Profile Analyses were conducted to identify the optimal number of profiles, in accordance with participants' scores on a set of variables prescribed by the Pathways Model and measured during early adolescence: depression, anxiety, impulsivity, hyperactivity, antisocial/aggressive behavior, and drug problems. A four-profile model fit the data best. Three profiles differed from each other in ways consistent with the Pathways Model (i.e., BC, EV, and BV gamblers). A fourth profile emerged, resembling a combination of EV and BV gamblers. Four profiles of at-risk and problem gamblers were identified. Three of these profiles closely resemble those suggested by the Pathways Model.

Intraspecific variability in allelopathy of Heracleum mantegazzianum is linked to the metabolic profile of root exudates

PubMed Central

Jandová, Kateřina; Dostál, Petr; Cajthaml, Tomáš; Kameník, Zdeněk

2015-01-01

Background and Aims Allelopathy may drive invasions of some exotic plants, although empirical evidence for this theory remains largely inconclusive. This could be related to the large intraspecific variability of chemically mediated plant–plant interactions, which is poorly studied. This study addressed intraspecific variability in allelopathy of Heracleum mantegazzianum (giant hogweed), an invasive species with a considerable negative impact on native communities and ecosystems. Methods Bioassays were carried out to test the alleopathic effects of H. mantegazzianum root exudates on germination of Arabidopsis thaliana and Plantago lanceolata. Populations of H. mantegazzianum from the Czech Republic were sampled and variation in the phytotoxic effects of the exudates was partitioned between areas, populations within areas, and maternal lines. The composition of the root exudates was determined by metabolic profiling using ultra-high-performance liquid chromatography with time-of-flight mass spectrometry, and the relationships between the metabolic profiles and the effects observed in the bioassays were tested using orthogonal partial least-squares analysis. Key Results Variance partitioning indicated that the highest variance in phytotoxic effects was within populations. The inhibition of germination observed in the bioassay for the co-occurring native species P. lanceolata could be predicted by the metabolic profiles of the root exudates of particular maternal lines. Fifteen compounds associated with this inhibition were tentatively identified. Conclusions The results present strong evidence that intraspecific variability needs to be considered in research on allelopathy, and suggest that metabolic profiling provides an efficient tool for studying chemically mediated plant–plant interactions whenever unknown metabolites are involved. PMID:25714817

An Analysis of Diet Quality, How It Controls Fatty Acid Profiles, Isotope Signatures and Stoichiometry in the Malaria Mosquito Anopheles arabiensis

PubMed Central

Hood-Nowotny, Rebecca; Schwarzinger, Bettina; Schwarzinger, Clemens; Soliban, Sharon; Madakacherry, Odessa; Aigner, Martina; Watzka, Margarete; Gilles, Jeremie

2012-01-01

Background Knowing the underlying mechanisms of mosquito ecology will ensure effective vector management and contribute to the overall goal of malaria control. Mosquito populations show a high degree of population plasticity in response to environmental variability. However, the principle factors controlling population size and fecundity are for the most part unknown. Larval habitat and diet play a crucial role in subsequent mosquito fitness. Developing the most competitive insects for sterile insect technique programmes requires a “production” orientated perspective, to deduce the most effective larval diet formulation; the information gained from this process offers us some insight into the mechanisms and processes taking place in natural native mosquito habitats. Methodology/Principal Findings Fatty acid profiles and de-novo or direct assimilation pathways, of whole-individual mosquitoes reared on a range of larval diets were determined using pyrolysis gas chromatograph/mass spectrometry. We used elemental analysis and isotope ratio mass spectrometry to measure individual-whole-body carbon, nitrogen and phosphorous values and to assess the impact of dietary quality on subsequent population stoichiometry, size, quality and isotopic signature. Diet had the greatest impact on fatty acid (FA) profiles of the mosquitoes, which exhibited a high degree of dietary routing, characteristic of generalist feeders. De-novo synthesis of a number of important FAs was observed. Mosquito C:N stoichiometry was fixed in the teneral stage. Dietary N content had significant influence on mosquito size, and P was shown to be a flexible pool which limited overall population size. Conclusions/Significance Direct routing of FAs was evident but there was ubiquitous de-novo synthesis suggesting mosquito larvae are competent generalist feeders capable of survival on diet with varying characteristics. It was concluded that nitrogen availability in the larval diet controlled teneral mosquito size and that teneral CN ratio is a sex- and species-specific fixed parameter. This finding has significant implications for overall mosquito competitiveness and environmental management. PMID:23133509

Rhizobium etli and Rhizobium gallicum Nodulate Common Bean (Phaseolus vulgaris) in a Traditionally Managed Milpa Plot in Mexico: Population Genetics and Biogeographic Implications

PubMed Central

Silva, Claudia; Vinuesa, Pablo; Eguiarte, Luis E.; Martínez-Romero, Esperanza; Souza, Valeria

2003-01-01

The stability of the genetic structure of rhizobial populations nodulating Phaseolus vulgaris cultivated in a traditionally managed milpa plot in Mexico was studied over three consecutive years. The set of molecular markers analyzed (including partial rrs, glnII, nifH, and nodB sequences), along with host range experiments, placed the isolates examined in Rhizobium etli bv. phaseoli and Rhizobium gallicum bv. gallicum. Cluster analysis of multilocus enzyme electrophoresis and plasmid profile data separated the two species and identified numerically dominant clones within each of them. Population genetic analyses showed that there was high genetic differentiation between the two species and that there was low intrapopulation differentiation of the species over the 3 years. The results of linkage disequilibrium analyses are consistent with an epidemic genetic structure for both species, with frequent genetic exchange taking place within conspecific populations but not between the R. etli and R. gallicum populations. A subsample of isolates was selected and used for 16S ribosomal DNA PCR-restriction fragment length polymorphism analysis, nifH copy number determination, and host range experiments. Plasmid profiles and nifH hybridization patterns also revealed the occurrence of lateral plasmid transfer among distinct multilocus genotypes within species but not between species. Both species were recovered from nodules of the same plants, indicating that mechanisms other than host, spatial, or temporal isolation may account for the genetic barrier between the species. The biogeographic implications of finding an R. gallicum bv. gallicum population nodulating common bean in America are discussed. PMID:12571008

Male Inmate Profiles and Their Biological Correlates

PubMed Central

Horn, Mathilde; Potvin, Stephane; Allaire, Jean-François; Côté, Gilles; Gobbi, Gabriella; Benkirane, Karim; Vachon, Jeanne; Dumais, Alexandre

2014-01-01

Objective: Borderline and antisocial personality disorders (PDs) share common clinical features (impulsivity, aggressiveness, substance use disorders [SUDs], and suicidal behaviours) that are greatly overrepresented in prison populations. These disorders have been associated biologically with testosterone and cortisol levels. However, the associations are ambiguous and the subject of controversy, perhaps because these heterogeneous disorders have been addressed as unitary constructs. A consideration of profiles of people, rather than of exclusive diagnoses, might yield clearer relationships. Methods: In our study, multiple correspondence analysis and cluster analysis were employed to identify subgroups among 545 newly convicted inmates. The groups were then compared in terms of clinical features and biological markers, including levels of cortisol, testosterone, estradiol, progesterone, and sulfoconjugated dehydroepiandrosterone (DHEA-S). Results: Four clusters with differing psychiatric, criminal, and biological profiles emerged. Clinically, one group had intermediate scores for each of the tested clinical features. Another group comprised people with little comorbidity. Two others displayed severe impulsivity, PD, and SUD. Biologically, cortisol levels were lowest in the last 2 groups and highest in the group with less comorbidity. In keeping with previous findings reported in the literature, testosterone was higher in a younger population with severe psychiatric symptoms. However, some apparently comparable behavioural outcomes were found to be related to distinct biological profiles. No differences were observed for estradiol, progesterone, or DHEA-S levels. Conclusions: The results not only confirm the importance of biological markers in the study of personality features but also demonstrate the need to consider the role of comorbidities and steroid coregulation. PMID:25161069

Mixture Modeling: Applications in Educational Psychology

ERIC Educational Resources Information Center

Harring, Jeffrey R.; Hodis, Flaviu A.

2016-01-01

Model-based clustering methods, commonly referred to as finite mixture modeling, have been applied to a wide variety of cross-sectional and longitudinal data to account for heterogeneity in population characteristics. In this article, we elucidate 2 such approaches: growth mixture modeling and latent profile analysis. Both techniques are…

Meta-Analysis on Near-Road Air Pollutants Concentrations for Developing Traffic Indicators for Exposure Assessment

EPA Science Inventory

Near-road air pollution has been associated with various health risks in human populations living near roadways. To better understand relationship between vehicle emissions and spatial profiles of traffic-related air pollutants we performed a comprehensive and systematic literat...

Cultural inter-population differences do not reflect biological distances: an example of interdisciplinary analysis of populations from Eastern Adriatic coast.

PubMed

Bašić, Željana; Fox, Ayano R; Anterić, Ivana; Jerković, Ivan; Polašek, Ozren; Anđelinović, Šimun; Holland, Mitchell M; Primorac, Dragan

2015-06-01

To compare the population group from the Šopot graveyard with population groups from traditional Croatian medieval graveyards by using anthropological, craniometrics, and mitochondrial (mtDNA) analysis and to examine if the cultural differences between population groups reflect biological differences. We determined sex, age at death, pathological, and traumatic changes of skeletal remains from the Šopot graveyard and compared them with a cumulative medieval sample from the same region. We also performed principal component analysis to compare skeletal remains from Šopot with those from Ostrovica and other Central European samples according to 8 cranial measurements. Finally, we compared 46 skeletons from Šopot with medieval (Ostrovica) and contemporary populations using mDNA haplogroup profiling. The remains from Šopot were similar to the cumulative sample in lifestyle and quality of life markers. Principal component analysis showed that they were closely related to Eastern Adriatic coast sites (including Ostrovica and Šopot) in terms of cranial morphology, indicating similar biological makeup. According to mDNA testing, Šopot population showed no significant differences in the haplogroup prevalence from either medieval or contemporary populations. This study shows that the Šopot population does not significantly differ from other medieval populations from this area. Besides similar quality of life markers, these populations also had similar biological markers. Substantial archeological differences can therefore be attributed to apparent cultural influences, which in this case do not reflect biological differences.

Cultural inter-population differences do not reflect biological distances: an example of interdisciplinary analysis of populations from Eastern Adriatic coast

PubMed Central

Bašić, Željana; Fox, Ayano R; Anterić, Ivana; Jerković, Ivan; Polašek, Ozren; Anđelinović, Šimun; Holland, Mitchell M; Primorac, Dragan

2015-01-01

Aim To compare the population group from the Šopot graveyard with population groups from traditional Croatian medieval graveyards by using anthropological, craniometrics, and mitochondrial (mtDNA) analysis and to examine if the cultural differences between population groups reflect biological differences. Methods We determined sex, age at death, pathological, and traumatic changes of skeletal remains from the Šopot graveyard and compared them with a cumulative medieval sample from the same region. We also performed principal component analysis to compare skeletal remains from Šopot with those from Ostrovica and other Central European samples according to 8 cranial measurements. Finally, we compared 46 skeletons from Šopot with medieval (Ostrovica) and contemporary populations using mDNA haplogroup profiling. Results The remains from Šopot were similar to the cumulative sample in lifestyle and quality of life markers. Principal component analysis showed that they were closely related to Eastern Adriatic coast sites (including Ostrovica and Šopot) in terms of cranial morphology, indicating similar biological makeup. According to mDNA testing, Šopot population showed no significant differences in the haplogroup prevalence from either medieval or contemporary populations. Conclusion This study shows that the Šopot population does not significantly differ from other medieval populations from this area. Besides similar quality of life markers, these populations also had similar biological markers. Substantial archeological differences can therefore be attributed to apparent cultural influences, which in this case do not reflect biological differences. PMID:26088847

Single Cell Gene Expression Profiling of Skeletal Muscle-Derived Cells.

PubMed

Gatto, Sole; Puri, Pier Lorenzo; Malecova, Barbora

2017-01-01

Single cell gene expression profiling is a fundamental tool for studying the heterogeneity of a cell population by addressing the phenotypic and functional characteristics of each cell. Technological advances that have coupled microfluidic technologies with high-throughput quantitative RT-PCR analyses have enabled detailed analyses of single cells in various biological contexts. In this chapter, we describe the procedure for isolating the skeletal muscle interstitial cells termed Fibro-Adipogenic Progenitors (FAPs ) and their gene expression profiling at the single cell level. Moreover, we accompany our bench protocol with bioinformatics analysis designed to process raw data as well as to visualize single cell gene expression data. Single cell gene expression profiling is therefore a useful tool in the investigation of FAPs heterogeneity and their contribution to muscle homeostasis.

Trace element analysis of rough diamond by LA-ICP-MS: a case of source discrimination?

PubMed

Dalpé, Claude; Hudon, Pierre; Ballantyne, David J; Williams, Darrell; Marcotte, Denis

2010-11-01

Current profiling of rough diamond source is performed using different physical and/or morphological techniques that require strong knowledge and experience in the field. More recently, chemical impurities have been used to discriminate diamond source and with the advance of laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) empirical profiling of rough diamonds is possible to some extent. In this study, we present a LA-ICP-MS methodology that we developed for analyzing ultra-trace element impurities in rough diamond for origin determination ("profiling"). Diamonds from two sources were analyzed by LA-ICP-MS and were statistically classified by accepted methods. For the two diamond populations analyzed in this study, binomial logistic regression produced a better overall correct classification than linear discriminant analysis. The results suggest that an anticipated matrix match reference material would improve the robustness of our methodology for forensic applications. © 2010 American Academy of Forensic Sciences.

Relationship between Oral Malodor and the Global Composition of Indigenous Bacterial Populations in Saliva ▿

PubMed Central

Takeshita, Toru; Suzuki, Nao; Nakano, Yoshio; Shimazaki, Yoshihiro; Yoneda, Masahiro; Hirofuji, Takao; Yamashita, Yoshihisa

2010-01-01

Oral malodor develops mostly from the metabolic activities of indigenous bacterial populations within the oral cavity, but whether healthy or oral malodor-related patterns of the global bacterial composition exist remains unclear. In this study, the bacterial compositions in the saliva of 240 subjects complaining of oral malodor were divided into groups based on terminal-restriction fragment length polymorphism (T-RFLP) profiles using hierarchical cluster analysis, and the patterns of the microbial community composition of those exhibiting higher and lower malodor were explored. Four types of bacterial community compositions were detected (clusters I, II, III, and IV). Two parameters for measuring oral malodor intensity (the concentration of volatile sulfur compounds in mouth air and the organoleptic score) were noticeably lower in cluster I than in the other clusters. Using multivariate analysis, the differences in the levels of oral malodor were significant after adjustment for potential confounding factors such as total bacterial count, mean periodontal pocket depth, and tongue coating score (P < 0.001). Among the four clusters with different proportions of indigenous members, the T-RFLP profiles of cluster I were implicated as the bacterial populations with higher proportions of Streptococcus, Granulicatella, Rothia, and Treponema species than those of the other clusters. These results clearly correlate the global composition of indigenous bacterial populations with the severity of oral malodor. PMID:20228112

[Analysis of 24-hour blood pressure profile, heart rate variability and carotid atherosclerosis in hypertensive patients among native and nonnative population living in Yamalo-Nenets autonomous district].

PubMed

Gapon, L I; Sereda, T V; Leont'eva, A V

2014-01-01

To study special characteristics of the course of arterial hypertension (AH) among native and nonnative population of Yamalo-Nenets autonomous district. We examined 100 residents of Far North with AH (men and women aged 21-55, mean age 44.08 ± 1.15 years). All patients were divided into 2 equal groups by 50 subjects: group I consisted of representatives of native and group II--nonnative population. Examination was carried out in outpatient clinic in Salekhard and included 24-hour ambulatory blood pressure monitoring (ABPM), registration of heart rate variability, duplex scanning of brachiocephalic arteries, and assessment of blood lipid profile. The groups were matched by age, gender and disease duration. Analysis of heart rate variability detected significant degree of strain of regulatory systems in most patients of both groups. According to results of ABPM "non-dipper" patients prevailed in group I compared to group II (p = 0.01). Common carotid artery intima-media complex was significantly greater compared to normal value in all patients; it was thicker in group I (p < 0.03), but number of carotid artery stenoses was similar in both groups. No dyslipoproteinemia was detected. Compared with group of representatives of nonnative (adopted) population group of native subjects with AH was characterized by greater carotid intima media thickness and prevalence of "non-dipper" patients.

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

Degrees of difference among minority female juvenile offenders' psychological functioning, risk behavior engagement, and health status: a latent profile investigation.

PubMed

Guthrie, Barbara J; Cooper, Shauna M; Brown, Charity; Metzger, Isha

2012-02-01

Given the increase in the number of female youth who come in contact with the juvenile justice system, particularly those from ethnic minority backgrounds, concerns have been raised about the health status of this population. Using a latent profile analysis, we identified health profiles using indicators of psychological well-being, health risk behaviors, and health status. Participants included 153 minority adolescent females (M=15.13, SD=1.70) who were currently in a juvenile diversion program. Results indicated that a three-class solution fit the data optimally. Profiles included girls with low to moderate health risks (n=35; 22.9%), higher mental health symptoms (n=68; 44.4%), and a combination of multiple health risks (n=50; 32.7%). Additionally, demographic, contextual and offense-related variation existed across health profiles. Treatment and policy implications are discussed.

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).

Yeast Diversity and Persistence in Botrytis-Affected Wine Fermentations

PubMed Central

Mills, David A.; Johannsen, Eric A.; Cocolin, Luca

2002-01-01

Culture-dependent and -independent methods were used to examine the yeast diversity present in botrytis-affected (“botrytized”) wine fermentations carried out at high (∼30°C) and ambient (∼20°C) temperatures. Fermentations at both temperatures possessed similar populations of Saccharomyces, Hanseniaspora, Pichia, Metschnikowia, Kluyveromyces, and Candida species. However, higher populations of non-Saccharomyces yeasts persisted in ambient-temperature fermentations, with Candida and, to a lesser extent, Kluyveromyces species remaining long after the fermentation was dominated by Saccharomyces. In general, denaturing gradient gel electrophoresis profiles of yeast ribosomal DNA or rRNA amplified from the fermentation samples correlated well with the plating data. The direct molecular methods also revealed a Hanseniaspora osmophila population not identified in the plating analysis. rRNA analysis also indicated a large population (>106 cells per ml) of a nonculturable Candida strain in the high-temperature fermentation. Monoculture analysis of the Candida isolate indicated an extreme fructophilic phenotype and correlated with an increased glucose/fructose ratio in fermentations containing higher populations of Candida. Analysis of wine fermentation microbial ecology by using both culture-dependent and -independent methods reveals the complexity of yeast interactions enriched during spontaneous fermentations. PMID:12324335

Tobacco, Marijuana, and Alcohol Use in University Students: A Cluster Analysis

ERIC Educational Resources Information Center

Primack, Brian A.; Kim, Kevin H.; Shensa, Ariel; Sidani, Jaime E.; Barnett, Tracey E.; Switzer, Galen E.

2012-01-01

Objective: Segmentation of populations may facilitate development of targeted substance abuse prevention programs. The authors aimed to partition a national sample of university students according to profiles based on substance use. Participants: The authors used 2008-2009 data from the National College Health Assessment from the American College…

State Size and Government Level Matter Most: A Structural Equation Model of Local Health Department Policy Behaviors.

PubMed

Meyerson, Beth E; Sayegh, M Aaron

2016-01-01

To explore relationships between local health department policy behaviors, levels of government activity, policy focus areas, and selected health department characteristics. Cross-sectional analysis of secondary data from the 2013 National Association of County & City Health Officials (NACCHO) Profile Survey. Local health departments throughout the United States. A total of 2000 local health departments responding to the 2013 Profile Survey of Local Health Departments. Survey data were gathered by the NACCHO. Secondary analysis of reported policy behaviors for the 2013 NACCHO Profile Survey. A structural equation model tested effects on and between state population size, rurality, census region and policy focus, and the latent variables of policy behavior formed from a confirmatory factor analysis. Policy behaviors, levels of government activity (local, state, and federal), policy focus areas, and selected local health department characteristics. The majority (85.1%) of health departments reported at least one of the possible policy behaviors. State population size increased the probability of local policy behavior, and local behavior increased the probability of state policy behavior. State size increased the likelihood of federal policy behavior and the focus on tobacco, emergency preparedness, and obesity/chronic disease. However, the more rural a state was, the more likely policy behavior was at the state and federal levels and not at local levels. Specific policy behaviors mattered less than the level of government activity. Size of state and rurality of health departments influence the government level of policy behavior.

Data Mining Applied to Analysis of Contraceptive Methods Among College Students.

PubMed

Simões, Priscyla Waleska; Cesconetto, Samuel; Dalló, Eduardo Daminelli; de Souza Pires, Maria Marlene; Comunello, Eros; Borges Tomaz, Felipe; Xavier, Eduardo Pícolo; da Rosa Brunel Alves, Pedro Antonio; Ceretta, Luciane Bisognin; Manenti, Sandra Aparecida

2017-01-01

The aim of this study was to use the Data Mining to analyze the profile of the use of contraceptive methods in a university population. We used a database about sexuality performed on a university population in southern Brazil. The results obtained by the generated rules are largely in line with the literature and epidemiology worldwide, showing significant points of vulnerability in the university population. Validation measures of the study, as such, accuracy, sensitivity, specificity, and area under the ROC curve were higher or at least similar as compared to recent studies using the same methodology.

Experimental design and quantitative analysis of microbial community multiomics.

PubMed

Mallick, Himel; Ma, Siyuan; Franzosa, Eric A; Vatanen, Tommi; Morgan, Xochitl C; Huttenhower, Curtis

2017-11-30

Studies of the microbiome have become increasingly sophisticated, and multiple sequence-based, molecular methods as well as culture-based methods exist for population-scale microbiome profiles. To link the resulting host and microbial data types to human health, several experimental design considerations, data analysis challenges, and statistical epidemiological approaches must be addressed. Here, we survey current best practices for experimental design in microbiome molecular epidemiology, including technologies for generating, analyzing, and integrating microbiome multiomics data. We highlight studies that have identified molecular bioactives that influence human health, and we suggest steps for scaling translational microbiome research to high-throughput target discovery across large populations.

Synteny analysis of genes and distribution of loci controlling oil content and fatty acid profile based on QTL alignment map in Brassica napus.

PubMed

Raboanatahiry, Nadia; Chao, Hongbo; Guo, Liangxing; Gan, Jianping; Xiang, Jun; Yan, Mingli; Zhang, Libin; Yu, Longjiang; Li, Maoteng

2017-10-12

Deciphering the genetic architecture of a species is a good way to understand its evolutionary history, but also to tailor its profile for breeding elite cultivars with desirable traits. Aligning QTLs from diverse population in one map and utilizing it for comparison, but also as a basis for multiple analyses assure a stronger evidence to understand the genetic system related to a given phenotype. In this study, 439 genes involved in fatty acid (FA) and triacylglycerol (TAG) biosyntheses were identified in Brassica napus. B. napus genome showed mixed gene loss and insertion compared to B. rapa and B. oleracea, and C genome had more inserted genes. Identified QTLs for oil (OC-QTLs) and fatty acids (FA-QTLs) from nine reported populations were projected on the physical map of the reference genome "Darmor-bzh" to generate a map. Thus, 335 FA-QTLs and OC-QTLs could be highlighted and 82 QTLs were overlapping. Chromosome C3 contained 22 overlapping QTLs with all trait studied except for C18:3. In total, 218 candidate genes which were potentially involved in FA and TAG were identified in 162 QTLs confidence intervals and some of them might affect many traits. Also, 76 among these candidate genes were found inside 57 overlapping QTLs, and candidate genes for oil content were in majority (61/76 genes). Then, sixteen genes were found in overlapping QTLs involving three populations, and the remaining 60 genes were found in overlapping QTLs of two populations. Interaction network and pathway analysis of these candidate genes indicated ten genes that might have strong influence over the other genes that control fatty acids and oil formation. The present results provided new information for genetic basis of FA and TAG formation in B. napus. A map including QTLs from numerous populations was built, which could serve as reference to study the genome profile of B. napus, and new potential genes emerged which might affect seed oil. New useful tracks were showed for the selection of population or/and selection of interesting genes for breeding improvement purpose.

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.

mRNA expression profiling of laser microbeam microdissected cells from slender embryonic structures.

PubMed

Scheidl, Stefan J; Nilsson, Sven; Kalén, Mattias; Hellström, Mats; Takemoto, Minoru; Håkansson, Joakim; Lindahl, Per

2002-03-01

Microarray hybridization has rapidly evolved as an important tool for genomic studies and studies of gene regulation at the transcriptome level. Expression profiles from homogenous samples such as yeast and mammalian cell cultures are currently extending our understanding of biology, whereas analyses of multicellular organisms are more difficult because of tissue complexity. The combination of laser microdissection, RNA amplification, and microarray hybridization has the potential to provide expression profiles from selected populations of cells in vivo. In this article, we present and evaluate an experimental procedure for global gene expression analysis of slender embryonic structures using laser microbeam microdissection and laser pressure catapulting. As a proof of principle, expression profiles from 1000 cells in the mouse embryonic (E9.5) dorsal aorta were generated and compared with profiles for captured mesenchymal cells located one cell diameter further away from the aortic lumen. A number of genes were overexpressed in the aorta, including 11 previously known markers for blood vessels. Among the blood vessel markers were endoglin, tie-2, PDGFB, and integrin-beta1, that are important regulators of blood vessel formation. This demonstrates that microarray analysis of laser microbeam micro-dissected cells is sufficiently sensitive for identifying genes with regulative functions.

Uncovering Longitudinal Health Care Behaviors for Millions of Medicaid Enrollees: A Multistate Comparison of Pediatric Asthma Utilization.

PubMed

Hilton, Ross; Zheng, Yuchen; Fitzpatrick, Anne; Serban, Nicoleta

2018-01-01

This study introduces a framework for analyzing and visualizing health care utilization for millions of children, with a focus on pediatric asthma, one of the major chronic respiratory conditions. The data source is the 2005 to 2012 Medicaid Analytic Extract claims for 10 Southeast states. The study population consists of Medicaid-enrolled children with persistent asthma. We translate multiyear, individual-level medical claims into sequences of discrete utilization events, which are modeled using Markov renewal processes and model-based clustering. Network analysis is used to visualize utilization profiles. The method is general, allowing the study of other chronic conditions. The study population consists of 1.5 million children with persistent asthma. All states have profiles with high probability of asthma controller medication, as large as 60.6% to 90.2% of the state study population. The probability of consecutive asthma controller prescriptions ranges between 0.75 and 0.95. All states have utilization profiles with uncontrolled asthma with 4.5% to 22.9% of the state study population. The probability for controller medication is larger than for short-term medication after a physician visit but not after an emergency department (ED) visit or hospitalization. Transitions from ED or hospitalization generally have a lower probability into physician office (between 0.11 and 0.38) than into ED or hospitalization (between 0.20 and 0.59). In most profiles, children who take asthma controller medication do so regularly. Follow-up physician office visits after an ED encounter or hospitalization are observed at a low rate across all states. Finally, all states have a proportion of children who have uncontrolled asthma, meaning they do not take controller medication while they have severe outcomes.

Metabolic and inflammatory profiles of biomarkers in obesity, metabolic syndrome, and diabetes in a Mediterranean population. DARIOS Inflammatory study.

PubMed

Fernández-Bergés, Daniel; Consuegra-Sánchez, Luciano; Peñafiel, Judith; Cabrera de León, Antonio; Vila, Joan; Félix-Redondo, Francisco Javier; Segura-Fragoso, Antonio; Lapetra, José; Guembe, María Jesús; Vega, Tomás; Fitó, Montse; Elosua, Roberto; Díaz, Oscar; Marrugat, Jaume

2014-08-01

There is a paucity of data regarding the differences in the biomarker profiles of patients with obesity, metabolic syndrome, and diabetes mellitus as compared to a healthy, normal weight population. We aimed to study the biomarker profile of the metabolic risk continuum defined by the transition from normal weight to obesity, metabolic syndrome, and diabetes mellitus. We performed a pooled analysis of data from 7 cross-sectional Spanish population-based surveys. An extensive panel comprising 20 biomarkers related to carbohydrate metabolism, lipids, inflammation, coagulation, oxidation, hemodynamics, and myocardial damage was analyzed. We employed age- and sex-adjusted multinomial logistic regression models for the identification of those biomarkers associated with the metabolic risk continuum phenotypes: obesity, metabolic syndrome, and diabetes mellitus. A total of 2851 subjects were included for analyses. The mean age was 57.4 (8.8) years, 1269 were men (44.5%), and 464 participants were obese, 443 had metabolic syndrome, 473 had diabetes mellitus, and 1471 had a normal weight (healthy individuals). High-sensitivity C-reactive protein, apolipoprotein B100, leptin, and insulin were positively associated with at least one of the phenotypes of interest. Apolipoprotein A1 and adiponectin were negatively associated. There are differences between the population with normal weight and that having metabolic syndrome or diabetes with respect to certain biomarkers related to the metabolic, inflammatory, and lipid profiles. The results of this study support the relevance of these mechanisms in the metabolic risk continuum. When metabolic syndrome and diabetes mellitus are compared, these differences are less marked. Copyright © 2013 Sociedad Española de Cardiología. Published by Elsevier Espana. All rights reserved.

Strategies for the profiling, characterisation and detailed structural analysis of N-linked oligosaccharides.

PubMed

Tharmalingam, Tharmala; Adamczyk, Barbara; Doherty, Margaret A; Royle, Louise; Rudd, Pauline M

2013-02-01

Many post-translational modifications, including glycosylation, are pivotal for the structural integrity, location and functional activity of glycoproteins. Sub-populations of proteins that are relocated or functionally changed by such modifications can change resting proteins into active ones, mediating specific effector functions, as in the case of monoclonal antibodies. To ensure safe and efficacious drugs it is essential to employ appropriate robust, quantitative analytical strategies that can (i) perform detailed glycan structural analysis, (ii) characterise specific subsets of glycans to assess known critical features of therapeutic activities (iii) rapidly profile glycan pools for at-line monitoring or high level batch to batch screening. Here we focus on these aspects of glycan analysis, showing how state-of-the-art technologies are required at all stages during the production of recombinant glycotherapeutics. These data can provide insights into processing pathways and suggest markers for intervention at critical control points in bioprocessing and also critical decision points in disease and drug monitoring in patients. Importantly, these tools are now enabling the first glycome/genome studies in large populations, allowing the integration of glycomics into other 'omics platforms in a systems biology context.

Kinematic analysis of total knee prosthesis designed for Asian population.

PubMed

Low, F H; Khoo, L P; Chua, C K; Lo, N N

2000-01-01

In designing a total knee replacement (TKR) prosthesis catering for the Asian population, 62 sets of femur were harvested and analyzed. The morphometrical data obtained were found to be in good agreement with dimensions typical of the Asian knee and has reaffirmed the fact that Caucasian knees are generally larger than Asian knees. Subsequently, these data when treated using a multivariate statistical technique resulted in the establishment of major design parameters for six different sizes of femoral implants. An extra-small implant size with established dimensions and geometrical shape has surfaced from the study. The differences between the Asian knees and the Caucasian knees are discussed. Employing the established femoral dimensions and motion path of the knee joint, the articulating tibia profile was generated. All the sizes of implants were modeled using a computer-aided software package. Thereupon, these models that accurately fits the local Asian knee were transported into a dynamic and kinematic analysis software package. The tibiofemoral joint was modeled successfully as a slide curve joint to study intuitively the motion of the femur when articulating on the tibia surface. An optimal tibia profile could be synthesized to mimic the natural knee path motion. Details of the analysis are presented and discussed.

Psychiatric symptom typology in a sample of youth receiving substance abuse treatment services: associations with self-reported child maltreatment and sexual risk behaviors.

PubMed

Oshri, Assaf; Tubman, Jonathan G; Jaccard, James

2011-11-01

Latent profile analysis (LPA) was used to classify 394 adolescents undergoing substance use treatment, based on past year psychiatric symptoms. Relations between profile membership and (a) self-reported childhood maltreatment experiences and (b) current sexual risk behavior were examined. LPA generated three psychiatric symptom profiles: Low-, High- Alcohol-, and High- Internalizing Symptoms profiles. Analyses identified significant associations between profile membership and childhood sexual abuse and emotional neglect ratings, as well as co-occurring sex with substance use and unprotected intercourse. Profiles with elevated psychiatric symptom scores (e.g., internalizing problems, alcohol abuse and dependence symptoms) and more severe maltreatment histories reported higher scores for behavioral risk factors for HIV/STI exposure. Heterogeneity in psychiatric symptom patterns among youth receiving substance use treatment services, and prior histories of childhood maltreatment, have significant implications for the design and delivery of HIV/STI prevention programs to this population.

[An analysis of the diabetic population in a Spanish rural are: morbidity profile, use of resources, complications and metabolic control].

PubMed

Inoriza, José M; Pérez, Marc; Cols, Montse; Sánchez, Inma; Carreras, Marc; Coderch, Jordi

2013-11-01

To describe the characteristics of a diabetic population, morbidity profile, resource consumption, complications and degree of metabolic control. Cross-sectional study during 2010. Four Health Areas (91.301 people) where the integrated management organization Serveis de Salut integrated Baix Empordà completely provide healthcare assistance. 4.985 diabetic individuals, identified through clinical codes using the ICD-9-MC classification and the 3M? Clinical Risk Groups software. Morbidity profile, related complications and degree of metabolic control were obtained for the target diabetic population. We analyzed the consumption of healthcare resources, pharmaceutical and blood glucose reagent strips. All measurements obtained at individual level. 99.3% of the diabetic population were attended at least once at a primary care center (14.9% of visits). 39.5% of primary care visits and less than 10% of the other scanned resources were related to the management of diabetes. The pharmaceutical expenditure was 25.4% of the population consumption (average cost ?1.014,57). 36.5% of diabetics consumed reagents strips (average cost ?120,65). The more frequent CRG are 5424-Diabetes (27%); 6144-Diabetes and Hypertension (25,5%) and 6143-Diabetes and Other Moderate Chronic Disease (17,2%). The degree of disease control is better in patients not consumers of antidiabetic drugs or treated with oral antidiabetic agents not secretagogues. Comorbidity is decisive in the consumption of resources. Just a few part of this consumption is specifically related to the management of diabetes. Results obtained provide a whole population approach to the main existing studies in our national and regional context. Copyright © 2012 Elsevier España, S.L. All rights reserved.

Genetic analysis of predicted fatty acid profiles of milk from Danish Holstein and Danish Jersey cattle populations.

PubMed

Hein, L; Sørensen, L P; Kargo, M; Buitenhuis, A J

2018-03-01

The objective of this study was to assess the genetic variability of the detailed fatty acid (FA) profiles of Danish Holstein (DH) and Danish Jersey (DJ) cattle populations. We estimated genetic parameters for 11 FA or groups of FA in milk samples from the Danish milk control system between May 2015 and October 2016. Concentrations of different FA and FA groups in milk samples were measured by mid-infrared spectroscopy. Data used for parameter estimation were from 132,732 first-parity DH cows and 21,966 first-parity DJ cows. We found the highest heritabilities for test day measurements in both populations for short-chain FA (DH = 0.16; DJ = 0.16) and C16:0 (DH = 0.14; DJ = 0.16). In DH, the highest heritabilities were also found for saturated FA and monounsaturated FA (both populations: 0.15). Genetic correlations between the fatty acid traits showed large differences between DH and DJ for especially short-chain FA with the other FA traits measured. Furthermore, genetic correlations of total fat with monounsaturated FA, polyunsaturated FA, short-chain FA, and C16:0 differed markedly between DH and DJ populations. In conclusion, we found genetic variation in the mid-infrared spectroscopy-predicted FA and FA groups of the DH and DJ cattle populations. This finding opens the possibility of using genetic selection to change the FA profiles of dairy cattle. The Authors. Published by FASS Inc. and Elsevier Inc. on behalf of the American Dairy Science Association®. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/3.0/).

Classification of municipal occupations.

PubMed

Ilmarinen, J; Suurnäkki, T; Nygård, C H; Landau, K

1991-01-01

Eighty-eight job titles were analyzed with the "ergonomic job analysis procedure" [Arbeitswissenschaftliche Erhebungsverfahren zur Tätigkeits-analyse abbreviated (AET) in German]. The objective was to classify the wide range of municipal jobs into homogeneous groups according to job demand and to provide better possibilities to study the relationships between work and health among the aging municipal working population. Altogether 216 items were classified. First, a hierarchical cluster analysis was made, and a dendrogram of the analyzed job titles was drawn. Second, a profile analysis was done in which the single items were grouped into 39 sum items, and a graphic profile was drawn. Finally, the stress factors were listed and drawn in ranking order. The cluster analysis formed 13 groups. Groups exposed to the highest stress factor level were kitchen supervisors, dentists, and physicians. More than 10 stress factors (greater than 50% of the maximum) were found in nursing, administration, installation, transport, and technical supervision.

Influence of anteroposterior mandibular positions on facial attractiveness in Japanese adults.

PubMed

Kuroda, Shingo; Sugahara, Takako; Takabatake, Souichirou; Taketa, Hiroaki; Ando, Ryoko; Takano-Yamamoto, Teruko

2009-01-01

Our aims in this study were to determine the anteroposterior facial relationship that is regarded as most attractive by Japanese laypersons in a questionnaire survey and to evaluate which analysis of the soft-tissue profile is most suitable for Japanese people. We showed 262 Japanese laypersons (121 male, 141 female) 9 morphed profile images with Point B and menton anteriorly or distally moved by software and asked them to number them sequentially according to their attractiveness. To examine which analysis best reflects facial attractiveness as judged by laypersons, we made 5 types of analyses of the facial profile with 11 variables in the 9 images. The normal face was judged favorably; however, an attractive profile might be different for each subject. The 3 highest ranking profiles (normal face and moderate mandibular retrusions) were often favorites, and 2 profiles (severe mandibular protrusions) were liked the least for most subjects. However, the other images showed a wide range of distribution. Mandibular retrusion was generally more favored than mandibular protrusion and bimaxillary protrusion (severe chin retrusion) had a high attractiveness ranking and was well accepted in the Japanese population. To evaluate the profiles of Japanese subjects, it is important to evaluate not only the esthetic line defined by the nose and chin, but also the balance of the upper and lower lips defined by the posterior reference line--ie, Burstone's Sn-Pog' line.

Profiles of children's social-emotional health at school entry and associated income, gender and language inequalities: a cross-sectional population-based study in British Columbia, Canada.

PubMed

Thomson, Kimberly C; Guhn, Martin; Richardson, Chris G; Ark, Tavinder K; Shoveller, Jean

2017-07-26

Early identification of distinct patterns of child social-emotional strengths and vulnerabilities has the potential to improve our understanding of child mental health and well-being; however, few studies have explored natural groupings of indicators of child vulnerability and strengths at a population level. The purpose of this study was to examine heterogeneity in the patterns of young children's social and emotional health and investigate the extent to which sociodemographic characteristics were associated. Cross-sectional study based on a population-level cohort. All kindergarten children attending public schools between 2004 and 2007 in British Columbia (BC), Canada. 35 818 kindergarten children (age of 5 years) with available linked data from the Early Development Instrument (EDI), BC Ministry of Health and BC Ministry of Education. We used latent profile analysis (LPA) to identify distinct profiles of social-emotional health according to children's mean scores across eight social-emotional subscales on the EDI, a teacher-rated measure of children's early development. Subscales measured children's overall social competence, responsibility and respect, approaches to learning, readiness to explore, prosocial behaviour, anxiety, aggression and hyperactivity. Six social-emotional profiles were identified: (1) overall high social-emotional functioning, (2) inhibited-adaptive (3) uninhibited-adaptive, (4) inhibited-disengaged, (5) uninhibited-aggressive/hyperactive and (6) overall low social-emotional functioning. Boys, children with English as a second language (ESL) status and children with lower household income had higher odds of membership to the lower social-emotional functioning groups; however, this association was less negative among boys with ESL status. Over 40% of children exhibited some vulnerability in early social-emotional health, and profiles were associated with sociodemographic factors. Approximately 9% of children exhibited multiple co-occurring vulnerabilities. This study adds to our understanding of population-level distributions of children's early social-emotional health and identifies profiles of strengths and vulnerabilities that can inform future intervention efforts. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Can profiles of poly- and Perfluoroalkyl substances (PFASs) in human serum provide information on major exposure sources?

PubMed

Hu, Xindi C; Dassuncao, Clifton; Zhang, Xianming; Grandjean, Philippe; Weihe, Pál; Webster, Glenys M; Nielsen, Flemming; Sunderland, Elsie M

2018-02-01

Humans are exposed to poly- and perfluoroalkyl substances (PFASs) from diverse sources and this has been associated with negative health impacts. Advances in analytical methods have enabled routine detection of more than 15 PFASs in human sera, allowing better profiling of PFAS exposures. The composition of PFASs in human sera reflects the complexity of exposure sources but source identification can be confounded by differences in toxicokinetics affecting uptake, distribution, and elimination. Common PFASs, such as perfluorooctanoic acid (PFOA), perfluorooctane sulfonic acid (PFOS) and their precursors are ubiquitous in multiple exposure sources. However, their composition varies among sources, which may impact associated adverse health effects. We use available PFAS concentrations from several demographic groups in a North Atlantic seafood consuming population (Faroe Islands) to explore whether chemical fingerprints in human sera provide insights into predominant exposure sources. We compare serum PFAS profiles from Faroese individuals to other North American populations to investigate commonalities in potential exposure sources. We compare individuals with similar demographic and physiological characteristics and samples from the same years to reduce confounding by toxicokinetic differences and changing environmental releases. Using principal components analysis (PCA) confirmed by hierarchical clustering, we assess variability in serum PFAS concentrations across three Faroese groups. The first principal component (PC)/cluster consists of C9-C12 perfluoroalkyl carboxylates (PFCAs) and is consistent with measured PFAS profiles in consumed seafood. The second PC/cluster includes perfluorohexanesulfonic acid (PFHxS) and the PFOS precursor N-ethyl perfluorooctane sulfonamidoacetate (N-EtFOSAA), which are directly used or metabolized from fluorochemicals in consumer products such as carpet and food packaging. We find that the same compounds are associated with the same exposure sources in two North American populations, suggesting generalizability of results from the Faroese population. We conclude that PFAS homologue profiles in serum provide valuable information on major exposure sources. It is essential to compare samples collected at similar time periods and to correct for demographic groups that are highly affected by differences in physiological processes (e.g., pregnancy). Information on PFAS homologue profiles is crucial for attributing adverse health effects to the proper mixtures or individual PFASs.

Profiles of children's social–emotional health at school entry and associated income, gender and language inequalities: a cross-sectional population-based study in British Columbia, Canada

PubMed Central

Guhn, Martin; Richardson, Chris G; Ark, Tavinder K; Shoveller, Jean

2017-01-01

Objectives Early identification of distinct patterns of child social–emotional strengths and vulnerabilities has the potential to improve our understanding of child mental health and well-being; however, few studies have explored natural groupings of indicators of child vulnerability and strengths at a population level. The purpose of this study was to examine heterogeneity in the patterns of young children's social and emotional health and investigate the extent to which sociodemographic characteristics were associated. Design Cross-sectional study based on a population-level cohort. Setting All kindergarten children attending public schools between 2004 and 2007 in British Columbia (BC), Canada. Participants 35 818 kindergarten children (age of 5 years) with available linked data from the Early Development Instrument (EDI), BC Ministry of Health and BC Ministry of Education. Outcome measure We used latent profile analysis (LPA) to identify distinct profiles of social–emotional health according to children's mean scores across eight social–emotional subscales on the EDI, a teacher-rated measure of children's early development. Subscales measured children's overall social competence, responsibility and respect, approaches to learning, readiness to explore, prosocial behaviour, anxiety, aggression and hyperactivity. Results Six social–emotional profiles were identified: (1) overall high social–emotional functioning, (2) inhibited-adaptive (3) uninhibited-adaptive, (4) inhibited-disengaged, (5) uninhibited-aggressive/hyperactive and (6) overall low social–emotional functioning. Boys, children with English as a second language (ESL) status and children with lower household income had higher odds of membership to the lower social–emotional functioning groups; however, this association was less negative among boys with ESL status. Conclusions Over 40% of children exhibited some vulnerability in early social–emotional health, and profiles were associated with sociodemographic factors. Approximately 9% of children exhibited multiple co-occurring vulnerabilities. This study adds to our understanding of population-level distributions of children's early social–emotional health and identifies profiles of strengths and vulnerabilities that can inform future intervention efforts. PMID:28751486

Population genetic analysis and trichothecene profiling of Fusarium graminearum from wheat in Uruguay.

PubMed

Pan, D; Mionetto, A; Calero, N; Reynoso, M M; Torres, A; Bettucci, L

2016-03-11

Fusarium graminearum sensu stricto (F. graminearum s.s.) is the major causal agent of Fusarium head blight of wheat worldwide, and contaminates grains with trichothecene mycotoxins that cause serious threats to food safety and animal health. An important aspect of managing this pathogen and reducing mycotoxin contamination of wheat is knowledge regarding its population genetics. Therefore, isolates of F. graminearum s.s. from the major wheat-growing region of Uruguay were analyzed by amplified fragment length polymorphism assays, PCR genotyping, and chemical analysis of trichothecene production. Of the 102 isolates identified as having the 15-ADON genotype via PCR genotyping, all were DON producers, but only 41 strains were also 15-ADON producers, as determined by chemical analysis. The populations were genotypically diverse but genetically similar, with significant genetic exchange occurring between them. Analysis of molecular variance indicated that most of the genetic variability resulted from differences between isolates within populations. Multilocus linkage disequilibrium analysis suggested that the isolates had a panmictic population genetic structure and that there is significant recombination occurs in F. graminearum s.s. In conclusion, tour findings provide the first detailed description of the genetic structure and trichothecene production of populations of F. graminearum s.s. from Uruguay, and expands our understanding of the agroecology of F. graminearum and of the correlation between genotypes and trichothecene chemotypes.

PO-58 - Cardiovascular risk profile in survivors of adult cancer - results from the general population study.

PubMed

Panova-Noeva, M; Hermanns, I M; Schulz, A; Laubert-Reh, D; Zeller, T; Blankenberg, S; Spronk, H M; Münzel, T; Lackner, K J; Ten Cate, H; Wild, P S

2016-04-01

The advancements in cancer treatment and detection of early cancer have resulted in steady increase of adult cancer survivors over the years. However, due to the long term toxic effects of chemotherapy and radiotherapy, the incidence of cardiovascular diseases (CVD) is increasing in survivors. Identifying risk factors and interventions to reduce the excess burden of CVD in this vulnerable population is urgently needed. To investigate the cardiovascular risk factors (CVRFs), inflammation and coagulation profile in cancer survivors from a large population-based study. Presence of CVRFs and laboratory markers have been compared in individuals with (n=1,359) and without (n=13,626) history of cancer. Standard laboratory profile, including blood glucose and lipid profile, has been evaluated in 15,010 individuals from the Gutenberg Health Study (GHS). Coagulation factors, D-dimer and von Willebrand factor (vWF) activity were available in N=4,993. The individuals with history of cancer were older compared to no history of cancer with mean age of 61,5years and 54.4years, respectively (p<0.001). Traditional CVRFs as diabetes (14% vs 8.8%), dyslipidemia (49.6% vs 43.7%) and hypertension (60.3 vs 48.7%) were more frequent whereas smoking was less frequent (14.5% vs 19.9%) in cancer survivors (p<0.001). The standard laboratory profile showed cancer survivors with lower erythrocyte, platelet and white blood cell counts and higher C-reactive protein (CRP), glucose, HbA1c and triglycerides levels (p<0.001). Multivariable logistic regression analysis adjusted for age, sex and CVRFs demonstrated an independent association with diabetes (odds ratio, OR: 1.24, 1.02-1.50; p=0.027) and higher CRP (OR: 1.01, 1.01-1.02; p=0.00071). Fibrinogen, FV, FVII, FVIII and FXI, D-dimer and vWF activity were higher in cancer survivors (p<0.001). Multivariable logistic regression confirmed an independent association with higher fibrinogen (OR: 1.002, 1.000-1.003) and vWF activity (OR: 1.005, 1.001-1.008). This is the first study investigating CVRFs, inflammation and coagulation profile in individuals with history of cancer from a well characterized population-representative adult sample. It gives evidence for higher prevalence of CVRFs, particularly diabetes in this vulnerable population. Markers of inflammation as CRP and fibrinogen and vWF activity were higher in cancer survivors independent of the cardiovascular risk profile. These results underline the increased risk of CVD and need for development of cardio-oncology programs offering cardiovascular prevention. © 2016 Elsevier Ltd. All rights reserved.

Pulsed-Field Gel Electrophoresis Analysis of Bordetella pertussis Isolates Circulating in Europe from 1998 to 2009

PubMed Central

Advani, Abdolreza; Hallander, Hans O.; Dalby, Tine; Krogfelt, Karen Angeliki; Guiso, Nicole; Njamkepo, Elisabeth; von Könnig, Carl Heinz Wirsing; Riffelmann, Marion; Mooi, Frits R.; Sandven, Per; Lutyńska, Anna; Fry, Norman K.; Mertsola, Jussi

2013-01-01

Between 1998 and 2009, Bordetella pertussis clinical isolates were collected during three periods, i.e., 1998 to 2001 (n = 102), 2004 to 2005 (n = 154), and 2007 to 2009 (n = 140), from nine countries with distinct vaccination programs, i.e., Denmark, Finland, France, Germany, The Netherlands, Norway, Poland, Sweden, and the United Kingdom. Pulsed-field gel electrophoresis (PFGE) analysis was performed according to standardized recommendations for epidemiological typing of B. pertussis. There were 81 different PFGE profiles, five of which (BpSR3, BpSR5, BpSR10, BpSR11, and BpSR12) were observed in 61% of the 396 isolates and shown to be predominant in almost all countries. The major profile, BpSR11, showed a decreasing trend from 25% to 30% in 1998 to 2005 to 13% in 2007 to 2009, and there were increases in BpSR3 and BpSR10 from 0% and 8% to 21% and 22%, respectively. One difference between these profiles is that BpSR11 contains isolates harboring the fim3-2 allele and BpSR3 and BpSR10 contain isolates harboring the fim3-1 allele. The total proportion of the five predominant profiles increased from 44% in 1998 to 2001 to 63% in 2004 to 2005 to 70% in 2007 to 2009. In conclusion, common PFGE profiles were identified in B. pertussis populations circulating in European countries with different vaccination programs and different vaccine coverages. These prevalent isolates contain the novel pertussis toxin promoter ptxP3 allele. However, there is evidence for diversifying selection between ptxP3 strains characterized by distinct PFGE profiles. This work shows that, even within a relatively short time span of 10 years, successful isolates which spread through Europe and cause large shifts in B. pertussis populations may emerge. PMID:23175253

THE STRUCTURE AND STELLAR CONTENT OF THE OUTER DISKS OF GALAXIES: A NEW VIEW FROM THE Pan-STARRS1 MEDIUM DEEP SURVEY

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

Zheng, Zheng; Thilker, David A.; Heckman, Timothy M.

2015-02-20

We present the results of an analysis of Pan-STARRS1 Medium Deep Survey multi-band (grizy) images of a sample of 698 low-redshift disk galaxies that span broad ranges in stellar mass, star-formation rate, and bulge/disk ratio. We use population synthesis spectral energy distribution fitting techniques to explore the radial distribution of the light, color, surface mass density, mass/light ratio, and age of the stellar populations. We characterize the structure and stellar content of the galaxy disks out to radii of about twice Petrosian r {sub 90}, beyond which the halo light becomes significant. We measure normalized radial profiles for sub-samples ofmore » galaxies in three bins each of stellar mass and concentration. We also fit radial profiles to each galaxy. The majority of galaxies have down-bending radial surface brightness profiles in the bluer bands with a break radius at roughly r {sub 90}. However, they typically show single unbroken exponentials in the reddest bands and in the stellar surface mass density. We find that the mass/light ratio and stellar age radial profiles have a characteristic 'U' shape. There is a good correlation between the amplitude of the down-bend in the surface brightness profile and the rate of the increase in the M/L ratio in the outer disk. As we move from late- to early-type galaxies, the amplitude of the down-bend and the radial gradient in M/L both decrease. Our results imply a combination of stellar radial migration and suppression of recent star formation can account for the stellar populations of the outer disk.« less

Anthocyanin profiling of wild maqui berries (Aristotelia chilensis [Mol.] Stuntz) from different geographical regions in Chile.

PubMed

Fredes, Carolina; Yousef, Gad G; Robert, Paz; Grace, Mary H; Lila, Mary Ann; Gómez, Miguel; Gebauer, Marlene; Montenegro, Gloria

2014-10-01

Maqui (Aristotelia chilensis) is a Chilean species which produces small berries that are collected from the wild. Anthocyanins, because of their health benefits, are the major focus of interest in maqui fruit. For this study, we examined anthocyanin and phenolic content of maqui fruits from individuals that belonged to four geographical areas in Chile, and used DNA marker analysis to examine the genetic variability of maqui populations that had distinctly different fruit anthocyanin content. Twelve primers generated a total of 145 polymorphic inter simple sequence repeat-polymerase chain reaction (ISSR-PCR) bands. ISSR-PCR showed different banding patterns for the individuals evaluated, confirming that maqui populations belonged to different genotypes. Maqui fruit from four different geographical regions during two consecutive growing seasons showed high total anthocyanin (6.6-15.0 g cy-3-glu kg⁻¹ fresh weight (FW)) and phenolic (10.7-20.5 g GAE kg⁻¹ FW) contents and different anthocyanin profiles. Three maqui genotypes exhibited significantly higher anthocyanin content than the others, as measured by pH differential method and high-performance liquid chromatography-mass spectrometry. Significant genetic diversity was noted within each ecological population. ISSR-PCR analysis provided a fingerprinting approach applicable for differentiation of maqui genotypes. © 2014 Society of Chemical Industry.

Genetic diversity of Pinus nigra Arn. populations in Southern Spain and Northern Morocco revealed by inter-simple sequence repeat profiles.

PubMed

Rubio-Moraga, Angela; Candel-Perez, David; Lucas-Borja, Manuel E; Tiscar, Pedro A; Viñegla, Benjamin; Linares, Juan C; Gómez-Gómez, Lourdes; Ahrazem, Oussama

2012-01-01

Eight Pinus nigra Arn. populations from Southern Spain and Northern Morocco were examined using inter-simple sequence repeat markers to characterize the genetic variability amongst populations. Pair-wise population genetic distance ranged from 0.031 to 0.283, with a mean of 0.150 between populations. The highest inter-population average distance was between PaCU from Cuenca and YeCA from Cazorla, while the lowest distance was between TaMO from Morocco and MA Sierra Mágina populations. Analysis of molecular variance (AMOVA) and Nei's genetic diversity analyses revealed higher genetic variation within the same population than among different populations. Genetic differentiation (Gst) was 0.233. Cuenca showed the highest Nei's genetic diversity followed by the Moroccan region, Sierra Mágina, and Cazorla region. However, clustering of populations was not in accordance with their geographical locations. Principal component analysis showed the presence of two major groups-Group 1 contained all populations from Cuenca while Group 2 contained populations from Cazorla, Sierra Mágina and Morocco-while Bayesian analysis revealed the presence of three clusters. The low genetic diversity observed in PaCU and YeCA is probably a consequence of inappropriate management since no estimation of genetic variability was performed before the silvicultural treatments. Data indicates that the inter-simple sequence repeat (ISSR) method is sufficiently informative and powerful to assess genetic variability among populations of P. nigra.

Genetic Diversity of Pinus nigra Arn. Populations in Southern Spain and Northern Morocco Revealed By Inter-Simple Sequence Repeat Profiles †

PubMed Central

Rubio-Moraga, Angela; Candel-Perez, David; Lucas-Borja, Manuel E.; Tiscar, Pedro A.; Viñegla, Benjamin; Linares, Juan C.; Gómez-Gómez, Lourdes; Ahrazem, Oussama

2012-01-01

Eight Pinus nigra Arn. populations from Southern Spain and Northern Morocco were examined using inter-simple sequence repeat markers to characterize the genetic variability amongst populations. Pair-wise population genetic distance ranged from 0.031 to 0.283, with a mean of 0.150 between populations. The highest inter-population average distance was between PaCU from Cuenca and YeCA from Cazorla, while the lowest distance was between TaMO from Morocco and MA Sierra Mágina populations. Analysis of molecular variance (AMOVA) and Nei’s genetic diversity analyses revealed higher genetic variation within the same population than among different populations. Genetic differentiation (Gst) was 0.233. Cuenca showed the highest Nei’s genetic diversity followed by the Moroccan region, Sierra Mágina, and Cazorla region. However, clustering of populations was not in accordance with their geographical locations. Principal component analysis showed the presence of two major groups—Group 1 contained all populations from Cuenca while Group 2 contained populations from Cazorla, Sierra Mágina and Morocco—while Bayesian analysis revealed the presence of three clusters. The low genetic diversity observed in PaCU and YeCA is probably a consequence of inappropriate management since no estimation of genetic variability was performed before the silvicultural treatments. Data indicates that the inter-simple sequence repeat (ISSR) method is sufficiently informative and powerful to assess genetic variability among populations of P. nigra. PMID:22754321

[Morbidity profile and hospital expenses with elderly patients in Paraná State, Brazil, 2008-2012].

PubMed

Kernkamp, Clarice da Luz; Costa, Cassia Kely Favoretto; Massuda, Ely Mitie; Silva, Eraldo Schunk; Yamaguchi, Mirian Ueda; Bernuci, Marcelo Picinin

2016-07-21

Growth in the elderly population has increased both the demand for health services and healthcare expenses, with relevant consequences for economic stability. The current study aimed to analyze the morbidity profile and hospital expenses with elderly patients in relation to socioeconomic and demographic conditions in Paraná State, Brazil, from 2008 to 2012, applying principal components analysis and groupings. Regions with higher and lower economic and human development showed high prevalence of hospitalizations and costs pertaining to the circulatory and respiratory systems and cardiac diseases for males and females. In regions with intermediary development, diseases of the nervous system in men and of the circulatory system in women had the highest morbidity and hospital expenses. Thus, measures for prevention and health promotion in this elderly population should be targeted to regional investigations.

[Psychosocial profile and family support perception in adults].

PubMed

Landeros-Herrera, Jesús Ernesto; Simental-Mendía, Luis E; Rodríguez-Durán, Juan Luis

2015-01-01

Psychosocial profile disturbances are the basis of personality disorders, which are frequent in México. Thus, the objective of this study was to determine if the family support perception is associated with the psychosocial profile in adults. A total of 450 men and non-pregnant women aged 18 to 60 years were enrolled in a population-based cross-sectional study. According psychosocial profile individuals were allocated into groups altered and unaltered. The presences of psychiatric illness, renal, hepatic, and cardiovascular disease, malignancy or any kind of disability were exclusion criteria. The family support perception was determined by family APGAR and the psychosocial profile using the Dr. Víctor Chávez test. A logistic regression analysis was used to compute the association between family support perception and psychosocial profile. A total of 344 (76.4 %) and 106 (23.5 %) subjects were included into the groups with altered and unaltered psychosocial profile, respectively. Both, moderate family dysfunction (OR = 1.80 95 % CI 1.01-3.23 p = 0.04), and high family dysfunction (OR = 3.88 95 % CI 1.09-12.09 p = 0.02) were significantly associated with altered psychosocial profile. Both, moderate and high family dysfunctions are associated with altered psychosocial profile in adults.

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

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.

Autism and Pitch Processing Splinter Skills: A Group and Subgroup Analysis

ERIC Educational Resources Information Center

Heaton, Pamela; Williams, Kerry; Cummins, Omar; Happe, Francesca

2008-01-01

Autism is characterized by an uneven profile of cognitive abilities and population studies show that approximately 10 percent of diagnosed individuals possess a skill that is significantly better than would be predicted by global IQ. Recent evidence suggests that individuals with autism who possess special skills may represent a distinct genetic…

Discovering and Meeting the Needs of Hispanic Hearing Impaired Children.

ERIC Educational Resources Information Center

Lerman, Alan; Cortez, Edmund

During the 1976-77 school year members of the Cooperative Research Endeavors in Education for the Deaf (CREED VII) project conducted a survey and analysis of the situation of Hispanic hearing impaired children in New York City. The demographic profile of this population, home background and language environment, the school environment, cultural…

Determinants of Employment Success Among Ex-Offenders

ERIC Educational Resources Information Center

Knox, George W.; Stacey, William A.

1978-01-01

Use of cost-benefit analysis in evaluation of seven manpower service programs for ex-offenders in Illinois shows these programs have benefit-cost ratios ranging from 4.24 to 16.88. Demographic profiles for the client flows differ somewhat, with Operation DARE's population being somewhat of a more "hard-core" group based on previous law…

Getting the Measure of the VET Professional

ERIC Educational Resources Information Center

Mlotkowski, Peter; Guthrie, Hugh

2010-01-01

This report draws on analyses of Australian Bureau of Statistics (ABS) data from the Survey of Education and Training (SET) and the Census of Population and Housing to provide an updated demographic profile of vocational education and training (VET) professionals and VET practitioners. A number of caveats are attached to this analysis, all…

All Different or All the Same? Exploring the Diversity of Professional Practices in Portuguese School Psychology

ERIC Educational Resources Information Center

Mendes, Sofia A.; Lasser, Jon; Abreu-Lima, Isabel M.; Almeida, Leandro S.

2017-01-01

Studies have generally characterized school psychologists as a relative homogenous population. Understanding the differences in professional practices and related variables is important for the development of the profession. Using a sample of 446 Portuguese school psychologists, this study used cluster analysis to identify distinct profiles of…

WISC-R Profile Analysis in Differentiating Learning Disabled from Emotionally Disabled Children.

ERIC Educational Resources Information Center

Vance, Booney

The paper examines the usefulness of the Wechsler Intelligence Scale for Children-Revised (WISC-R) subtest score pattern for distinguishing between groups of handicapped children, specifically learning disabled and emotionally disturbed students. The author asserts that no single clear cut pattern characteristic of either population is likely to…

Behavioral Profiles in 4-5 Year-Old Children: Normal and Pathological Variants

ERIC Educational Resources Information Center

Larsson, Jan-Olov; Bergman, Lars R.; Earls, Felton; Rydelius, Per-Anders

2004-01-01

Normal and psychopathological patterns of behavior symptoms in preschool children were described by a classification approach using cluster analysis. The behavior of 406 children, average age 4 years 9 months, from the general population was evaluated at home visits. Seven clusters were identified based on empirically defined dimensions:…

The American Freshman: National Norms for Fall 2000.

ERIC Educational Resources Information Center

Sax, Linda J.; Astin, Alexander W.; Korn, William S.; Mahoney, Kathryn M.

This 35th annual report of national normative data on college freshmen is part of the Cooperative Institutional Research Program (CIRP) longitudinal study to assess the effects of college on students. The freshman data reported here are weighted to provide a normative profile of the U.S. freshman population for use in policy analysis, human…

Ambulatory glucose profile analysis of the juvenile diabetes research foundation continuous glucose monitoring dataset-Applications to the pediatric diabetes population.

PubMed

Forlenza, Gregory P; Pyle, Laura L; Maahs, David M; Dunn, Timothy C

2017-11-01

Increased continuous glucose monitor (CGM) use presents both the benefit and burden of increased data for clinicians to rapidly analyze. The ambulatory glucose profile (AGP) is an evolving a universal software report for CGM data analysis. We utilized the Juvenile Diabetes Research Foundation-CGM dataset to evaluate the AGP across a broad spectrum of patients to show how AGP can be used clinically to assist with CGM-related decision making. We hypothesized that AGP metrics would be different across age and HbA1c strata. AGPs were generated from the JDRF-CGM trial dataset for all periods during which there were ≥10 days of CGM coverage in the 2 weeks adjacent to an HbA1c measurement yielding 1101 AGPs for 393 unique subjects. AGPs were stratified by age group (8-14, 15-24, and ≥25 years) and HbA1c (within or above target for age) and compared for between group differences in AGP metrics via two-factor ANOVA. Glycemic differences between time periods were analyzed via segmented regression analysis. Glucose exposure (average and estimated A1c) and variability (standard deviation and interquartile range) were different between the low and high HbA1c levels. Within a given HbA1c level all age groups were significantly different from each other with older patients having lower averages with less variability than younger patients. AGP analysis of the JDRF-CGM data highlights significant differences in glycemic profiles between pediatric and adult age groups and between well and less well-controlled patient populations. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

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.

Transit profiles : agencies in urbanized areas exceeding 200,000 population for the 1993 National Transit Database section 15 report year

DOT National Transportation Integrated Search

1994-12-01

This publication consists of individual profiles for each reporting transit agency located in an urbanized area with a population exceeding 200,000. The data contained in each profile consists of general and summary reports, as well as modal, perform...

Transit profiles : agencies in urbanized areas exceeding 200,000 population for the 1994 National Transit Database report year

DOT National Transportation Integrated Search

1995-12-01

This publication consists of individual profiles for each reporting transit agency located in an urbanized area with a population exceeding 200,000. The data contained in each profile consists of general and summary reports, as well as modal, perform...

Correspondence regarding Zhong et al., BMC Bioinformatics 2013 Mar 7;14:89.

PubMed

Kuhn, Alexandre

2014-11-28

Computational expression deconvolution aims to estimate the contribution of individual cell populations to expression profiles measured in samples of heterogeneous composition. Zhong et al. recently proposed Digital Sorting Algorithm (BMC Bioinformatics 2013 Mar 7;14:89) and showed that they could accurately estimate population-specific expression levels and expression differences between two populations. They compared DSA with Population-Specific Expression Analysis (PSEA), a previous deconvolution method that we developed to detect expression changes occurring within the same population between two conditions (e.g. disease versus non-disease). However, Zhong et al. compared PSEA-derived specific expression levels across different cell populations. Specific expression levels obtained with PSEA cannot be directly compared across different populations as they are on a relative scale. They are accurate as we demonstrate by deconvolving the same dataset used by Zhong et al. and, importantly, allow for comparison of population-specific expression across conditions.

Variability of the needle essential oils of Pinus heldreichii from different populations in Montenegro and Serbia.

PubMed

Nikolić, Biljana; Ristić, Mihailo; Bojović, Srdjan; Marin, Petar D

2007-05-01

The essential-oil compositions of Pinus heldreichii Christ. from Montenegro and Serbia are reported at the population level. Whitebark pine is a sub-endemic high-mountain Balkan pine relict of an anthropogenically reduced area, with large morphological diversity and insufficiently clear taxonomic position. In the pine-needle terpene profile from three populations from Montenegro, and one from Serbia, 101 compounds were detected, 72 of which could be identified (Table 3). The dominant constituents are limonene (26.3%), alpha-pinene (17.5%), germacrene D (13.5%), and beta-caryophyllene (10.4%), comprising ca. 67.7% of the essential oil. Medium-to-high contents (0.5-10%) of the following 16 additional components were found: beta-pinene, beta-myrcene, alpha-humulene, delta-cadinene, alpha-muurolene, (E)-hex-2-enal, beta-gurjunene, gamma-muurolene, isopimarol, camphene, gamma-cadinene, aromadendrene, beta-bisabolene, trans-beta-farnesene, alpha-cadinene, and (Z)-hex-3-en-1-ol. The similarity of the populations and the within-population variability was visualized by principle-component analysis (PCA) of eleven selected terpenes in 97 tree samples. Cluster and genetic analyses suggest closest connection between the two spatially most-distant populations I (Montenegro) and IV (Serbia). Based on the profile of the main sesquiterpene components, the studied populations from Montenegro and Serbia are more similar to the populations from Greece and the Central Balkan peninsula (Bosnia and Serbia-Kosovo) than to those on the furthest eastern margin of their natural range (Bulgaria).

Antimicrobial Resistance Profiles and Diversity in Salmonella from Humans and Cattle, 2004-2011.

PubMed

Afema, J A; Mather, A E; Sischo, W M

2015-11-01

Analysis of long-term anti-microbial resistance (AMR) data is useful to understand source and transmission dynamics of AMR. We analysed 5124 human clinical isolates from Washington State Department of Health, 391 cattle clinical isolates from the Washington Animal Disease Diagnostic Laboratory and 1864 non-clinical isolates from foodborne disease research on dairies in the Pacific Northwest. Isolates were assigned profiles based on phenotypic resistance to 11 anti-microbials belonging to eight classes. Salmonella Typhimurium (ST), Salmonella Newport (SN) and Salmonella Montevideo (SM) were the most common serovars in both humans and cattle. Multinomial logistic regression showed ST and SN from cattle had greater probability of resistance to multiple classes of anti-microbials than ST and SN from humans (P < 0.0001). While these findings could be consistent with the belief that cattle are a source of resistant ST and SN for people, occurrence of profiles unique to cattle and not observed in temporally related human isolates indicates these profiles are circulating in cattle only. We used various measures to assess AMR diversity, conditional on the weighting of rare versus abundant profiles. AMR profile richness was greater in the common serovars from humans, although both source data sets were dominated by relatively few profiles. The greater profile richness in human Salmonella may be due to greater diversity of sources entering the human population compared to cattle or due to continuous evolution in the human environment. Also, AMR diversity was greater in clinical compared to non-clinical cattle Salmonella, and this could be due to anti-microbial selection pressure in diseased cattle that received treatment. The use of bootstrapping techniques showed that although there were shared profiles between humans and cattle, the expected and observed number of profiles was different, suggesting Salmonella and associated resistance from humans and cattle may not be wholly derived from a common population. © 2014 The Authors. Zoonoses and Public Health Published by Blackwell Verlag GmbH.

Clusterons as a tool for monitoring populations of tick-borne encephalitis virus.

PubMed

Kovalev, Sergey Y; Mukhacheva, Tatyana A

2014-02-01

Tick-borne encephalitis (TBE) is a natural focal viral neuroinfection that is widespread in the temperate zone of Eurasia. Knowledge of the genetic structure of tick-borne encephalitis virus (TBEV) populations is important for understanding, not only the origin and evolution of the virus, but also the formation and maintenance of natural foci. A new approach to the differentiation of TBEV strains within subtype, with clusterons as the basis of analysis, has recently been proposed. In the present study, the genetic structure of TBEV-Sib populations has been investigated based on 387 strains isolated in the Middle Urals (Sverdlovsk region). Fourteen of the 18 currently known TBEV-Sib clusterons were identified. They belong to the Asian and Eastern European (Baltic) groups. It was shown that each TBE foci could be characterized by a unique clusteron profile. Three clusterons that emerged within the last 50 years have been identified which implies an active evolutionary process in the TBEV-Sib populations. The greatest diversity of clusterons was observed in the south of the Middle Urals along the Trans-Siberian Way. Such a pattern could reflect the history of colonization of the area and is closely related to the roads passing from Siberia to the European part of Russia through the Urals. In this article, the principles of continuous monitoring in the regional and local TBE foci are proposed, based on the quantitative and qualitative analysis of TBEV-Sib clusteron profiles. © 2013 Wiley Periodicals, Inc.

Navigating natural variation in herbivory-induced secondary metabolism in coyote tobacco populations using MS/MS structural analysis

PubMed Central

Li, Dapeng; Baldwin, Ian T.; Gaquerel, Emmanuel

2015-01-01

Natural variation can be extremely useful in unraveling the determinants of phenotypic trait evolution but has rarely been analyzed with unbiased metabolic profiling to understand how its effects are organized at the level of biochemical pathways. Native populations of Nicotiana attenuata, a wild tobacco species, have been shown to be highly genetically diverse for traits important for their interactions with insects. To resolve the chemodiversity existing in these populations, we developed a metabolomics and computational pipeline to annotate leaf metabolic responses to Manduca sexta herbivory. We selected seeds from 43 accessions of different populations from the southwestern United States—including the well-characterized Utah 30th generation inbred accession—and grew 183 plants in the glasshouse for standardized herbivory elicitation. Metabolic profiles were generated from elicited leaves of each plant using a high-throughput ultra HPLC (UHPLC)-quadrupole TOFMS (qTOFMS) method, processed to systematically infer covariation patterns among biochemically related metabolites, as well as unknown ones, and finally assembled to map natural variation. Navigating this map revealed metabolic branch-specific variations that surprisingly only partly overlapped with jasmonate accumulation polymorphisms and deviated from canonical jasmonate signaling. Fragmentation analysis via indiscriminant tandem mass spectrometry (idMS/MS) was conducted with 10 accessions that spanned a large proportion of the variance found in the complete accession dataset, and compound spectra were computationally assembled into spectral similarity networks. The biological information captured by this networking approach facilitates the mining of the mass spectral data of unknowns with high natural variation, as demonstrated by the annotation of a strongly herbivory-inducible phenolic derivative, and can guide pathway analysis. PMID:26170304

Relationship Between Soil and Essential Oil Profiles in Salvia desoleana Populations: Preliminary Results.

PubMed

Rapposelli, Emma; Melito, Sara; Barmina, Giovanni Gabriele; Foddai, Marzia; Azara, Emanuela; Scarpa, Grazia Maria

2015-09-01

Salvia desoleana is a herbaceous perennial shrub endemic of Sardinia (Italy). The leaves are a source of essential oil, used in pharmaceutical and cosmetic industries. The therapeutic function of this species has been associated to the presence of essential oils rich in α/β-pinene, p-cimene, linalool, linalyl acetate and 1,8-cineole. Today.the industrial request of Salvia essential oils is increasing and most of the biomass is exploited from the natural populations which are under severe risk of genetic erosion. In order to improve the essential oil production, the study of the environmental parameters that influence composition, quality and quantity of the essential oils, turns out to be necessary. Soil physical and chemical structure represents one of the determinant factors in secondary metabolites production, and could also be involved in volatiles fraction composition in the same species. The main aim of this research was to explore the relationship between essential oil profiles and soil characteristics in S. desoleana populations. GC/MS analysis performed on the essential oil extracts identified 22 principal compounds, which were extremely variable among the five S. desoleana populations studied. The analysis of the essential oils revealed different compositions in the terpenes fractions: 68.2% of monoterpenes, 27.3% of sesquiterpenes and 4.5% of diterpenes. Analysis of chemical and physical soil parameters at the collection sites revealed that silt and sand contents were correlated with α-pinene and sclareol fractions and the total K20 was significantly correlated to several compounds belonging to the three terpene fractions identified. These results will provide guidelines for the in site conservation and for the improvement of the commercial value of the species.

Population structure and diversity of citrus tristeza virus (CTV) isolates in Hunan province, China.

PubMed

Xiao, Cui; Yao, Run-Xian; Li, Fang; Dai, Su-Ming; Licciardello, Grazia; Catara, Antonino; Gentile, Alessandra; Deng, Zi-Niu

2017-02-01

Stem-pitting (SP) is the main type of citrus tristeza virus (CTV) that causes severe damage to citrus trees, especially those of sweet orange, in Hunan province, China. Understanding the local CTV population structure should provide clues for effective mild strain cross-protection (MSCP) of the SP strain of CTV. In this study, markers for the p23 gene, multiple molecular markers (MMMs), and sequence analysis of the three silencing suppressor genes (p20, p23 and p25) were employed to analyze the genetic diversity and genotype composition of the CTV population based on 51 CTV-positive samples collected from 14 citrus orchards scattered around six major citrus-growing areas of Hunan. The results indicated that the CTV population structure was extremely complex and that infection was highly mixed. In total, p23 gene markers resulted in six profiles, and MMMs demonstrated 25 profiles. The severe VT and T3 types appeared to be predominantly associated with SP, while the mild T30 and RB types were related to asymptomatic samples. Based on phylogenetic analysis of the amino acid sequences of p20, p23 and p25, 19 representative CTV samples were classified into seven recently established CTV groups and a potentially novel one. A high level of genetic diversity, as well as potential recombination, was revealed among different CTV isolates. Five pure SP severe and two pure mild strains were identified by genotype composition analysis. Taken together, the results update the genetic diversity of CTV in Hunan with the detection of one possible novel strain, and this information might be applicable for the selection of appropriate mild CTV strains for controlling citrus SP disease through cross-protection.

Inhibition of Thrombopoietin/Mpl Signaling in Adult Hematopoiesis Identifies New Candidates for Hematopoietic Stem Cell Maintenance.

PubMed

Kohlscheen, Saskia; Wintterle, Sabine; Schwarzer, Adrian; Kamp, Christel; Brugman, Martijn H; Breuer, Daniel C; Büsche, Guntram; Baum, Christopher; Modlich, Ute

2015-01-01

Thrombopoietin (Thpo) signals via its receptor Mpl and regulates megakaryopoiesis, hematopoietic stem cell (HSC) maintenance and post-transplant expansion. Mpl expression is tightly controlled and deregulation of Thpo/Mpl-signaling is linked to hematological disorders. Here, we constructed an intracellular-truncated, signaling-deficient Mpl protein which is presented on the cell surface (dnMpl). The transplantation of bone marrow cells retrovirally transduced to express dnMpl into wildtype mice induced thrombocytopenia, and a progressive loss of HSC. The aplastic BM allowed the engraftment of a second BM transplant without further conditioning. Functional analysis of the truncated Mpl in vitro and in vivo demonstrated no internalization after Thpo binding and the inhibition of Thpo/Mpl-signaling in wildtype cells due to dominant-negative (dn) effects by receptor competition with wildtype Mpl for Thpo binding. Intracellular inhibition of Mpl could be excluded as the major mechanism by the use of a constitutive-dimerized dnMpl. To further elucidate the molecular changes induced by Thpo/Mpl-inhibition on the HSC-enriched cell population in the BM, we performed gene expression analysis of Lin-Sca1+cKit+ (LSK) cells isolated from mice transplanted with dnMpl transduced BM cells. The gene expression profile supported the exhaustion of HSC due to increased cell cycle progression and identified new and known downstream effectors of Thpo/Mpl-signaling in HSC (namely TIE2, ESAM1 and EPCR detected on the HSC-enriched LSK cell population). We further compared gene expression profiles in LSK cells of dnMpl mice with human CD34+ cells of aplastic anemia patients and identified similar deregulations of important stemness genes in both cell populations. In summary, we established a novel way of Thpo/Mpl inhibition in the adult mouse and performed in depth analysis of the phenotype including gene expression profiling.

Inhibition of Thrombopoietin/Mpl Signaling in Adult Hematopoiesis Identifies New Candidates for Hematopoietic Stem Cell Maintenance

PubMed Central

Schwarzer, Adrian; Kamp, Christel; Brugman, Martijn H.; Breuer, Daniel C.; Büsche, Guntram; Baum, Christopher; Modlich, Ute

2015-01-01

Thrombopoietin (Thpo) signals via its receptor Mpl and regulates megakaryopoiesis, hematopoietic stem cell (HSC) maintenance and post-transplant expansion. Mpl expression is tightly controlled and deregulation of Thpo/Mpl-signaling is linked to hematological disorders. Here, we constructed an intracellular-truncated, signaling-deficient Mpl protein which is presented on the cell surface (dnMpl). The transplantation of bone marrow cells retrovirally transduced to express dnMpl into wildtype mice induced thrombocytopenia, and a progressive loss of HSC. The aplastic BM allowed the engraftment of a second BM transplant without further conditioning. Functional analysis of the truncated Mpl in vitro and in vivo demonstrated no internalization after Thpo binding and the inhibition of Thpo/Mpl-signaling in wildtype cells due to dominant-negative (dn) effects by receptor competition with wildtype Mpl for Thpo binding. Intracellular inhibition of Mpl could be excluded as the major mechanism by the use of a constitutive-dimerized dnMpl. To further elucidate the molecular changes induced by Thpo/Mpl-inhibition on the HSC-enriched cell population in the BM, we performed gene expression analysis of Lin-Sca1+cKit+ (LSK) cells isolated from mice transplanted with dnMpl transduced BM cells. The gene expression profile supported the exhaustion of HSC due to increased cell cycle progression and identified new and known downstream effectors of Thpo/Mpl-signaling in HSC (namely TIE2, ESAM1 and EPCR detected on the HSC-enriched LSK cell population). We further compared gene expression profiles in LSK cells of dnMpl mice with human CD34+ cells of aplastic anemia patients and identified similar deregulations of important stemness genes in both cell populations. In summary, we established a novel way of Thpo/Mpl inhibition in the adult mouse and performed in depth analysis of the phenotype including gene expression profiling. PMID:26147434

Characterising the latent structure and organisation of self-reported thoughts, feelings and behaviours in adolescents and young adults

PubMed Central

Neufeld, Sharon; Jones, Peter B.; Fonagy, Peter; Bullmore, Edward T.; Dolan, Raymond J.; Moutoussis, Michael; Toseeb, Umar; Goodyer, Ian M.

2017-01-01

Little is known about the underlying relationships between self-reported mental health items measuring both positive and negative emotional and behavioural symptoms at the population level in young people. Improved measurement of the full range of mental well-being and mental illness may aid in understanding the aetiological substrates underlying the development of both mental wellness as well as specific psychiatric diagnoses. A general population sample aged 14 to 24 years completed self-report questionnaires on anxiety, depression, psychotic-like symptoms, obsessionality and well-being. Exploratory and confirmatory factor models for categorical data and latent profile analyses were used to evaluate the structure of both mental wellness and illness items. First order, second order and bifactor structures were evaluated on 118 self-reported items obtained from 2228 participants. A bifactor solution was the best fitting latent variable model with one general latent factor termed ‘distress’ and five ‘distress independent’ specific factors defined as self-confidence, antisocial behaviour, worry, aberrant thinking, and mood. Next, six distinct subgroups were derived from a person-centred latent profile analysis of the factor scores. Finally, concurrent validity was assessed using information on hazardous behaviours (alcohol use, substance misuse, self-harm) and treatment for mental ill health: both discriminated between the latent traits and latent profile subgroups. The findings suggest a complex, multidimensional mental health structure in the youth population rather than the previously assumed first or second order factor structure. Additionally, the analysis revealed a low hazardous behaviour/low mental illness risk subgroup not previously described. Population sub-groups show greater validity over single variable factors in revealing mental illness risks. In conclusion, our findings indicate that the structure of self reported mental health is multidimensional in nature and uniquely finds improved prediction to mental illness risk within person-centred subgroups derived from the multidimensional latent traits. PMID:28403164

Characterising the latent structure and organisation of self-reported thoughts, feelings and behaviours in adolescents and young adults.

PubMed

St Clair, Michelle C; Neufeld, Sharon; Jones, Peter B; Fonagy, Peter; Bullmore, Edward T; Dolan, Raymond J; Moutoussis, Michael; Toseeb, Umar; Goodyer, Ian M

2017-01-01

Little is known about the underlying relationships between self-reported mental health items measuring both positive and negative emotional and behavioural symptoms at the population level in young people. Improved measurement of the full range of mental well-being and mental illness may aid in understanding the aetiological substrates underlying the development of both mental wellness as well as specific psychiatric diagnoses. A general population sample aged 14 to 24 years completed self-report questionnaires on anxiety, depression, psychotic-like symptoms, obsessionality and well-being. Exploratory and confirmatory factor models for categorical data and latent profile analyses were used to evaluate the structure of both mental wellness and illness items. First order, second order and bifactor structures were evaluated on 118 self-reported items obtained from 2228 participants. A bifactor solution was the best fitting latent variable model with one general latent factor termed 'distress' and five 'distress independent' specific factors defined as self-confidence, antisocial behaviour, worry, aberrant thinking, and mood. Next, six distinct subgroups were derived from a person-centred latent profile analysis of the factor scores. Finally, concurrent validity was assessed using information on hazardous behaviours (alcohol use, substance misuse, self-harm) and treatment for mental ill health: both discriminated between the latent traits and latent profile subgroups. The findings suggest a complex, multidimensional mental health structure in the youth population rather than the previously assumed first or second order factor structure. Additionally, the analysis revealed a low hazardous behaviour/low mental illness risk subgroup not previously described. Population sub-groups show greater validity over single variable factors in revealing mental illness risks. In conclusion, our findings indicate that the structure of self reported mental health is multidimensional in nature and uniquely finds improved prediction to mental illness risk within person-centred subgroups derived from the multidimensional latent traits.

Profiles of sedentary and non-sedentary young men - a population-based MOPO study.

PubMed

Pyky, Riitta; Jauho, Anna-Maiju; Ahola, Riikka; Ikäheimo, Tiina M; Koivumaa-Honkanen, Heli; Mäntysaari, Matti; Jämsä, Timo; Korpelainen, Raija

2015-11-23

Sedentary behavior is associated with poor well-being in youth with adverse trajectories spanning to adulthood. Still, its determinants are poorly known. Our aim was to profile sedentary and non-sedentary young men and to clarify their differences in a population-based setting. A total of 616 men (mean age 17.9, SD 0.6) attending compulsory conscription for military service completed a questionnaire on health, health behavior, socioeconomic situation and media use. They underwent a physical (body composition, muscle and aerobic fitness) and medical examination. Profiles were formed by principal component analysis (PCA). A total of 30.1 % men were sedentary (daily leisure-time sitting ≥5 h) and 28.9 % non-sedentary (sitting ≤2 h). The sedentary men had more body fat, more depressive symptoms, but lower fitness and life satisfaction than non-sedentary men. However, according to PCA, profiles of unhealthy eating, life-dissatisfaction, and gaming were detected both among sedentary and non-sedentary men, as well as high self-rated PA and motives to exercise. Determinants of sedentary and non-sedentary lifestyles were multiple and partially overlapping. Recognizing individual patterns and underlying factors of the sedentary lifestyle is essential for tailored health promotion and interventions.

The moderating impact of childhood adversity profiles and conflict on psychological health and suicidal behaviour in the Northern Ireland population.

PubMed

McLafferty, Margaret; O'Neill, Siobhan; Murphy, Sam; Armour, Cherie; Ferry, Finola; Bunting, Brendan

2018-04-01

Childhood adversities are key etiological factors in the onset and persistence of psychopathology. In Northern Ireland the Troubles also impacted on the population's psychological health. This study used data from the Northern Ireland Study of Health and Stress a collaborative epidemiological study which used the WMH-CIDI to assess mental health disorders in a nationally representative sample (Part 2, n = 1986). The aims of the study were to assess co-occurrences of childhood adversities and investigate the impact of adversity profiles and conflict experience on psychopathology and suicidal behaviour. Latent Class Analysis uncovered 3 discrete childhood adversity profiles, a low, medium, and high risk class. Individuals from higher risk adversity profiles displayed significantly increased odds of having psychological problems, with conflict exposure also impacting on psychopathology. However, the study revealed that the impact of conflict exposure on suicidal behaviour was moderated by latent class membership and that some adversity may actually be protective. The findings highlight the need to consider that, while adversity can have a negative impact on psychopathology, a lack of adversity early in life may hinder some people from developing adequate coping strategies. Further research is required to identify adversity patterns and other interacting factors that are protective. Copyright © 2018 Elsevier B.V. All rights reserved.

Chemical analysis of essential oils from different parts of Ferula communis L. growing in central Italy.

PubMed

Maggi, Filippo; Papa, Fabrizio; Dall'Acqua, Stefano; Nicoletti, Marcello

2016-01-01

Ferula communis is a showy herbaceous plant typical of the Mediterranean area where it is used as a traditional medicine. The plant is a source of bioactive compounds such as daucane sesquiterpenes and prenylated coumarins. In Italy, most of phytochemical studies focused on Sardinian populations where poisonous and nonpoisonous chemotypes were found, while investigations on peninsular populations are scarce. In this work, we report the chemical characterisation of the essential oils obtained from different parts of F. communis growing in central Italy. The chemical profiles of the plant parts, as detected by GC-FID and GC-MS, were different from each other and from those reported in insular populations. Notably, α-pinene (10.5%), γ-terpinene (7.6%) and hedycariol (8.4%) were the major volatile constituents in flowers; α-pinene (55.9%), β-pinene (16.8%) and myrcene (5.9%) in fruits; β-eudesmol (12.1%), α-eudesmol (12.1%) and hedycariol (10.3%) in leaves; (E)-β-farnesene (9.5%), β-cubebene (8.2%) and (E)-caryophyllene (7.2%) in roots. The volatile profiles detected did not allow to classify the investigated central Italy population into the poisonous and nonpoisonous chemotypes previously described in Sardinia.

Analysis on a diffusive SIS epidemic model with logistic source

NASA Astrophysics Data System (ADS)

Li, Bo; Li, Huicong; Tong, Yachun

2017-08-01

In this paper, we are concerned with an SIS epidemic reaction-diffusion model with logistic source in spatially heterogeneous environment. We first discuss some basic properties of the parabolic system, including the uniform upper bound of solutions and global stability of the endemic equilibrium when spatial environment is homogeneous. Our primary focus is to determine the asymptotic profile of endemic equilibria (when exist) if the diffusion (migration) rate of the susceptible or infected population is small or large. Combined with the results of Li et al. (J Differ Equ 262:885-913, 2017) where the case of linear source is studied, our analysis suggests that varying total population enhances persistence of infectious disease.

Assessment of diversity among populations of Rauvolfia serpentina Benth. Ex. Kurtz. from Southern Western Ghats of India, based on chemical profiling, horticultural traits and RAPD analysis.

PubMed

Nair, Vadakkemuriyil Divya; Raj, Rajan Pillai Dinesh; Panneerselvam, Rajaram; Gopi, Ragupathi

2014-01-01

Genetic, morphological and chemical variations of ten natural populations of Rauvolfia serpentina Benth. Ex. Kurtz. from Southern Western Ghats of India were assessed using RAPD markers reserpine content and morphological traits. An estimate of genetic diversity and differentiation between genotypes of breeding germplasm is of key importance for its improvement. Populations were collected from different geographical regions. Data obtained through three different methods were compared and the correlation among them was estimated. Statistical analysis showed significant differences for all horticultural characteristics among the accessions suggesting that selection for relevant characteristics could be possible. Variation in the content of Reserpine ranges from 0.192 g/100 g (population from Tusharagiri) to 1.312 g/100 g (population from Aryankavu). A high diversity within population and high genetic differentiation among them based on RAPDs were revealed caused both by habitat fragmentation of the low size of most populations and the low level of gene flow among them. The UPGMA dendrogram and PCA analysis based on reserpine content yielded higher separation among populations indicated specific adaptation of populations into clusters each of them including populations closed to their geographical origin. Genetic, chemical and morphological data were correlated based on Mantel test. Given the high differentiation among populations conservation strategies should take into account genetic diversity and chemical variation levels in relation to bioclimatic and geographic location of populations. Our results also indicate that RAPD approach along with horticultural analysis seemed to be best suited for assessing with high accuracy the genetic relationships among distinct R. serpentina accessions. © 2013.

Average probability that a "cold hit" in a DNA database search results in an erroneous attribution.

PubMed

Song, Yun S; Patil, Anand; Murphy, Erin E; Slatkin, Montgomery

2009-01-01

We consider a hypothetical series of cases in which the DNA profile of a crime-scene sample is found to match a known profile in a DNA database (i.e., a "cold hit"), resulting in the identification of a suspect based only on genetic evidence. We show that the average probability that there is another person in the population whose profile matches the crime-scene sample but who is not in the database is approximately 2(N - d)p(A), where N is the number of individuals in the population, d is the number of profiles in the database, and p(A) is the average match probability (AMP) for the population. The AMP is estimated by computing the average of the probabilities that two individuals in the population have the same profile. We show further that if a priori each individual in the population is equally likely to have left the crime-scene sample, then the average probability that the database search attributes the crime-scene sample to a wrong person is (N - d)p(A).

Dyslipidaemia and undernutrition in children from impoverished areas of Maceió, state of Alagoas, Brazil.

PubMed

Veiga, Gabriela R S; Ferreira, Haroldo S; Sawaya, Ana L; Calado, Jairo; Florêncio, Telma M M T

2010-12-01

Chronic undernutrition causes reduced growth and endocrine adaptations in order to maintain basic life processes. In the present study, the biochemical profiles of chronically undernourished children were determined in order to test the hypothesis that chronic undernutrition also causes changes in lipid profile in pre-school children. The study population comprised 80 children aged between 12 and 71 months, including 60 with moderate undernutrition [height-for-age Z (HAZ) scores ≤ -2 and > -3] and 20 with severe undernutrition (HAZ scores ≤ -3). Socioeconomic, demographic and environmental data were obtained by application of a questionnaire, and anthropometric measurements and information relating to sex, age and feeding habits were collected by a trained nutritionist. Blood samples were analysed for haemoglobin, vitamin A, insulin-like growth factor 1 (IGF-1) and serum lipids, while cortisol was assayed in the saliva. Faecal samples were submitted to parasitological investigation. Analysis of variance and χ² methods were employed in order to select the variables that participated in the multivariate logistic regression analysis. The study population was socioeconomically homogeneous, while the lack of a treated water supply was clearly associated with the degree of malnutrition. Most children were parasitised and anaemia was significantly more prevalent among the severely undernourished. Levels of IGF-1 decreased significantly with increasing severity of undernutrition. Lipid analysis revealed that almost all of the children had dyslipidemia, while low levels of high-density lipoprotein were associated with the degree of undernutrition. It is concluded that chronic malnutrition causes endocrine changes that give rise to alterations in the metabolic profile of pre-school children.

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.

The analysis of ensembles of moderately saturated interstellar lines

NASA Technical Reports Server (NTRS)

Jenkins, E. B.

1986-01-01

It is shown that the combined equivalent widths for a large population of Gaussian-like interstellar line components, each with different central optical depths tau(0) and velocity dispersions b, exhibit a curve of growth (COG) which closely mimics that of a single, pure Gaussian distribution in velocity. Two parametric distributions functions for the line populations are considered: a bivariate Gaussian for tau(0) and b and a power law distribution for tau(0) combined with a Gaussian dispersion for b. First, COGs for populations having an extremely large number of nonoverlapping components are derived, and the implications are shown by focusing on the doublet-ratio analysis for a pair of lines whose f-values differ by a factor of two. The consequences of having, instead of an almost infinite number of lines, a relatively small collection of components added together for each member of a doublet are examined. The theory of how the equivalent widths grow for populations of overlapping Gaussian profiles is developed. Examples of the composite COG analysis applied to existing collections of high-resolution interstellar line data are presented.

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

Effects of geodemographic profiles on healthcare service utilization: a case study on cardiac care in Ontario, Canada

PubMed Central

2013-01-01

Background Although literature has associated geodemographic factors with healthcare service utilization, little is known about how these factors — such as population size, age profile, service accessibility, and educational profile — interact to influence service utilization. This study fills this gap in the literature by examining both the direct and the moderating effects of geodemographic profiles on the utilization of cardiac surgery services. Methods We aggregated secondary data obtained from Statistics Canada and Cardiac Care Network of Ontario to derive the geodemographic profiles of Ontario and the corresponding cardiac surgery service utilization in the years between 2004 and 2007. We conducted a two-step test using Partial Least Squares-based structural equation modeling to investigate the relationships between geodemographic profiles and healthcare service utilization. Results Population size and age profile have direct positive effects on service utilization (β=0.737, p<0.01; β=0.284, p<0.01, respectively), whereas service accessibility is negatively associated with service utilization (β=−0.210, p<0.01). Service accessibility decreases the effect of population size on service utilization (β=−0.606, p<0.01), and educational profile weakens the effects of population size and age profile on service utilization (β=−0.595, p<0.01; β=−0.286, p<0.01, respectively). Conclusions In this study, we found that (1) service accessibility has a moderating effect on the relationship between population size and service utilization, and (2) educational profile has moderating effects on both the relationship between population size and service utilization, and the relationship between age profile and service utilization. Our findings suggest that reducing regional disparities in healthcare service utilization should take into account the interaction of geodemographic factors such as service accessibility and education. In addition, the allocation of resources for a particular healthcare service in one area should consider the geographic distribution of the same services in neighboring areas, as patients may be willing to utilize these services in areas not far from where they reside. PMID:23816201

Transit profiles : agencies in urbanized areas with a population of less than 200,000 for the 1994 National Transit Database report year

DOT National Transportation Integrated Search

1995-12-01

This publication consists of individual profiles for each reporting transit agency located in an urbanized area with a population less than 200,000. The data contained in each profile consists of general and summary reports, as well as modal, perform...

Genetic Relationships among Different Chemotypes of Lupinus sulphureus.

PubMed

Cook, Daniel; Mott, Ivan W; Larson, Steven R; Lee, Stephen T; Johnson, Robert; Stonecipher, Clinton A

2018-02-28

Lupines (Lupinus spp.) are a common plant legume species found on western U.S. rangelands. Lupinus spp. may contain quinolizidine and/or piperidine alkaloids that can be toxic and/or teratogenic to grazing livestock. Alkaloid profiles may vary between and within a species. The objectives of this study were to (1) further explore the characteristic alkaloid profiles of Lupinus sulphureus using field collections and (2) explore the phylogenetic relationship of the different populations and chemotypes of L. sulphureus using the amplified fragment length polymorphism method of DNA fingerprinting, thus providing possible explanations to the phenomena of multiple chemotypes within a species. A total of 49 accessions of L. sulphureus were classified into seven chemotypes. The DNA profiles showed that one L. sulphureus chemotype, chemotype A, is genetically divergent from the other chemotypes of L. sulphureus, suggesting that it represents an unresolved lupine taxon, possibly a new lupine species. Additionally, the different chemotypes of L. sulphureus represented different genetic groups, as shown by Bayesian cluster analysis and principle component analysis.

Screening for prenatal substance use: development of the Substance Use Risk Profile-Pregnancy scale.

PubMed

Yonkers, Kimberly A; Gotman, Nathan; Kershaw, Trace; Forray, Ariadna; Howell, Heather B; Rounsaville, Bruce J

2010-10-01

To report on the development of a questionnaire to screen for hazardous substance use in pregnant women and to compare the performance of the questionnaire with other drug and alcohol measures. Pregnant women were administered a modified TWEAK (Tolerance, Worried, Eye-openers, Amnesia, K[C] Cut Down) questionnaire, the 4Ps Plus questionnaire, items from the Addiction Severity Index, and two questions about domestic violence (N=2,684). The sample was divided into "training" (n=1,610) and "validation" (n=1,074) subsamples. We applied recursive partitioning class analysis to the responses from individuals in the training subsample that resulted in a three-item Substance Use Risk Profile-Pregnancy scale. We examined sensitivity, specificity, and the fit of logistic regression models in the validation subsample to compare the performance of the Substance Use Risk Profile-Pregnancy scale with the modified TWEAK and various scoring algorithms of the 4Ps. The Substance Use Risk Profile-Pregnancy scale is comprised of three informative questions that can be scored for high- or low-risk populations. The Substance Use Risk Profile-Pregnancy scale algorithm for low-risk populations was mostly highly predictive of substance use in the validation subsample (Akaike's Information Criterion=579.75, Nagelkerke R=0.27) with high sensitivity (91%) and adequate specificity (67%). The high-risk algorithm had lower sensitivity (57%) but higher specificity (88%). The Substance Use Risk Profile-Pregnancy scale is simple and flexible with good sensitivity and specificity. The Substance Use Risk Profile-Pregnancy scale can potentially detect a range of substances that may be abused. Clinicians need to further assess women with a positive screen to identify those who require treatment for alcohol or illicit substance use in pregnancy. III.

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

Differential absorption lidar measurements of atmospheric temperature and pressure profiles

NASA Technical Reports Server (NTRS)

Korb, C. L.

1981-01-01

The theory and methodology of using differential absorption lidar techniques for the remote measurement of atmospheric pressure profiles, surface pressure, and temperature profiles from ground, air, and space-based platforms are presented. Pressure measurements are effected by means of high resolution measurement of absorption at the edges of the oxygen A band lines where absorption is pressure dependent due to collisional line broadening. Temperature is assessed using measurements of the absorption at the center of the oxygen A band line originating from a quantum state with high ground state energy. The population of the state is temperature dependent, allowing determination of the temperature through the Boltzmann term. The results of simulations of the techniques using Voigt profile and variational analysis are reported for ground-based, airborne, and Shuttle-based systems. Accuracies in the 0.5-1.0 K and 0.1-0.3% range are projected.

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

mRNA Expression Profiling of Laser Microbeam Microdissected Cells from Slender Embryonic Structures

PubMed Central

Scheidl, Stefan J.; Nilsson, Sven; Kalén, Mattias; Hellström, Mats; Takemoto, Minoru; Håkansson, Joakim; Lindahl, Per

2002-01-01

Microarray hybridization has rapidly evolved as an important tool for genomic studies and studies of gene regulation at the transcriptome level. Expression profiles from homogenous samples such as yeast and mammalian cell cultures are currently extending our understanding of biology, whereas analyses of multicellular organisms are more difficult because of tissue complexity. The combination of laser microdissection, RNA amplification, and microarray hybridization has the potential to provide expression profiles from selected populations of cells in vivo. In this article, we present and evaluate an experimental procedure for global gene expression analysis of slender embryonic structures using laser microbeam microdissection and laser pressure catapulting. As a proof of principle, expression profiles from 1000 cells in the mouse embryonic (E9.5) dorsal aorta were generated and compared with profiles for captured mesenchymal cells located one cell diameter further away from the aortic lumen. A number of genes were overexpressed in the aorta, including 11 previously known markers for blood vessels. Among the blood vessel markers were endoglin, tie-2, PDGFB, and integrin-β1, that are important regulators of blood vessel formation. This demonstrates that microarray analysis of laser microbeam micro-dissected cells is sufficiently sensitive for identifying genes with regulative functions. PMID:11891179

Indoor tanning facility density in eighty U.S. cities.

PubMed

Palmer, Richard C; Mayer, Joni A; Woodruff, Susan I; Eckhardt, Laura; Sallis, James F

2002-06-01

The purpose of this study was to examine the number of tanning facilities in select U.S. cities. The twenty most populated cities from each of 4 U.S. regions were selected for the sample. For each city, data on the number of tanning facilities, climate, and general demographic profile were collected. Data for state tanning facility legislation also were collected. A tanning facility density variable was created by dividing the city's number of facilities by its population size. The 80 cities had an average of 50 facilities each. Results of linear regression analysis indicated that higher density was significantly associated with colder climate, lower median income, and higher proportion of Whites. These data indicate that indoor tanning facilities are prevalent in the environments of U.S. urban-dwellers. Cities having the higher density profile may be logical targets for interventions promoting less or safer use of these facilities.

Black Females in High School: A Statistical Educational Profile

ERIC Educational Resources Information Center

Muhammad, Crystal Gafford; Dixson, Adrienne D.

2008-01-01

In life as in literature, both the mainstream public and the Black community writ large, overlook the Black female experiences, both adolescent and adult. In order to contribute to the knowledge base regarding this population, we present through our study a statistical portrait of Black females in high school. To do so, we present an analysis of…

Energy and greenhouse gas life cycle assessment and cost analysis of aerobic and anaerobic membrane bioreactor systems: Influence of scale, population density, climate, and methane recovery

EPA Science Inventory

This study calculated the energy and greenhouse gas life cycle and cost profiles of transitional aerobic membrane bioreactors (AeMBR) and anaerobic membrane bioreactors (AnMBR). Membrane bioreactors (MBR) represent a promising technology for decentralized wastewater treatment and...

The Disappeared Ones: Female Student Veterans at a Four-Year College

ERIC Educational Resources Information Center

Heitzman, Amy Claire; Somers, Patricia

2015-01-01

Since the end of the military draft in 1973, women have entered military service in greater numbers: Women currently account for 16 percent of active-duty service personnel; by 2035, they will account for 15 percent of the total veteran population (National Center for Veterans Analysis and Statistics 2011). The profile of female veterans differs…

Influenza vaccine response profiles are affected by vaccine preparation and preexisting immunity, but not HIV infection.

PubMed

Berger, Christoph T; Greiff, Victor; Mehling, Matthias; Fritz, Stefanie; Meier, Marc A; Hoenger, Gideon; Conen, Anna; Recher, Mike; Battegay, Manuel; Reddy, Sai T; Hess, Christoph

2015-01-01

Vaccines dramatically reduce infection-related morbidity and mortality. Determining factors that modulate the host response is key to rational vaccine design and demands unsupervised analysis. To longitudinally resolve influenza-specific humoral immune response dynamics we constructed vaccine response profiles of influenza A- and B-specific IgM and IgG levels from 42 healthy and 31 HIV infected influenza-vaccinated individuals. Pre-vaccination antibody levels and levels at 3 predefined time points after vaccination were included in each profile. We performed hierarchical clustering on these profiles to study the extent to which HIV infection associated immune dysfunction, adaptive immune factors (pre-existing influenza-specific antibodies, T cell responses), an innate immune factor (Mannose Binding Lectin, MBL), demographic characteristics (gender, age), or the vaccine preparation (split vs. virosomal) impacted the immune response to influenza vaccination. Hierarchical clustering associated vaccine preparation and pre-existing IgG levels with the profiles of healthy individuals. In contrast to previous in vitro and animal data, MBL levels had no impact on the adaptive vaccine response. Importantly, while HIV infected subjects with low CD4 T cell counts showed a reduced magnitude of their vaccine response, their response profiles were indistinguishable from those of healthy controls, suggesting quantitative but not qualitative deficits. Unsupervised profile-based analysis ranks factors impacting the vaccine-response by relative importance, with substantial implications for comparing, designing and improving vaccine preparations and strategies. Profile similarity between HIV infected and HIV negative individuals suggests merely quantitative differences in the vaccine response in these individuals, offering a rationale for boosting strategies in the HIV infected population.

A neural measure of precision in visual working memory.

PubMed

Ester, Edward F; Anderson, David E; Serences, John T; Awh, Edward

2013-05-01

Recent studies suggest that the temporary storage of visual detail in working memory is mediated by sensory recruitment or sustained patterns of stimulus-specific activation within feature-selective regions of visual cortex. According to a strong version of this hypothesis, the relative "quality" of these patterns should determine the clarity of an individual's memory. Here, we provide a direct test of this claim. We used fMRI and a forward encoding model to characterize population-level orientation-selective responses in visual cortex while human participants held an oriented grating in memory. This analysis, which enables a precise quantitative description of multivoxel, population-level activity measured during working memory storage, revealed graded response profiles whose amplitudes were greatest for the remembered orientation and fell monotonically as the angular distance from this orientation increased. Moreover, interparticipant differences in the dispersion-but not the amplitude-of these response profiles were strongly correlated with performance on a concurrent memory recall task. These findings provide important new evidence linking the precision of sustained population-level responses in visual cortex and memory acuity.

Risk Profile of Hepatitis E Virus from Pigs or Pork in Canada.

PubMed

Wilhelm, B; Fazil, A; Rajić, A; Houde, A; McEwen, S A

2017-12-01

The role and importance of pigs and pork as sources of zoonotic hepatitis E virus (HEV) has been debated in Canada and abroad for over 20 years. To further investigate this question, we compiled data to populate a risk profile for HEV in pigs or pork in Canada. We organized the risk profile (RP) using the headings prescribed for a foodborne microbial risk assessment and used research synthesis methods and inputs wherever possible in populating the fields of this RP. A scoping review of potential public health risks of HEV, and two Canadian field surveys sampling finisher pigs, and retail pork chops and pork livers, provided inputs to inform this RP. We calculated summary estimates of prevalence using the Comprehensive Meta-analysis 3 software, employing the method of moments. Overall, we found the incidence of sporadic locally acquired hepatitis E in Canada, compiled from peer-reviewed literature or from diagnosis at the National Microbiology Laboratory to be low relative to other non-endemic countries. In contrast, we found the prevalence of detection of HEV RNA in pigs and retail pork livers, to be comparable to that reported in the USA and Europe. We drafted risk categories (high/medium/low) for acquiring clinical hepatitis E from exposure to pigs or pork in Canada and hypothesize that the proportion of the Canadian population at high risk from either exposure is relatively small. © 2016 Crown copyright.

Spermatozoa from patients with seminal alterations exhibit a differential micro-ribonucleic acid profile.

PubMed

Salas-Huetos, Albert; Blanco, Joan; Vidal, Francesca; Godo, Anna; Grossmann, Mark; Pons, Maria Carme; F-Fernández, Silvia; Garrido, Nicolás; Anton, Ester

2015-09-01

To compare the microRNA (miRNA) expression profile in spermatozoa from three infertile populations vs. a group of fertile men. Evaluation of the expression level of 736 miRNAs in human spermatozoa using TaqMan quantitative reverse transcription-polymerase chain reaction. University research facility. Semen samples with a single seminal alteration were collected from infertile individuals: asthenozoospermic (n = 10), teratozoospermic (n = 10), and oligozoospermic (n = 10). None. Correlation of the expression level of each miRNA with seminal parameters, age, and chromosome instability; clustering of the individuals according to their miRNA expression profiles and influence of the seminogram, age, chromosome instability, and assisted reproductive technology outcome in the clustering; analysis of the differentially expressed miRNAs (DE-miRNAs) in each infertile population; genome annotation of these DE-miRNAs; and ontological analysis of their predicted targets. The hsa-miR-34b-3p correlated with age, the hsa-miR-629-3p with sperm motility, and the hsa-miR-335-5p, hsa-miR-885-5p, and hsa-miR-152-3p with sperm concentration. The individuals clustered into two groups, and only the seminogram was differentially distributed. We identified 32 DE-miRNAs in the asthenozoospermic group, 19 in the teratozoospermic group, and 18 in the oligozoospermic group. The up-regulated miRNAs presented an enriched localization in introns, affecting relevant genes for spermatogenesis. The predicted targets of the DE-miRNAs contained critical genes associated to infertility, and their ontological analysis revealed significantly associated functions related to the seminal alterations of each group. Spermatozoa from patients with seminal alterations exhibit a differential miRNA profile. This provides new evidence that miRNAs have an essential role in spermatogenesis, contributing to the mechanisms involved in human fertility. Copyright © 2015 American Society for Reproductive Medicine. Published by Elsevier Inc. All rights reserved.

Genetic diversity in natural populations of mangaba in Sergipe, the largest producer State in Brazil.

PubMed

Soares, A N R; Vitória, M F; Nascimento, A L S; Ledo, A S; Rabbani, A R C; Silva, A V C

2016-08-19

Mangaba (Hancornia speciosa Gomes) is found in areas of coastal tablelands in the Brazilian Northeast and Cerrado regions. This species has been subjected to habitat fragmentation that is mainly due to human activity, and requires conservation strategies. The aim of this study was to analyze the structure and inter- and intrapopulation genetic diversity of natural populations of H. speciosa Gomes using inter-simple sequence repeat (ISSR) molecular markers. A total of 155 individuals were sampled in 10 natural populations (ITA, PAC, IND, EST, BC, PIR, JAP, BG, NEO, and SANT) in the State of Sergipe, Brazil. Fifteen primers were used to generate 162 fragments with 100% polymorphism. Genetic analysis showed that the variability between populations (77%) was higher than within populations (23%). It was possible to identify five different groups by the unweighted pair group method with arithmetic mean and principal coordinate analysis, and only one individual (E10) remained isolated. Using ISSR markers it was possible to obtain a molecular profile of the populations evaluated, showing that these markers were effective and exhibited sufficient polymorphism to estimate the genetic variability of natural populations of H. speciosa Gomes.

Genetic differentiation and origin of the Jordanian population: an analysis of Alu insertion polymorphisms.

PubMed

Bahri, Raoudha; El Moncer, Wifak; Al-Batayneh, Khalid; Sadiq, May; Esteban, Esther; Moral, Pedro; Chaabani, Hassen

2012-05-01

Although much of Jordan is covered by desert, its north-western region forms part of the Fertile Crescent region that had given a rich past to Jordanians. This past, scarcely described by historians, is not yet clarified by sufficient genetic data. Thus in this paper we aim to determine the genetic differentiation of the Jordanian population and to discuss its origin. A total of 150 unrelated healthy Jordanians were investigated for ten Alu insertion polymorphisms. Genetic relationships among populations were estimated by a principal component (PC) plot based on the analyses of the R-matrix software. Statistical analysis showed that the Jordanian population is not significantly different from the United Arab Emirates population or the North Africans. This observation, well represented in PC plot, suggests a common origin of these populations belonging respectively to ancient Mesopotamia, Arabia, and North Africa. Our results are compatible with ancient peoples' movements from Arabia to ancient Mesopotamia and North Africa as proposed by historians and supported by previous genetic results. The original genetic profile of the Jordanian population, very likely Arabian Semitic, has not been subject to significant change despite the succession of several civilizations.

Profile of the elderly in physical therapy and its relation to functional disability.

PubMed

Rossi, Ana L S; Pereira, Vanessa S; Driusso, Patrícia; Rebelatto, José R; Ricci, Natalia A

2013-01-01

As the population ages, changes occur in the epidemiological profile towards the current predominance of chronic degenerative diseases which, when untreated, lead to loss of functional capacity and require long-term assistance. To describe the profile of the elderly attending the geriatric physical therapy service and to identify factors associated with functional disability. A cross-sectional descriptive analytical study was conducted. The medical records of elderly individuals were analyzed using the first physical therapy assessment, which included sociodemographic, clinical and mobility data. To determine the degree of disability (mild/moderate), the Brazilian Multidimensional Functional Assessment Questionnaire (BOMFAQ) was used. Descriptive analysis and univariate logistic regression were performed, followed by multivariate logistic regression. The sample comprised 130 elderly patients with a mean age of 73.3 [standar deviation (SD)=7.2] years-old, predominantly female (63.9%), sedentary (71.5%) and presenting three to four diseases (47.7%). The mean of activities with difficulty in the BOMFAQ was 6.7 (SD=4.8), 35 (26.9%) individuals presented mild disability and 95 (73.1%) moderate. The participant characteristic that presented a greatest risk of disability was self-reporting of poor health (OR=12.4). The factors identified, which together can determine functional decline, were sedentary lifestyle, presence of dizziness, polypharmacy and high pain intensity. Elderly individuals attended by the geriatric physical therapy service showed a profile associated with disability, characterized by potentially modifiable factors. This profile also reinforces the demand for long-term care for this population.

Single Cell Profiling using Ionic Liquid Matrix-Enhanced Secondary Ion Mass Spectrometry for Neuronal Cell Type Differentiation

PubMed Central

Do, Thanh D.; Comi, Troy J.; Dunham, Sage J. B.; Rubakhin, Stanislav S.; Sweedler, Jonathan V.

2017-01-01

A high-throughput single cell profiling method has been developed for matrix-enhanced secondary ion mass spectrometry (ME-SIMS) to investigate the lipid profiles of neuronal cells. Populations of cells are dispersed onto the substrate, their locations determined using optical microscopy, and the cell locations used to guide the acquisition of SIMS spectra from the cells. Up to 2,000 cells can be assayed in one experiment at a rate of 6 s per cell. Multiple saturated and unsaturated phosphatidylcholines (PCs) and their fragments are detected and verified with tandem mass spectrometry from individual cells when ionic liquids are employed as a matrix. Optically guided single cell profiling with ME-SIMS is suitable for a range of cell sizes, from Aplysia californica neurons larger than 75 μm to 7-μm rat cerebellar neurons. ME-SIMS analysis followed by t-distributed stochastic neighbor embedding of peaks in the lipid molecular mass range (m/z 700–850) distinguishes several cell types from the rat central nervous system, largely based on the relative proportions of the four dominant lipids, PC(32:0), PC(34:1), PC(36:1), and PC(38:5). Furthermore, subpopulations within each cell type are tentatively classified consistent with their endogenous lipid ratios. The results illustrate the efficacy of a new approach to classify single cell populations and subpopulations using SIMS profiling of lipid and metabolite contents. These methods are broadly applicable for high throughput single cell chemical analyses. PMID:28194949

Transit profiles : agencies in urbanized areas with a population of less than 200,000 for the 1993 National Transit Database section 15 report year

DOT National Transportation Integrated Search

1994-12-01

This publication consists of individual profiles for each reporting transit agency located in an urbanized area with a population less than 200,000. The data contained in each profile consists of general and summary reports, as well as modal, perform...

Ancient DNA reveals kinship burial patterns of a pre-Columbian Andean community

PubMed Central

2012-01-01

Background A detailed genetic study of the pre-Columbian population inhabiting the Tompullo 2 archaeological site (department Arequipa, Peru) was undertaken to resolve the kin relationships between individuals buried in six different chullpas. Kin relationships were an important factor shaping the social organization in the pre-Columbian Andean communities, centering on the ayllu, a group of relatives that shared a common land and responsibilities. The aim of this study was to evaluate whether this Andean model of a social organization had an influence on mortuary practices, in particular to determine whether chullpas served as family graves. Results The remains of forty-one individuals were analyzed with both uniparental (mtDNA, Y–chromosome) and biparental (autosomal microsatellites) markers. Reproducible HVRI sequences, autosomal and Y chromosomal STR profiles were obtained for 24, 16 and 11 individuals, respectively. Mitochondrial DNA diversity was comparable to that of ancient and contemporary Andean populations. The Tompullo 2 population exhibited the closest relationship with the modern population from the same region. A kinship analysis revealed complex pattern of relations within and between the graves. However mean relatedness coefficients regarding the pairs of individuals buried in the same grave were significantly higher than those regarding pairs buried in different graves. The Y chromosome profiles of 11 males suggest that only members of one male line were buried in the same grave. Conclusions Genetic investigation of the population that inhabited Tompullo 2 site shows continuity between pre-Columbian and modern Native Amerindian populations inhabiting the Arequipa region. This suggests that no major demographic processes have influenced the mitochondrial DNA diversity of these populations during the past five hundred years. The kinship analysis involving uni- and biparental markers suggests that the community that inhabited the Tompullo 2 site was organized into extended family groups that were buried in different graves. This finding is in congruence with known models of social organization of Andean communities. PMID:22524324

Measuring health-promoting behaviors: cross-cultural validation of the Health-Promoting Lifestyle Profile-II.

PubMed

Sousa, Pedro; Gaspar, Pedro; Vaz, Daniela C; Gonzaga, Sílvia; Dixe, M Anjos

2015-04-01

Individual lifestyles have emerged as valuable health constructs. This study aims to psychometrically test the Portuguese (European) version of the Health-Promoting Lifestyle Profile-II. After an adequate linguistic and cultural adaptation of the Health-Promoting Lifestyle Profile-II scale, their psychometric properties were assessed (N = 889) by Cronbach's alpha and confirmatory factor analysis. Results showed an adequate fit to a 52-item, six-factor structure. A global alpha of .925 was obtained. The Portuguese version demonstrated good validity and reliability in a wide adult sample, and can thus be applied to the Portuguese population. This instrument is useful as an evaluation tool for health-promoting lifestyles and as an instrument for testing the effectiveness of health-promoting programs. © 2014 NANDA International, Inc.

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.

Psychological profiles in patients with Sjögren's syndrome related to fatigue: a cluster analysis.

PubMed

van Leeuwen, Ninke; Bossema, Ercolie R; Knoop, Hans; Kruize, Aike A; Bootsma, Hendrika; Bijlsma, Johannes W J; Geenen, Rinie

2015-05-01

Fatigue is a highly prevalent and debilitating symptom in the autoimmune disease SS. Although the disease process plays a role in fatigue, psychological factors may influence fatigue and the ability to deal with its consequences. Profiles of co-occurring psychological factors may suggest potential targets for the treatment of fatigue. The aim of this study was to identify psychological profiles in patients with SS and the accompanying levels of fatigue. Three hundred patients with primary SS (mean age 57 years, 93% female) completed questionnaires on fatigue (multidimensional fatigue inventory), physical activity cognitions (TAMPA-SK), illness cognitions, cognitive regulation, emotion processing and regulation [Toronto Alexithymia Scale 20, Emotion Regulation Questionnaire (ERQ), Berkeley Expressivity Questionnaire], coping strategies (Brief COPE) and social support. Principal axis factor analysis (oblimin rotation) yielded six psychological factors: social support, negative thinking, positive thinking, emotional expressivity, avoidance and alexithymia (i.e. the inability to differentiate emotions). Using cluster analyses, these factors were grouped in four psychological profiles: functional (39%), alexithymic (27%), self-reliant (23%) and dysfunctional (11%). Irrespective of the psychological profile, the level of fatigue was substantially higher in patients than in the general population. Patients with a dysfunctional or an alexithymic profile reported more fatigue than those with a self-reliant profile. Our study in SS yielded four psychological profiles that were differentially associated with fatigue. These profiles can be used to examine determinants and prognosis of fatigue as well as the possibility of customizing cognitive behavioural interventions for chronic fatigue. © The Author 2014. Published by Oxford University Press on behalf of the British Society for Rheumatology. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Genetic profile based upon 15 microsatellites of four caste groups of the eastern Indian state, Bihar.

PubMed

Ashma, R; Kashyap, V K

2003-01-01

The formation of caste groups among the Hindu community and the practice of endogamy exert a great impact on the genetic structure and diversity of the Indian population. Allele frequency data of 15 microsatellite loci clearly portray the genetic diversity and relatedness among four socio-culturally advanced caste groups: Brahmin, Bhumihar, Rajput and Kayasth of Caucasoid ethnicity of Bihar. The study seeks to understand the impact of the man-made caste system on the genetic profile of the four major caste groups of Bihar. Computation of average heterozygosity, most frequent allele, allele diversity and coefficient of gene differentiation (Gst), along with genetic distance (DA)and principal coordinate analysis were performed to assess intra-population and inter-population diversity. The average Gst value for all the loci was 0.012 +/- 0.0033, and the level of average heterozygosity was approximately 75.5%, indicating genetic similarity and intra-population diversity. Genetic distance (DA) values and the phylogenetic tree along with other higher caste groups of India indicate the relative distance between them. The present study clearly depicts the genetic profile of these caste groups, their inherent closeness in the past, and the impact of the imposed caste system that later restricted the gene flow. The study highlights the status of Bhumihar and Kayasth in the Hindu caste system. The former was found clustering with the Brahmin group (as expected, since Bhumihar is known to be a subclass of Brahmin), whereas the distance between the Brahmin and Kayasth caste groups was found to be large. North-eastern Indian Mongoloids form a separate cluster.

Nonlinear mixed effects modeling of the diurnal blood pressure profile in a multiracial population.

PubMed

van Rijn-Bikker, Petra C; Snelder, Nelleke; Ackaert, Oliver; van Hest, Reinier M; Ploeger, Bart A; van Montfrans, Gert A; Koopmans, Richard P; Mathôt, Ron A

2013-09-01

Cardiac and cerebrovascular events in hypertensive patients are related to specific features of the 24-hour diurnal blood pressure (BP) profile (i.e., daytime and nighttime BP, nocturnal dip (ND), and morning surge (MS)). This investigation aimed to characterize 24-hour diurnal systolic BP (SBP) with parameters that correlate directly with daytime and nighttime SBP, ND, and MS using nonlinear mixed effects modeling. Ambulatory 24-hour SBP measurements (ABPM) of 196 nontreated subjects from three ethnic groups were available. A population model was parameterized in NONMEM to estimate and evaluate the parameters baseline SBP (BSL), nadir (minimum SBP during the night), and change (SBP difference between day and night). Associations were tested between these parameters and patient-related factors to explain interindividual variability. The diurnal SBP profile was adequately described as the sum of 2 cosine functions. The following typical values (interindividual variability) were found: BSL = 139 mm Hg (11%); nadir = 122 mm Hg (14%); change = 25 mm Hg (52%), and residual error = 12 mm Hg. The model parameters correlate well with daytime and nighttime SBP, ND, and MS (R (2) = 0.50-0.92). During covariate analysis, ethnicity was found to be associated with change; change was 40% higher in white Dutch subjects and 26.8% higher in South Asians than in blacks. The developed population model allows simultaneous estimation of BSL, nadir, and change for all individuals in the investigated population, regardless of individual number of SBP measurements. Ethnicity was associated with change. The model provides a tool to evaluate and optimize the sampling frequency for 24-hour ABPM.

Country Demographic Profiles: Thailand.

ERIC Educational Resources Information Center

Bureau of the Census (DOC), Suitland, MD. Population Div.

This profile of the population of Thailand contains 35 tables of selected demographic information, including size of population and estimates of fertility and mortality, beginning in 1950. An adjusted distribution of the population by age and sex is given for the latest census year, as well as for 1976. Projections of the number of women of…

Using Fatty-Acid Profile Analysis as an Ecologic Indicator in the Management of Tourist Impacts on Marine Wildlife: A Case of Stingray-Feeding in the Caribbean

NASA Astrophysics Data System (ADS)

Semeniuk, Christina A. D.; Speers-Roesch, Ben; Rothley, Kristina D.

2007-10-01

Feeding marine wildlife as a tourism experience has become a popular means by which to attract both people and wildlife, although management efforts are still in their infancy. “Stingray City Sandbar” in the Cayman Islands, where visitors can hand feed free-ranging Southern Stingrays ( Dasyatis americana), is a world-famous attraction currently undergoing visitor and wildlife management. One plan is to decrease the amount of nonnatural food provided by tourists with the intention of decreasing stingray habituation to the artificial food source and promoting stingray health. However, the effectiveness of this action is uncertain given that neither the extent of squid composition in the stingray diet nor the degree of nutrient similarity between the fed and natural diets is unknown. We used fatty acid (FA) profile analysis to address these questions by assessing the serum nonesterified FA composition of fed and unfed stingrays around the island and compared them with FA profiles of (1) the provisioned food source (squid) and (2) other warm- and cold-water elasmobranchs (sharks and rays). Our results indicated that fed stingrays were distinct. The FA profiles of the fed stingray population were expressly different from those of the unfed populations and showed a remarkable similarity to the FA composition of squid, suggesting that squid is the main food source. The tropical fed stingrays also exhibited essential FA ratios, specific to both species and habitat, comparable with those of elasmobranchs and squid from cold-water environs, implying that the provisioned food does not provide a similar nutritional lipid composition to that eaten in the wild. Our results suggest that FA profiles are a valuable indicator for the management and monitoring of fed Southern Stingrays because they can be used to assess differences in diet composition and provide an index of nutritional similarity. Our findings are currently being used by Caymanian stakeholders in designing practical management actions for their wildlife attraction.

Metabolic Profiling of a Mapping Population Exposes New Insights in the Regulation of Seed Metabolism and Seed, Fruit, and Plant Relations

PubMed Central

Toubiana, David; Semel, Yaniv; Tohge, Takayuki; Beleggia, Romina; Cattivelli, Luigi; Rosental, Leah; Nikoloski, Zoran; Zamir, Dani; Fernie, Alisdair R.; Fait, Aaron

2012-01-01

To investigate the regulation of seed metabolism and to estimate the degree of metabolic natural variability, metabolite profiling and network analysis were applied to a collection of 76 different homozygous tomato introgression lines (ILs) grown in the field in two consecutive harvest seasons. Factorial ANOVA confirmed the presence of 30 metabolite quantitative trait loci (mQTL). Amino acid contents displayed a high degree of variability across the population, with similar patterns across the two seasons, while sugars exhibited significant seasonal fluctuations. Upon integration of data for tomato pericarp metabolite profiling, factorial ANOVA identified the main factor for metabolic polymorphism to be the genotypic background rather than the environment or the tissue. Analysis of the coefficient of variance indicated greater phenotypic plasticity in the ILs than in the M82 tomato cultivar. Broad-sense estimate of heritability suggested that the mode of inheritance of metabolite traits in the seed differed from that in the fruit. Correlation-based metabolic network analysis comparing metabolite data for the seed with that for the pericarp showed that the seed network displayed tighter interdependence of metabolic processes than the fruit. Amino acids in the seed metabolic network were shown to play a central hub-like role in the topology of the network, maintaining high interactions with other metabolite categories, i.e., sugars and organic acids. Network analysis identified six exceptionally highly co-regulated amino acids, Gly, Ser, Thr, Ile, Val, and Pro. The strong interdependence of this group was confirmed by the mQTL mapping. Taken together these results (i) reflect the extensive redundancy of the regulation underlying seed metabolism, (ii) demonstrate the tight co-ordination of seed metabolism with respect to fruit metabolism, and (iii) emphasize the centrality of the amino acid module in the seed metabolic network. Finally, the study highlights the added value of integrating metabolic network analysis with mQTL mapping. PMID:22479206

The rural bite in population pyramids: what are the implications for responsiveness of health systems in middle income countries?

PubMed Central

2014-01-01

Background Health services can only be responsive if they are designed to service the needs of the population at hand. In many low and middle income countries, the rate of urbanisation can leave the profile of the rural population quite different from the urban population. As a consequence, the kinds of services required for an urban population may be quite different from that required for a rural population. This is examined using data from the South East Asia Community Observatory in rural Malaysia and contrasting it with the national Malaysia population profile. Methods Census data were collected from 10,373 household and the sex and age of household members was recorded. Approximate Malaysian national age and sex profiles were downloaded from the US Census Bureau. The population pyramids, and the dependency and support ratios for the whole population and the SEACO sub-district population are compared. Results Based on the population profiles and the dependency ratios, the rural sub-district shows need for health services in the under 14 age group similar to that required nationally. In the older age group, however, the rural sub-district shows twice the need for services as the national data indicate. Conclusion The health services needs of an older population will tend towards chronic conditions, rather than the typically acute conditions of childhood. The relatively greater number of older people in the rural population suggest a very different health services mix need. Community based population monitoring provides critical information to inform health systems. PMID:25081203

Indication of two Pacific walrus stocks from whole tooth elemental analysis

USGS Publications Warehouse

Jay, C.V.; Outridge, P.M.; Garlich-Miller, J. L.

2008-01-01

The Pacific walrus (Odobenus rosmarus divergens) is considered to be a single panmictic population for management purposes. However, studies on population structuring in this species are limited; in part, because portions of the population's range are often inaccessible. Therefore, alternative and complementary methods for investigating stock structure in the Pacific walrus are of particular interest. We used measures of elemental concentrations in whole tooth sections from ICP-MS in a discriminant analysis to investigate evidence of stock separation between walruses from two of three known breeding areas (S.E. Bering, St Lawrence, and Anadyr Gulf). Elemental compositions of teeth from female and male walruses from the S.E. Bering and St Lawrence breeding areas were significantly different, providing evidence of separate stocks. We also obtained insights into the potential relation of walruses from non-breeding areas to walruses from these breeding groups based on similarities in their dental elemental profiles. ?? 2008 Springer-Verlag.

Patterns of genetic diversity at the nine forensically approved STR loci in the Indian populations.

PubMed

Dutta, Ranjan; Reddy, B Mohan; Chattopadhyay, P; Kashyap, V K; Sun, Guangyun; Deka, Ranjan

2002-02-01

Genetic diversity at the nine short tandem repeat (STR) loci, which are universally approved and widely used for forensic investigations, has been studied among nine Indian populations with diverse ethnic, linguistic, and geographic backgrounds. The nine STR loci were profiled on 902 individuals using fluorescent detection methods on an ABI377 System, with the aid of an Amp-F1 Profiler Plus Kit. The studied populations include two upper castes, Brahmin and Kayastha; a tribe, Garo, from West Bengal; a Hindu caste, Meitei, with historical links to Bengal Brahmins; a migrant group of Muslims; three tribal groups, Naga, Kuki and Hmar, from Manipur in northeast India; and a middle-ranking caste, Golla, who are seminomadic herders from Andhra Pradesh. Gene diversity analysis suggests that the average heterozygosity is uniformly high (>0.8) in the studied populations, with the coefficient of gene differentiation at 0.050 +/- 0.0054. Both neighbor-joining (NJ) and unweighted pair group method with arithmetic mean (UPGMA) trees based on DA distances bring out distinct clusters that are consistent with ethnic, linguistic, and/or geographic backgrounds of the populations. The fit of the Harpending and Ward model of regression of average heterozygosity on the gene frequency centroid is found to be good, and the observed outliers are consistent with the population structure and history of the studied populations. Our study suggests that the nine STR loci, used so far mostly for forensic investigations, can be used fruitfully for microevolutionary studies as well, and for reconstructing the phylogenetic history of human populations, at least at the local level.

Fundamental limits on dynamic inference from single-cell snapshots

PubMed Central

Weinreb, Caleb; Tusi, Betsabeh K.; Socolovsky, Merav

2018-01-01

Single-cell expression profiling reveals the molecular states of individual cells with unprecedented detail. Because these methods destroy cells in the process of analysis, they cannot measure how gene expression changes over time. However, some information on dynamics is present in the data: the continuum of molecular states in the population can reflect the trajectory of a typical cell. Many methods for extracting single-cell dynamics from population data have been proposed. However, all such attempts face a common limitation: for any measured distribution of cell states, there are multiple dynamics that could give rise to it, and by extension, multiple possibilities for underlying mechanisms of gene regulation. Here, we describe the aspects of gene expression dynamics that cannot be inferred from a static snapshot alone and identify assumptions necessary to constrain a unique solution for cell dynamics from static snapshots. We translate these constraints into a practical algorithmic approach, population balance analysis (PBA), which makes use of a method from spectral graph theory to solve a class of high-dimensional differential equations. We use simulations to show the strengths and limitations of PBA, and then apply it to single-cell profiles of hematopoietic progenitor cells (HPCs). Cell state predictions from this analysis agree with HPC fate assays reported in several papers over the past two decades. By highlighting the fundamental limits on dynamic inference faced by any method, our framework provides a rigorous basis for dynamic interpretation of a gene expression continuum and clarifies best experimental designs for trajectory reconstruction from static snapshot measurements. PMID:29463712

Tumour xenograft detection through quantitative analysis of the metabolic profile of urine in mice

NASA Astrophysics Data System (ADS)

Moroz, Jennifer; Turner, Joan; Slupsky, Carolyn; Fallone, Gino; Syme, Alasdair

2011-02-01

The metabolic content of urine from NIH III nude mice (n = 22) was analysed before and after inoculation with human glioblastoma multiforme (GBM) cancer cells. An age- and gender-matched control population (n = 14) was also studied to identify non-tumour-related changes. Urine samples were collected daily for 6 weeks, beginning 1 week before cell injection. Metabolite concentrations were obtained via targeted profiling with Chenomx Suite 5.1, based on nuclear magnetic resonance (NMR) spectra acquired on an Oxford 800 MHz cold probe NMR spectrometer. The Wilcoxon rank sum test was used to evaluate the significance of the change in metabolite concentration between the two time points. Both the metabolite concentrations and the ratios of pairs of metabolites were studied. The complicated inter-relationships between metabolites were assessed through partial least-squares discriminant analysis (PLS-DA). Receiver operating characteristic (ROC) curves were generated for all variables and the area under the curve (AUC) calculated. The data indicate that the number of statistically significant changes in metabolite concentrations was more pronounced in the tumour-bearing population than in the control animals. This was also true of the ratios of pairs of metabolites. ROC analysis suggests that the ratios were better able to differentiate between the pre- and post-injection samples compared to the metabolite concentrations. PLS-DA models produced good separation between the populations and had the best AUC results (all models exceeded 0.937). These results demonstrate that metabolomics may be used as a screening tool for GBM cells grown in xenograft models in mice.

Microbial analysis in primary and persistent endodontic infections by using pyrosequencing.

PubMed

Hong, Bo-Young; Lee, Tae-Kwon; Lim, Sang-Min; Chang, Seok Woo; Park, Joonhong; Han, Seung Hyun; Zhu, Qiang; Safavi, Kamran E; Fouad, Ashraf F; Kum, Kee Yeon

2013-09-01

The aim of this study was to investigate the bacterial community profile of intracanal microbiota in primary and persistent endodontic infections associated with asymptomatic chronic apical periodontitis by using GS-FLX Titanium pyrosequencing. The null hypothesis was that there is no difference in diversity of overall bacterial community profiles between primary and persistent infections. Pyrosequencing analysis from 10 untreated and 8 root-filled samples was conducted. Analysis from 18 samples yielded total of 124,767 16S rRNA gene sequences (with a mean of 6932 reads per sample) that were taxonomically assigned into 803 operational taxonomic units (3% distinction), 148 genera, and 10 phyla including unclassified. Bacteroidetes was the most abundant phylum in both primary and persistent infections. There were no significant differences in bacterial diversity between the 2 infection groups (P > .05). The bacterial community profile that was based on dendrogram showed that bacterial population in both infections was not significantly different in their structure and composition (P > .05). The present pyrosequencing study demonstrates that persistent infections have as diverse bacterial community as primary infections. Copyright © 2013 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

The absorption profile of pregabalin in chronic pancreatitis.

PubMed

Olesen, Anne E; Olofsen, Erik; Olesen, Søren S; Staahl, Camilla; Andresen, Trine; Dahan, Albert; Drewes, Asbjørn M

2012-12-01

It was recently shown that pregabalin decreased pain associated with chronic pancreatitis. It is well known that pancreatitis patients suffer from fat malabsorption with accompanying diarrhoea because of loss of exocrine pancreatic enzyme production. This may lead to changes in the mucosal surface in the small intestine and possibly affect the absorption of pregabalin. The pharmacokinetics of pregabalin has never been investigated in patients suffering from chronic pancreatitis. The aim of this study was to develop a population pharmacokinetic model of pregabalin administered to patients with chronic pancreatitis. The pregabalin population pharmacokinetic analysis was conducted on data from fifteen patients with chronic pancreatitis. Each patient received 75 mg of pregabalin (oral capsule). Pregabalin concentrations were measured using a validated liquid chromatographic method. Data analysis was performed using non-linear mixed effects modelling methodology as implemented by NONMEM. A one-compartment model with first-order absorption and elimination adequately described pregabalin pharmacokinetics. Time to maximum observed plasma concentration (T(max) ) was 1.53 (95% CI 1.09-2.05). The maximum plasma concentration (C(max) ) was 1.98 μg/ml (95% CI 1.69-2.34), and area under the plasma concentration-time profile (area under the curve) was 18.2 μg*hr/ml (95% CI 14.7-26.3). Pregabalin is well absorbed in patients with chronic pancreatitis, and the pharmacokinetic profile of pregabalin is not extensively affected by chronic pancreatitis. © 2012 The Authors Basic & Clinical Pharmacology & Toxicology © 2012 Nordic Pharmacological Society.

Single cell gene expression profiling in Alzheimer's disease.

PubMed

Ginsberg, Stephen D; Che, Shaoli; Counts, Scott E; Mufson, Elliott J

2006-07-01

Development and implementation of microarray techniques to quantify expression levels of dozens to hundreds to thousands of transcripts simultaneously within select tissue samples from normal control subjects and neurodegenerative diseased brains has enabled scientists to create molecular fingerprints of vulnerable neuronal populations in Alzheimer's disease (AD) and related disorders. A goal is to sample gene expression from homogeneous cell types within a defined region without potential contamination by expression profiles of adjacent neuronal subpopulations and nonneuronal cells. The precise resolution afforded by single cell and population cell RNA analysis in combination with microarrays and real-time quantitative polymerase chain reaction (qPCR)-based analyses allows for relative gene expression level comparisons across cell types under different experimental conditions and disease progression. The ability to analyze single cells is an important distinction from global and regional assessments of mRNA expression and can be applied to optimally prepared tissues from animal models of neurodegeneration as well as postmortem human brain tissues. Gene expression analysis in postmortem AD brain regions including the hippocampal formation and neocortex reveals selectively vulnerable cell types share putative pathogenetic alterations in common classes of transcripts, for example, markers of glutamatergic neurotransmission, synaptic-related markers, protein phosphatases and kinases, and neurotrophins/neurotrophin receptors. Expression profiles of vulnerable regions and neurons may reveal important clues toward the understanding of the molecular pathogenesis of various neurological diseases and aid in identifying rational targets toward pharmacotherapeutic interventions for progressive, late-onset neurodegenerative disorders such as mild cognitive impairment (MCI) and AD.

Profiling antibody responses by multiparametric analysis of primary B cells

PubMed Central

Story, Craig M.; Papa, Eliseo; Hu, Chih-Chi Andrew; Ronan, Jehnna L.; Herlihy, Kara; Ploegh, Hidde L.; Love, J. Christopher

2008-01-01

Determining the efficacy of a vaccine generally relies on measuring neutralizing antibodies in sera. This measure cannot elucidate the mechanisms responsible for the development of immunological memory at the cellular level, however. Quantitative profiles that detail the cellular origin, extent, and diversity of the humoral (antibody-based) immune response would improve both the assessment and development of vaccines. Here, we describe a novel approach to collect multiparametric datasets that describe the specificity, isotype, and apparent affinity of the antibodies secreted from large numbers of individual primary B cells (≈103-104). The antibody/antigen binding curves obtained by this approach can be used to classify closely related populations of cells using algorithms for data clustering, and the relationships among populations can be visualized graphically using affinity heatmaps. The technique described was used to evaluate the diversity of antigen-specific antibody-secreting cells generated during an in vivo humoral response to a series of immunizations designed to mimic a multipart vaccination. Profiles correlating primary antibody-producing cells with the molecular characteristics of their secreted antibodies should facilitate both the evaluation of candidate vaccines and, broadly, studies on the repertoires of antibodies generated in response to infectious or autoimmune diseases. PMID:19004776

Population and genetic outcomes 20 years after reintroducing bobcats (Lynx rufus) to Cumberland Island, Georgia USA

USGS Publications Warehouse

Diefenbach, Duane R.; Hansen, Leslie A.; Bohling, Justin H.; Miller-Butterworth, Cassandra

2015-01-01

In 1988–1989, 32 bobcats Lynx rufus were reintroduced to Cumberland Island (CUIS), Georgia, USA, from which they had previously been extirpated. They were monitored intensively for 3 years immediately post-reintroduction, but no estimation of the size or genetic diversity of the population had been conducted in over 20 years since reintroduction. We returned to CUIS in 2012 to estimate abundance and effective population size of the present-day population, as well as to quantify genetic diversity and inbreeding. We amplified 12 nuclear microsatellite loci from DNA isolated from scats to establish genetic profiles to identify individuals. We used spatially explicit capture–recapture population estimation to estimate abundance. From nine unique genetic profiles, we estimate a population size of 14.4 (SE = 3.052) bobcats, with an effective population size (Ne) of 5–8 breeding individuals. This is consistent with predictions of a population viability analysis conducted at the time of reintroduction, which estimated the population would average 12–13 bobcats after 10 years. We identified several pairs of related bobcats (parent-offspring and full siblings), but ~75% of the pairwise comparisons were typical of unrelated individuals, and only one individual appeared inbred. Despite the small population size and other indications that it has likely experienced a genetic bottleneck, levels of genetic diversity in the CUIS bobcat population remain high compared to other mammalian carnivores. The reintroduction of bobcats to CUIS provides an opportunity to study changes in genetic diversity in an insular population without risk to this common species. Opportunities for natural immigration to the island are limited; therefore, continued monitoring and supplemental bobcat reintroductions could be used to evaluate the effect of different management strategies to maintain genetic diversity and population viability. The successful reintroduction and maintenance of a bobcat population on CUIS illustrates the suitability of translocation as a management tool for re-establishing felid populations.

Analysis of the effect of spatial and temporal sampling densities on accuracy of predicting the heating profile in windrowed broiler litter

USDA-ARS?s Scientific Manuscript database

A standard method for monitoring temperature in windrow piles of broiler litter to predict microbial population reductions is described. Temperature data collected every 2 min on a 10 cm x 10 cm spatial sampling grid in five identically-constructed litter windrow piles was utilized in this study. ...

Universal Temporal Profile of Replication Origin Activation in Eukaryotes

NASA Astrophysics Data System (ADS)

Goldar, Arach

2011-03-01

The complete and faithful transmission of eukaryotic genome to daughter cells involves the timely duplication of mother cell's DNA. DNA replication starts at multiple chromosomal positions called replication origin. From each activated replication origin two replication forks progress in opposite direction and duplicate the mother cell's DNA. While it is widely accepted that in eukaryotic organisms replication origins are activated in a stochastic manner, little is known on the sources of the observed stochasticity. It is often associated to the population variability to enter S phase. We extract from a growing Saccharomyces cerevisiae population the average rate of origin activation in a single cell by combining single molecule measurements and a numerical deconvolution technique. We show that the temporal profile of the rate of origin activation in a single cell is similar to the one extracted from a replicating cell population. Taking into account this observation we exclude the population variability as the origin of observed stochasticity in origin activation. We confirm that the rate of origin activation increases in the early stage of S phase and decreases at the latter stage. The population average activation rate extracted from single molecule analysis is in prefect accordance with the activation rate extracted from published micro-array data, confirming therefore the homogeneity and genome scale invariance of dynamic of replication process. All these observations point toward a possible role of replication fork to control the rate of origin activation.

Disproportionate Tobacco Use in the Puerto Rico Lesbian, Gay, Bisexual, and Transgender Community of 18 Years and Over-A Descriptive Profile.

PubMed

Cabrera-Serrano, Alex; Felici-Giovanini, Marcos E; Díaz-Toro, Elba C; Cases-Rosario, Antonio L

2014-06-01

Tobacco use is currently one of the most critical public health issues affecting sexual and gender minority individuals. The primary objective of this research was to provide the first population-based epidemiological profile of tobacco use in the LGBT community in Puerto Rico. The secondary objective was to identify differences between LGBT smokers (LGBT-S) versus LGBT nonsmokers (LGBT-NS). We conducted a secondary data analysis of the 2011 Puerto Rico Behavioral Risk Surveillance System database through a cross-sectional study methodology. A univariate analysis was performed to obtain an epidemiological profile of the LGBT-S. Through a bivariate analysis, we compared LGBT-S with LGBT-NS to identify differences. A higher prevalence of tobacco use was found in the Puerto Rico LGBT community (20.8%) compared with the Puerto Rico general population (14.8%). The groups with higher prevalence were females (23.2%), bisexuals (23.9%), people aged 25-34 years (52.0%), people with some years in university or technical school (23.9%), people who reported being out of work for more than 1 year (45.5%), and people who reported an annual income of $50,000 or more (12.5%). LGBT-S were more likely to report a history of cancer, arthritis, kidney disease, overweight or obesity, depressive disorder, and anxiety disorder than LGBT-NS. Health surveys should incorporate sexual and gender identity questions in order to learn more about the health status of the LGBT community, especially given the disproportionate use of tobacco. The data may be useful to implement health promotion strategies related to tobacco control in this community.

Bacterial community structure in the hyperarid core of the Atacama Desert, Chile

USGS Publications Warehouse

Drees, Kevin P.; Neilson, Julia W.; Betancourt, Julio L.; Quade, Jay; Henderson, David A.; Pryor, Barry M.; Maier, Raina M.

2006-01-01

Soils from the hyperarid Atacama Desert of northern Chile were sampled along an east-west elevational transect (23.75 to 24.70 degrees S) through the driest sector to compare the relative structure of bacterial communities. Analysis of denaturing gradient gel electrophoresis (DGGE) profiles from each of the samples revealed that microbial communities from the extreme hyperarid core of the desert clustered separately from all of the remaining communities. Bands sequenced from DGGE profiles of two samples taken at a 22-month interval from this core region revealed the presence of similar populations dominated by bacteria from the Gemmatimonadetes and Planctomycetes phyla.

Motivational profiles in physical education and their relation to the theory of planned behavior.

PubMed

Moreno-Murcia, Juan Antonio; Cervelló Gimeno, Eduardo; Hernández, Elisa Huéscar; Pedreño, Noelia Belan-do; Rodríguez Marín, Jesús Jesus

2013-01-01

The aim of this study was to establish motivational profiles for doing physical activity according to the variables from the theory of planned action in a sample of 698 students aged 14 to 16. The instruments used were the Questionnaire of Behavioral Regulation in Sport (BRQ-R) and the Questionnaire of the Theory of Planned Behavior (TCP). Cluster analysis revealed two motivational profiles: a "self-determined "profile with high scores in intrinsic motivation and low scores in extrinsic motivation and amotivation, and a "non self- determined "profile with low scores in intrinsic motivation and high scores in extrinsic motivation and amotivation. Positive significant differences in attitudes, norms, and intent to control were found for the self-determined profile related to "non self-determined "profile. Key PointsA "self-determined "profile was found with higher scores for the four types of intrinsic motivations (general, knowledge, stimulation and achievement) and identified regulation than for introjected and external regulation.A "non self-determined "profile was found with higher scores for external, introjected regulation and amotivation than for the four types of intrinsic motivation (general, knowledge, stimulation and achievement).In the context of the "non self-determined profile "we could encourage programs that adapt to these needs in such a way that they contribute to increasing the rates of doing physical activity in the population.

Comparing Stellar Populations Across the Hubble Sequence

NASA Astrophysics Data System (ADS)

Loeffler, Shane; Kaleida, Catherine C.; Parkash, Vaishali

2015-01-01

Previous work (Jansen et al., 2000, Taylor et al., 2005) has revealed trends in the optical wavelength radial profiles of galaxies across the Hubble Sequence. Radial profiles offer insight into stellar populations, metallicity, and dust concentrations, aspects which are deeply tied to the individual evolution of a galaxy. The Nearby Field Galaxy Survey (NFGS) provides a sampling of nearby galaxies that spans the range of morphological types, luminosities, and masses. Currently available NFGS data includes optical radial surface profiles and spectra of 196 nearby galaxies. We aim to look for trends in the infrared portion of the spectrum for these galaxies, but find that existing 2MASS data is not sufficiently deep. Herein, we expand the available data for the NGFS galaxy IC1639 deeper into the infrared using new data taken with the Infrared Sideport Imager (ISPI) on the 4-m Blanco Telescope at the Cerro Tololo Inter-American Observatory (CTIO) in Chile. Images taken in J, H, and Ks were reduced using standard IRAF and IDL procedures. Photometric calibrations were completed by using the highest quality (AAA) 2MASS stars in the field. Aperture photometry was then performed on the galaxy and radial profiles of surface brightness, J-H color, and H-Ks color were produced. For IC1639, the new ISPI data reveals flat color gradients and surface brightness gradients that decrease with radius. These trends reveal an archetypal elliptical galaxy, with a relatively homogeneous stellar population, stellar density decreasing with radius, and little-to-no obscuration by dust. We have obtained ISPI images for an additional 8 galaxies, and further reduction and analysis of these data will allow for investigation of radial trends in the infrared for galaxies across the Hubble Sequence.

Screening for Prenatal Substance Use

PubMed Central

Yonkers, Kimberly A.; Gotman, Nathan; Kershaw, Trace; Forray, Ariadna; Howell, Heather B.; Rounsaville, Bruce J.

2011-01-01

OBJECTIVE To report on the development of a questionnaire to screen for hazardous substance use in pregnant women and to compare the performance of the questionnaire with other drug and alcohol measures. METHODS Pregnant women were administered a modified TWEAK (Tolerance, Worried, Eye-openers, Amnesia, K[C] Cut Down) questionnaire, the 4Ps Plus questionnaire, items from the Addiction Severity Index, and two questions about domestic violence (N=2,684). The sample was divided into “training” (n=1,610) and “validation” (n=1,074) subsamples. We applied recursive partitioning class analysis to the responses from individuals in the training subsample that resulted in a three-item Substance Use Risk Profile-Pregnancy scale. We examined sensitivity, specificity, and the fit of logistic regression models in the validation subsample to compare the performance of the Substance Use Risk Profile-Pregnancy scale with the modified TWEAK and various scoring algorithms of the 4Ps. RESULTS The Substance Use Risk Profile-Pregnancy scale is comprised of three informative questions that can be scored for high- or low-risk populations. The Substance Use Risk Profile-Pregnancy scale algorithm for low-risk populations was mostly highly predictive of substance use in the validation subsample (Akaike’s Information Criterion=579.75, Nagelkerke R2=0.27) with high sensitivity (91%) and adequate specificity (67%). The high-risk algorithm had lower sensitivity (57%) but higher specificity (88%). CONCLUSION The Substance Use Risk Profile-Pregnancy scale is simple and flexible with good sensitivity and specificity. The Substance Use Risk Profile-Pregnancy scale can potentially detect a range of substances that may be abused. Clinicians need to further assess women with a positive screen to identify those who require treatment for alcohol or illicit substance use in pregnancy. PMID:20859145

How convincing is a matching Y-chromosome profile?

PubMed Central

2017-01-01

The introduction of forensic autosomal DNA profiles was controversial, but the problems were successfully addressed, and DNA profiling has gone on to revolutionise forensic science. Y-chromosome profiles are valuable when there is a mixture of male-source and female-source DNA, and interest centres on the identity of the male source(s) of the DNA. The problem of evaluating evidential weight is even more challenging for Y profiles than for autosomal profiles. Numerous approaches have been proposed, but they fail to deal adequately with the fact that men with matching Y-profiles are related in extended patrilineal clans, many of which may not be represented in available databases. The higher mutation rates of modern profiling kits have led to increased discriminatory power but they have also exacerbated the problem of fairly conveying evidential value. Because the relevant population is difficult to define, yet the number of matching relatives is fixed as population size varies, it is typically infeasible to derive population-based match probabilities relevant to a specific crime. We propose a conceptually simple solution, based on a simulation model and software to approximate the distribution of the number of males with a matching Y profile. We show that this distribution is robust to different values for the variance in reproductive success and the population growth rate. We also use importance sampling reweighting to derive the distribution of the number of matching males conditional on a database frequency, finding that this conditioning typically has only a modest impact. We illustrate the use of our approach to quantify the value of Y profile evidence for a court in a way that is both scientifically valid and easily comprehensible by a judge or juror. PMID:29099833

Using forensic microsatellites to decipher the genetic structure of linguistic and geographic isolates: A survey in the eastern Italian Alps.

PubMed

Montinaro, Francesco; Boschi, Ilaria; Trombetta, Federica; Merigioli, Sara; Anagnostou, Paolo; Battaggia, Cinzia; Capocasa, Marco; Crivellaro, Federica; Destro Bisol, Giovanni; Coia, Valentina

2012-12-01

The study of geographically and/or linguistically isolated populations could represent a potential area of interaction between population and forensic genetics. These investigations may be useful to evaluate the suitability of loci which have been selected using forensic criteria for bio-anthropological studies. At the same time, they give us an opportunity to evaluate the efficiency of forensic tools for parentage testing in groups with peculiar allele frequency profiles. Within the frame of a long-term project concerning Italian linguistic isolates, we studied 15 microsatellite loci (Identifiler kit) comprising the CODIS panel in 11 populations from the north-eastern Italian Alps (Veneto, Trentino and Friuli Venezia Giulia regions). All our analyses of inter-population differentiation highlight the genetic distinctiveness of most Alpine populations comparing them either to each other or with large and non-isolated Italian populations. Interestingly, we brought to light some aspects of population genetic structure which cannot be detected using unilinear polymorphisms. In fact, the analysis of genotypic disequilibrium between loci detected signals of population substructure when all the individuals of Alpine populations are pooled in a single group. Furthermore, despite the relatively low number of loci analyzed, genetic differentiation among Alpine populations was detected at individual level using a Bayesian method to cluster multilocus genotypes. Among the various populations studied, the four linguistic minorities (Fassa Valley, Luserna, Sappada and Sauris) showed the most pronounced diversity and signatures of a peculiar genetic ancestry. Finally, we show that database replacement may affect estimates of probability of paternity even when the local database is replaced by another based on populations which share a common genetic background but which differ in their demographic history. These findings point to the importance of considering the demographic and cultural profile of populations in forensic applications, even in a context of substantial genetic homogeneity such as that of European populations. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

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

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.

Genetic structure of Cantharellus formosus populations in a second-growth temperate rain forest of the Pacific Northwest

USGS Publications Warehouse

Redman, Regina S.; Ranson, Judith; Rodriguez, Rusty J.

2006-01-01

Cantharellus formosus growing on the Olympic Peninsula of the Pacific Northwest was sampled from September – November 1995 for genetic analysis. A total of ninety-six basidiomes from five clusters separated from one another by 3 - 25 meters were genetically characterized by PCR analysis of 13 arbitrary loci and rDNA sequences. The number of basidiomes in each cluster varied from 15 to 25 and genetic analysis delineated 15 genets among the clusters. Analysis of variance utilizing thirteen apPCR generated genetic molecular markers and PCR amplification of the ribosomal ITS regions indicated that 81.41% of the genetic variation occurred between clusters and 18.59% within clusters. Proximity of the basidiomes within a cluster was not an indicator of genotypic similarity. The molecular profiles of each cluster were distinct and defined as unique populations containing 2 - 6 genets. The monitoring and analysis of this species through non-lethal sampling and future applications is discussed.

Latinos in Colorado: A Profile of Culture, Changes, and Challenges. Volume V.

ERIC Educational Resources Information Center

Pappas, Georgia, Ed.; Guajardo, Maria, Ed.

It is projected that the population of Colorado will increase by 25% between 1990 and 2000. The Latino community will experience a slight increase in the proportion of Colorado's population, and will remain the largest ethnic group over the next 30 years. The chapters in this profile describe the Latino population of Colorado. The following essays…

Population Profiles; A Series of 14 Units, Plus Extras, for the Study of Demography. Numbers 8 and 9.

ERIC Educational Resources Information Center

Lee, Everett S.; Bouvier, Leon F.

"Growth and Future of Cities" and "The Nation's Minorities" are units eight and nine, respectively from the fourteen-units series Population Profiles. The former initiates its consideration of our urban future with two divergent points of view on population distribution. Those views are brought into perspective by an historical investigation of…

Databases for rRNA gene profiling of microbial communities

DOEpatents

Ashby, Matthew

2013-07-02

The present invention relates to methods for performing surveys of the genetic diversity of a population. The invention also relates to methods for performing genetic analyses of a population. The invention further relates to methods for the creation of databases comprising the survey information and the databases created by these methods. The invention also relates to methods for analyzing the information to correlate the presence of nucleic acid markers with desired parameters in a sample. These methods have application in the fields of geochemical exploration, agriculture, bioremediation, environmental analysis, clinical microbiology, forensic science and medicine.

Study of Opacity Effects on Emission Lines at EXTRAP T2R RFP

NASA Astrophysics Data System (ADS)

Stancalie, Viorica; Rachlew, Elisabeth

We have investigated the influence of opacity on hydrogen (H-α and Ly-β) and Li-like oxygen emission lines from the EXTRAP T2R reversed field pinch. We used the Atomic Data Analysis System (AzDAS) based on the escape factor approximation for radiative transfer to calculate metastable and excited population densities via a collisional-radiative model. Population escape factor, emergent escape factor and modified line profiles are plotted vs. optical depth. The simulated emission line ratios in the density/temperature plane are in good agreement with experimental data for electron density and temperature measurements.

Diversity of Wolbachia pipientis strain wPip in a genetically admixtured, above-ground Culex pipiens (Diptera: Culicidae) population: association with form molestus ancestry and host selection patterns.

PubMed

Morningstar, Rebecca J; Hamer, Gabriel L; Goldberg, Tony L; Huang, Shaoming; Andreadis, Theodore G; Walker, Edward D

2012-05-01

Analysis of molecular genetic diversity in nine marker regions of five genes within the bacteriophage WO genomic region revealed high diversity of the Wolbachia pipentis strain wPip in a population of Culex pipiens L. sampled in metropolitan Chicago, IL. From 166 blood fed females, 50 distinct genetic profiles of wPip were identified. Rarefaction analysis suggested a maximum of 110 profiles out of a possible 512 predicted by combinations of the nine markers. A rank-abundance curve showed that few strains were common and most were rare. Multiple regression showed that markers associated with gene Gp2d, encoding a partial putative capsid protein, were significantly associated with ancestry of individuals either to form molestus or form pipiens, as determined by prior microsatellite allele frequency analysis. None of the other eight markers was associated with ancestry to either form, nor to ancestry to Cx. quinquefasciatus Say. Logistic regression of host choice (mammal vs. avian) as determined by bloodmeal analysis revealed that significantly fewer individuals that had fed on mammals had the Gp9a genetic marker (58.5%) compared with avian-fed individuals (88.1%). These data suggest that certain wPip molecular genetic types are associated with genetic admixturing in the Cx. pipiens complex of metropolitan Chicago, IL, and that the association extends to phenotypic variation related to host preference.

Laser Capture Microdissection for Protein and NanoString RNA analysis

PubMed Central

Golubeva, Yelena; Salcedo, Rosalba; Mueller, Claudius; Liotta, Lance A.; Espina, Virginia

2013-01-01

Laser capture microdissection (LCM) allows the precise procurement of enriched cell populations from a heterogeneous tissue, or live cell culture, under direct microscopic visualization. Histologically enriched cell populations can be procured by harvesting cells of interest directly, or isolating specific cells by ablating unwanted cells. The basic components of laser microdissection technology are a) visualization of cells via light microscopy, b) transfer of laser energy to a thermolabile polymer with either the formation of a polymer-cell composite (capture method) or transfer of laser energy via an ultraviolet laser to photovolatize a region of tissue (cutting method), and c) removal of cells of interest from the heterogeneous tissue section. The capture and cutting methods (instruments) for laser microdissection differ in the manner by which cells of interest are removed from the heterogeneous sample. Laser energy in the capture method is infrared (810nm), while in the cutting mode the laser is ultraviolet (355nm). Infrared lasers melt a thermolabile polymer that adheres to the cells of interest, whereas ultraviolet lasers ablate cells for either removal of unwanted cells or excision of a defined area of cells. LCM technology is applicable to an array of applications including mass spectrometry, DNA genotyping and loss-of-heterozygosity analysis, RNA transcript profiling, cDNA library generation, proteomics discovery, and signal kinase pathway profiling. This chapter describes laser capture microdissection using an ArcturusXT instrument for protein LCM sample analysis, and using a mmi CellCut Plus® instrument for RNA analysis via NanoString technology. PMID:23027006

Mutation analysis of the COL1A1 and COL1A2 genes in Vietnamese patients with osteogenesis imperfecta.

PubMed

Ho Duy, Binh; Zhytnik, Lidiia; Maasalu, Katre; Kändla, Ivo; Prans, Ele; Reimann, Ene; Märtson, Aare; Kõks, Sulev

2016-08-12

The genetics of osteogenesis imperfecta (OI) have not been studied in a Vietnamese population before. We performed mutational analysis of the COL1A1 and COL1A2 genes in 91 unrelated OI patients of Vietnamese origin. We then systematically characterized the mutation profiles of these two genes which are most commonly related to OI. Genomic DNA was extracted from EDTA-preserved blood according to standard high-salt extraction methods. Sequence analysis and pathogenic variant identification was performed with Mutation Surveyor DNA variant analysis software. Prediction of the pathogenicity of mutations was conducted using Alamut Visual software. The presence of variants was checked against Dalgleish's osteogenesis imperfecta mutation database. The sample consisted of 91 unrelated osteogenesis imperfecta patients. We identified 54 patients with COL1A1/2 pathogenic variants; 33 with COL1A1 and 21 with COL1A2. Two patients had multiple pathogenic variants. Seventeen novel COL1A1 and 10 novel COL1A2 variants were identified. The majority of identified COL1A1/2 pathogenic variants occurred in a glycine substitution (36/56, 64.3 %), usually serine (23/36, 63.9 %). We found two pathogenic variants of the COL1A1 gene c.2461G > A (p.Gly821Ser) in four unrelated patients and one, c.2005G > A (p.Ala669Thr), in two unrelated patients. Our data showed a lower number of collagen OI pathogenic variants in Vietnamese patients compared to reported rates for Asian populations. The OI mutational profile of the Vietnamese population is unique and related to the presence of a high number of recessive mutations in non-collagenous OI genes. Further analysis of OI patients negative for collagen mutations, is required.

UIT Observations of Early-Type Galaxies and Analysis of the FUSE Spectrum of a Subdwarf B Star

NASA Technical Reports Server (NTRS)

Ohl, Raymond G.; Krebs, Carolyn (Technical Monitor)

2001-01-01

This work covers Ultraviolet Imaging Telescope (UIT) observations of early-type galaxies (155 nm) and Far Ultraviolet Spectroscopic Explorer (FUSE) spectra of a Galactic subdwarf B star (sdB). Early UV space astronomy missions revealed that early-type galaxies harbor a population of stars with effective temperatures greater than that of the main sequence turn-off (about 6,000 K) and UV emission that is very sensitive to characteristics of the stellar population. We present UV (155 nm) surface photometry and UV-B color profiles for 8 E and SO galaxies observed by UIT. Some objects have de Vaucouleurs surface brightness profiles, while others have disk-like profiles, but we find no other evidence for the presence of a disk or young, massive stars. There is a wide range of UV-B color gradients, but there is no correlation with metallicity gradients. SdB stars are the leading candidate UV emitters in old, high metallicity stellar populations (e.g., early-type galaxies). We observed the Galactic sdB star PG0749+658 with FUSE and derived abundances with the aim of constraining models of the heavy element distribution in sdB atmospheres. All of the elements measured are depleted with respect to solar, except for Cr and Mn, which are about solar, and Ni, which is enhanced. This work was supported in part by NASA grants NAG5-700 and NAG5-6403 to the University of Virginia and NAS5-32985 to Johns Hopkins University.

Stem cell and neurogenic gene-expression profiles link prostate basal cells to aggressive prostate cancer

PubMed Central

Zhang, Dingxiao; Park, Daechan; Zhong, Yi; Lu, Yue; Rycaj, Kiera; Gong, Shuai; Chen, Xin; Liu, Xin; Chao, Hsueh-Ping; Whitney, Pamela; Calhoun-Davis, Tammy; Takata, Yoko; Shen, Jianjun; Iyer, Vishwanath R.; Tang, Dean G.

2016-01-01

The prostate gland mainly contains basal and luminal cells constructed as a pseudostratified epithelium. Annotation of prostate epithelial transcriptomes provides a foundation for discoveries that can impact disease understanding and treatment. Here we describe a genome-wide transcriptome analysis of human benign prostatic basal and luminal epithelial populations using deep RNA sequencing. Through molecular and biological characterizations, we show that the differential gene-expression profiles account for their distinct functional properties. Strikingly, basal cells preferentially express gene categories associated with stem cells, neurogenesis and ribosomal RNA (rRNA) biogenesis. Consistent with this profile, basal cells functionally exhibit intrinsic stem-like and neurogenic properties with enhanced rRNA transcription activity. Of clinical relevance, the basal cell gene-expression profile is enriched in advanced, anaplastic, castration-resistant and metastatic prostate cancers. Therefore, we link the cell-type-specific gene signatures to aggressive subtypes of prostate cancer and identify gene signatures associated with adverse clinical features. PMID:26924072

Stem cell and neurogenic gene-expression profiles link prostate basal cells to aggressive prostate cancer.

PubMed

Zhang, Dingxiao; Park, Daechan; Zhong, Yi; Lu, Yue; Rycaj, Kiera; Gong, Shuai; Chen, Xin; Liu, Xin; Chao, Hsueh-Ping; Whitney, Pamela; Calhoun-Davis, Tammy; Takata, Yoko; Shen, Jianjun; Iyer, Vishwanath R; Tang, Dean G

2016-02-29

The prostate gland mainly contains basal and luminal cells constructed as a pseudostratified epithelium. Annotation of prostate epithelial transcriptomes provides a foundation for discoveries that can impact disease understanding and treatment. Here we describe a genome-wide transcriptome analysis of human benign prostatic basal and luminal epithelial populations using deep RNA sequencing. Through molecular and biological characterizations, we show that the differential gene-expression profiles account for their distinct functional properties. Strikingly, basal cells preferentially express gene categories associated with stem cells, neurogenesis and ribosomal RNA (rRNA) biogenesis. Consistent with this profile, basal cells functionally exhibit intrinsic stem-like and neurogenic properties with enhanced rRNA transcription activity. Of clinical relevance, the basal cell gene-expression profile is enriched in advanced, anaplastic, castration-resistant and metastatic prostate cancers. Therefore, we link the cell-type-specific gene signatures to aggressive subtypes of prostate cancer and identify gene signatures associated with adverse clinical features.

Serum trace element differences between Schizophrenia patients and controls in the Han Chinese population.

PubMed

Cai, Lei; Chen, Tianlu; Yang, Jinglei; Zhou, Kejun; Yan, Xiaomei; Chen, Wenzhong; Sun, Liya; Li, Linlin; Qin, Shengying; Wang, Peng; Yang, Ping; Cui, Donghong; Burmeister, Margit; He, Lin; Jia, Wei; Wan, Chunling

2015-10-12

Little is known about the trace element profile differences between Schizophrenia patients and healthy controls; previous studies about the association of certain elements with Schizophrenia have obtained conflicting results. To identify these differences in the Han Chinese population, inductively coupled plasma-mass spectrometry was used to quantify the levels of 35 elements in the sera of 111 Schizophrenia patients and 110 healthy participants, which consisted of a training (61/61 for cases/controls included) and a test group including remaining participants. An orthogonal projection to latent structures model was constructed from the training group (R(2)Y = 0.465, Q(2)cum = 0.343) had a sensitivity of 76.0% and a specificity of 71.4% in the test group. Single element analysis indicated that the concentrations of cesium, zinc, and selenium were significantly reduced in patients with Schizophrenia in both the training and test groups. The meta-analysis including 522 cases and 360 controls supported that Zinc was significantly associated with Schizophrenia (standardized mean difference [SMD], -0.81; 95% confidence intervals [CI], -1.46 to -0.16, P = 0.01) in the random-effect model. Information theory analysis indicated that Zinc could play roles independently in Schizophrenia. These results suggest clear element profile differences between patients with Schizophrenia and healthy controls, and reduced Zn level is confirmed in the Schizophrenia patients.

Risk Factors for Serious Prescription Opioid-Induced Respiratory Depression or Overdose: Comparison of Commercially Insured and Veterans Health Affairs Populations

PubMed Central

Nadpara, Pramit A; Joyce, Andrew R; Murrelle, E Lenn; Carroll, Nathan W; Carroll, Norman V; Barnard, Marie; Zedler, Barbara K

2018-01-01

Abstract Objective To characterize the risk factors associated with overdose or serious opioid-induced respiratory depression (OIRD) among medical users of prescription opioids in a commercially insured population (CIP) and to compare risk factor profiles between the CIP and Veterans Health Administration (VHA) population. Subjects and Methods Analysis of data from 18,365,497 patients in the IMS PharMetrics Plus health plan claims database (CIP) who were dispensed a prescription opioid in 2009 to 2013. Baseline factors associated with an event of serious OIRD among 7,234 cases and 28,932 controls were identified using multivariable logistic regression. The CIP risk factor profile was compared with that from a corresponding logistic regression among 817 VHA cases and 8,170 controls in 2010 to 2012. Results The strongest associations with serious OIRD in CIP were diagnosed substance use disorder (odds ratio [OR] = 10.20, 95% confidence interval [CI] = 9.06–11.40) and depression (OR = 3.12, 95% CI = 2.84–3.42). Other strongly associated factors included other mental health disorders; impaired liver, renal, vascular, and pulmonary function; prescribed fentanyl, methadone, and morphine; higher daily opioid doses; and concurrent psychoactive medications. These risk factors, except depression, vascular disease, and specific opioids, largely aligned with VHA despite CIP being substantially younger, including more females and less chronic disease, and having greater prescribing prevalence of higher daily opioid doses, specific opioids, and most selected nonopioids. Conclusions Risk factor profiles for serious OIRD among US medical users of prescription opioids with private or public health insurance were largely concordant despite substantial differences between the populations in demographics, clinical conditions, health care delivery systems, and clinical practices. PMID:28419384

Risk Factors for Serious Prescription Opioid-Induced Respiratory Depression or Overdose: Comparison of Commercially Insured and Veterans Health Affairs Populations.

PubMed

Nadpara, Pramit A; Joyce, Andrew R; Murrelle, E Lenn; Carroll, Nathan W; Carroll, Norman V; Barnard, Marie; Zedler, Barbara K

2018-01-01

To characterize the risk factors associated with overdose or serious opioid-induced respiratory depression (OIRD) among medical users of prescription opioids in a commercially insured population (CIP) and to compare risk factor profiles between the CIP and Veterans Health Administration (VHA) population. Analysis of data from 18,365,497 patients in the IMS PharMetrics Plus health plan claims database (CIP) who were dispensed a prescription opioid in 2009 to 2013. Baseline factors associated with an event of serious OIRD among 7,234 cases and 28,932 controls were identified using multivariable logistic regression. The CIP risk factor profile was compared with that from a corresponding logistic regression among 817 VHA cases and 8,170 controls in 2010 to 2012. The strongest associations with serious OIRD in CIP were diagnosed substance use disorder (odds ratio [OR] = 10.20, 95% confidence interval [CI] = 9.06-11.40) and depression (OR = 3.12, 95% CI = 2.84-3.42). Other strongly associated factors included other mental health disorders; impaired liver, renal, vascular, and pulmonary function; prescribed fentanyl, methadone, and morphine; higher daily opioid doses; and concurrent psychoactive medications. These risk factors, except depression, vascular disease, and specific opioids, largely aligned with VHA despite CIP being substantially younger, including more females and less chronic disease, and having greater prescribing prevalence of higher daily opioid doses, specific opioids, and most selected nonopioids. Risk factor profiles for serious OIRD among US medical users of prescription opioids with private or public health insurance were largely concordant despite substantial differences between the populations in demographics, clinical conditions, health care delivery systems, and clinical practices. © 2017 American Academy of Pain Medicine.

Automatic genetic optimization approach to two-dimensional blade profile design for steam turbines

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

Trigg, M.A.; Tubby, G.R.; Sheard, A.G.

1999-01-01

In this paper a systematic approach to the optimization of two-dimensional blade profiles is presented. A genetic optimizer has been developed that modifies the blade profile and calculates its profile loss. This process is automatic, producing profile designs significantly faster and with significantly lower loss than has previously been possible. The optimizer developed uses a genetic algorithm to optimize a two-dimensional profile, defined using 17 parameters, for minimum loss with a given flow condition. The optimizer works with a population of two-dimensional profiles with varied parameters. A CFD mesh is generated for each profile, and the result is analyzed usingmore » a two-dimensional blade-to-blade solver, written for steady viscous compressible flow, to determine profile loss. The loss is used as the measure of a profile`s fitness. The optimizer uses this information to select the members of the next population, applying crossovers, mutations, and elitism in the process. Using this method, the optimizer tends toward the best values for the parameters defining the profile with minimum loss.« less

An abundant tissue macrophage population in the adult murine heart with a distinct alternatively-activated macrophage profile.

PubMed

Pinto, Alexander R; Paolicelli, Rosa; Salimova, Ekaterina; Gospocic, Janko; Slonimsky, Esfir; Bilbao-Cortes, Daniel; Godwin, James W; Rosenthal, Nadia A

2012-01-01

Cardiac tissue macrophages (cTMs) are a previously uncharacterised cell type that we have identified and characterise here as an abundant GFP(+) population within the adult Cx(3)cr1(GFP/+) knock-in mouse heart. They comprise the predominant myeloid cell population in the myocardium, and are found throughout myocardial interstitial spaces interacting directly with capillary endothelial cells and cardiomyocytes. Flow cytometry-based immunophenotyping shows that cTMs exhibit canonical macrophage markers. Gene expression analysis shows that cTMs (CD45(+)CD11b(+)GFP(+)) are distinct from mononuclear CD45(+)CD11b(+)GFP(+) cells sorted from the spleen and brain of adult Cx(3)cr1(GFP/+) mice. Gene expression profiling reveals that cTMs closely resemble alternatively-activated anti-inflammatory M2 macrophages, expressing a number of M2 markers, including Mrc1, CD163, and Lyve-1. While cTMs perform normal tissue macrophage homeostatic functions, they also exhibit a distinct phenotype, involving secretion of salutary factors (including IGF-1) and immune modulation. In summary, the characterisation of cTMs at the cellular and molecular level defines a potentially important role for these cells in cardiac homeostasis.

[Comparative analysis of ISSR markers polymorphism in populations of yak (Bos mutus) and in F1 hybrids between yak and cattle in the Sayan-Altai region].

PubMed

Stolpovsky, Yu A; Kol, N V; Evsyukov, A N; Nesteruk, L V; Dorzhu, Ch M; Tsendsuren, Ts; Sulimova, G E

2014-10-01

The genetic variability in seven yak populations from the Sayan-Altai region and in F1 hybrids between yak and cattle (khainags) was investigated with the help of a technique that involves the use of inter simple sequence repeat (ISSR) markers generated with PCR primers (AG)9C and (GA)9C. Samples for the analysis were collected in Mongolia, Tuva, and Altai from 2008 through 2012. The examined yak populations differed in in the presence/absence of ISSR fragments, as well as in their frequency. In total, 46 ISSR fragments were identified using two marker systems; the proportion of polymorphic loci constituted 76% and 90% for the AG-ISSR and GA-ISSR markers, respectively. For the total sample of yaks, total genetic diversity (Ht), within-population diversity (Hs), and interpopulation diversity (Gst) constituted 0.081, 0.044, and 0.459 for the AG-ISSR and 0.137, 0.057, and 0.582 for the GA-ISSR markers, respectively. Based on ISSR finger printing, species- and breed-specific DNA patterns were described for the three groups of animals (yaks, cattle, khainags). For the domestic yak, the species-specific profile was represented by eight ISSR fragments. Genetic relationships between the yak populations, cattle breeds, and khainags were examined with the help of four different approaches used in the analysis of population structure: estimation of phylogenetic similarity, multidimensional scaling, principal component analysis, and cluster analysis. Clear evidence on the differentiation of the populations examined at the interspecific, as well as at intraspecific, level were obtained. Similar (relative); as well as remote (isolated), yak populations were identified. Khainags occupy an intermediate position between yak and cattle. However, the data on the ISSR-PCR marker polymorphism (genome polymorphism, population structure).indicate that part of the analyzed khainag genome was more similar to the yak genome than to the cattle genome.

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

High-resolution metabolic mapping of cell types in plant roots

PubMed Central

Moussaieff, Arieh; Rogachev, Ilana; Brodsky, Leonid; Malitsky, Sergey; Toal, Ted W.; Belcher, Heather; Yativ, Merav; Brady, Siobhan M.; Benfey, Philip N.; Aharoni, Asaph

2013-01-01

Metabolite composition offers a powerful tool for understanding gene function and regulatory processes. However, metabolomics studies on multicellular organisms have thus far been performed primarily on whole organisms, organs, or cell lines, losing information about individual cell types within a tissue. With the goal of profiling metabolite content in different cell populations within an organ, we used FACS to dissect GFP-marked cells from Arabidopsis roots for metabolomics analysis. Here, we present the metabolic profiles obtained from five GFP-tagged lines representing core cell types in the root. Fifty metabolites were putatively identified, with the most prominent groups being glucosinolates, phenylpropanoids, and dipeptides, the latter of which is not yet explored in roots. The mRNA expression of enzymes or regulators in the corresponding biosynthetic pathways was compared with the relative metabolite abundance. Positive correlations suggest that the rate-limiting steps in biosynthesis of glucosinolates in the root are oxidative modifications of side chains. The current study presents a work flow for metabolomics analyses of cell-type populations. PMID:23476065

A phylo-functional core of gut microbiota in healthy young Chinese cohorts across lifestyles, geography and ethnicities.

PubMed

Zhang, Jiachao; Guo, Zhuang; Xue, Zhengsheng; Sun, Zhihong; Zhang, Menghui; Wang, Lifeng; Wang, Guoyang; Wang, Fang; Xu, Jie; Cao, Hongfang; Xu, Haiyan; Lv, Qiang; Zhong, Zhi; Chen, Yongfu; Qimuge, Sudu; Menghe, Bilige; Zheng, Yi; Zhao, Liping; Chen, Wei; Zhang, Heping

2015-09-01

Structural profiling of healthy human gut microbiota across heterogeneous populations is necessary for benchmarking and characterizing the potential ecosystem services provided by particular gut symbionts for maintaining the health of their hosts. Here we performed a large structural survey of fecal microbiota in 314 healthy young adults, covering 20 rural and urban cohorts from 7 ethnic groups living in 9 provinces throughout China. Canonical analysis of unweighted UniFrac principal coordinates clustered the subjects mainly by their ethnicities/geography and less so by lifestyles. Nine predominant genera, all of which are known to contain short-chain fatty acid producers, co-occurred in all individuals and collectively represented nearly half of the total sequences. Interestingly, species-level compositional profiles within these nine genera still discriminated the subjects according to their ethnicities/geography and lifestyles. Therefore, a phylogenetically diverse core of gut microbiota at the genus level may be commonly shared by distinctive healthy populations as functionally indispensable ecosystem service providers for the hosts.

A phylo-functional core of gut microbiota in healthy young Chinese cohorts across lifestyles, geography and ethnicities

PubMed Central

Zhang, Jiachao; Guo, Zhuang; Xue, Zhengsheng; Sun, Zhihong; Zhang, Menghui; Wang, Lifeng; Wang, Guoyang; Wang, Fang; Xu, Jie; Cao, Hongfang; Xu, Haiyan; Lv, Qiang; Zhong, Zhi; Chen, Yongfu; Qimuge, Sudu; Menghe, Bilige; Zheng, Yi; Zhao, Liping; Chen, Wei; Zhang, Heping

2015-01-01

Structural profiling of healthy human gut microbiota across heterogeneous populations is necessary for benchmarking and characterizing the potential ecosystem services provided by particular gut symbionts for maintaining the health of their hosts. Here we performed a large structural survey of fecal microbiota in 314 healthy young adults, covering 20 rural and urban cohorts from 7 ethnic groups living in 9 provinces throughout China. Canonical analysis of unweighted UniFrac principal coordinates clustered the subjects mainly by their ethnicities/geography and less so by lifestyles. Nine predominant genera, all of which are known to contain short-chain fatty acid producers, co-occurred in all individuals and collectively represented nearly half of the total sequences. Interestingly, species-level compositional profiles within these nine genera still discriminated the subjects according to their ethnicities/geography and lifestyles. Therefore, a phylogenetically diverse core of gut microbiota at the genus level may be commonly shared by distinctive healthy populations as functionally indispensable ecosystem service providers for the hosts. PMID:25647347

A comparative study of the risk profile of hemodialysis patients in a for profit network and in two regional registries of the Italian Society of Nephrology.

PubMed

Postorino, Maurizio; Amato, Claudia; Mancini, Elena; Carioni, Paola; D'Arrigo, Graziella; Di Benedetto, Attilio; Cerino, Fabrizio; Marino, Carmela; Vilasi, Antonio; Tripepi, Giovanni; Stuard, Stefano; Capasso, Giovanbattista; Santoro, Antonio; Zoccali, Carmine

2018-02-01

In 2013, the Italian Society of Nephrology joined forces with Nephrocare-Italy to create a clinical research cohort of patients on file in the data-rich clinical management system (EUCLID) of this organization for the performance of observational studies in the hemodialysis (HD) population. To see whether patients in EUCLID are representative of the HD population in Italy, we set out to compare the whole EUCLID population with patients included in the regional HD registries in Emilia-Romagna (Northern Italy) and in Calabria (Southern Italy), the sole regions in Italy which have systematically collected an enlarged clinical data set allowing comparison with the data-rich EUCLID system. An analysis of prevalent and incident patients in 2010 and 2011 showed that EUCLID patients had a lower prevalence of coronary heart disease, peripheral vascular disease, heart failure, valvular heart disease, liver disease, peptic ulcer and other comorbidities and risk factors and a higher fractional urea clearance (Kt/V) than those in the Emilia Romagna and Calabria registries. Accordingly, survival analysis showed a lower mortality risk in the EUCLID 2010 and 2011 cohorts than in the combined two regional registries in the corresponding years: for 2010, hazard ratio (HR) EUCLID vs. Regional registries: 0.80 [95% confidence interval: 0.71-0.90]; for 2011, HR: 0.76 [0.65-0.90]. However, this difference was nullified by statistical adjustment for the difference in comorbidities and risk factors, indicating that the longer survival in the EUCLID database was attributable to the lower risk profile of patients included in that database. This preliminary analysis sets the stage for future observational studies and indicates that appropriate adjustment for difference in comorbidities and risk factors is needed to generalize to the Italian HD population analyses based on the data-rich EUCLID database.

Gene expression profiling of human mesenchymal stem cells derived from bone marrow during expansion and osteoblast differentiation.

PubMed

Kulterer, Birgit; Friedl, Gerald; Jandrositz, Anita; Sanchez-Cabo, Fatima; Prokesch, Andreas; Paar, Christine; Scheideler, Marcel; Windhager, Reinhard; Preisegger, Karl-Heinz; Trajanoski, Zlatko

2007-03-12

Human mesenchymal stem cells (MSC) with the capacity to differentiate into osteoblasts provide potential for the development of novel treatment strategies, such as improved healing of large bone defects. However, their low frequency in bone marrow necessitate ex vivo expansion for further clinical application. In this study we asked if MSC are developing in an aberrant or unwanted way during ex vivo long-term cultivation and if artificial cultivation conditions exert any influence on their stem cell maintenance. To address this question we first developed human oligonucleotide microarrays with 30.000 elements and then performed large-scale expression profiling of long-term expanded MSC and MSC during differentiation into osteoblasts. The results showed that MSC did not alter their osteogenic differentiation capacity, surface marker profile, and the expression profiles of MSC during expansion. Microarray analysis of MSC during osteogenic differentiation identified three candidate genes for further examination and functional analysis: ID4, CRYAB, and SORT1. Additionally, we were able to reconstruct the three developmental phases during osteoblast differentiation: proliferation, matrix maturation, and mineralization, and illustrate the activation of the SMAD signaling pathways by TGF-beta2 and BMPs. With a variety of assays we could show that MSC represent a cell population which can be expanded for therapeutic applications.

A Comparative Genomic Study in Schizophrenic and in Bipolar Disorder Patients, Based on Microarray Expression Profiling Meta-Analysis

PubMed Central

Logotheti, Marianthi; Papadodima, Olga; Venizelos, Nikolaos; Chatziioannou, Aristotelis; Kolisis, Fragiskos

2013-01-01

Schizophrenia affecting almost 1% and bipolar disorder affecting almost 3%–5% of the global population constitute two severe mental disorders. The catecholaminergic and the serotonergic pathways have been proved to play an important role in the development of schizophrenia, bipolar disorder, and other related psychiatric disorders. The aim of the study was to perform and interpret the results of a comparative genomic profiling study in schizophrenic patients as well as in healthy controls and in patients with bipolar disorder and try to relate and integrate our results with an aberrant amino acid transport through cell membranes. In particular we have focused on genes and mechanisms involved in amino acid transport through cell membranes from whole genome expression profiling data. We performed bioinformatic analysis on raw data derived from four different published studies. In two studies postmortem samples from prefrontal cortices, derived from patients with bipolar disorder, schizophrenia, and control subjects, have been used. In another study we used samples from postmortem orbitofrontal cortex of bipolar subjects while the final study was performed based on raw data from a gene expression profiling dataset in the postmortem superior temporal cortex of schizophrenics. The data were downloaded from NCBI's GEO datasets. PMID:23554570

Method of LSD profile asymmetry for estimating the center of mass velocities of pulsating stars

NASA Astrophysics Data System (ADS)

Britavskiy, Nikolay; Pancino, Elena; Romano, Donatella; Tsymbal, Vadim

2015-08-01

We present radial velocity analysis for 20 solar neighborhood RR Lyrae and 3 Population II Cepheids. High-resolution spectra were observed with either TNG/SARG or VLT/UVES over varying phases. To estimate the center of mass (barycentric) velocities of the program stars, we utilized two independent methods. First, the 'classic' method was employed, which is based on RR Lyrae radial velocity curve templates. Second, we provide the new method that used absorption line profile asymmetry to determine both the pulsation and the barycentric velocities even with a low number of high-resolution spectra and in cases where the phase of the observations is uncertain. This new method is based on a Least Squares Deconvolution (LSD) of the line profiles in order to analyze line asymmetry that occurs in the spectra of pulsating stars. By applying this method to our sample stars we attain accurate measurements (± 1 km/s) of the pulsation component of the radial velocity. This results in determination of the barycentric velocity to within 5 km/s even with a low number of high-resolution spectra. A detailed investigation of LSD profile asymmetry shows the variable nature of the project factor at different pulsation phases, which should be taken into account in the detailed spectroscopic analysis of pulsating stars.

Method of LSD profile asymmetry for estimating the center of mass velocities of pulsating stars

NASA Astrophysics Data System (ADS)

Britavskiy, N.; Pancino, E.; Tsymbal, V.; Romano, D.; Cacciari, C.; Clementini, C.

2016-05-01

We present radial velocity analysis for 20 solar neighborhood RR Lyrae and 3 Population II Cepheids. High-resolution spectra were observed with either TNG/SARG or VLT/UVES over varying phases. To estimate the center of mass (barycentric) velocities of the program stars, we utilized two independent methods. First, the 'classic' method was employed, which is based on RR Lyrae radial velocity curve templates. Second, we provide the new method that used absorption line profile asymmetry to determine both the pulsation and the barycentric velocities even with a low number of high-resolution spectra and in cases where the phase of the observations is uncertain. This new method is based on a least squares deconvolution (LSD) of the line profiles in order to an- alyze line asymmetry that occurs in the spectra of pulsating stars. By applying this method to our sample stars we attain accurate measurements (+- 2 kms^-1) of the pulsation component of the radial velocity. This results in determination of the barycentric velocity to within 5 kms^-1 even with a low number of high- resolution spectra. A detailed investigation of LSD profile asymmetry shows the variable nature of the project factor at different pulsation phases, which should be taken into account in the detailed spectroscopic analysis of pulsating stars.

Environmental and Risk Factors of Leptospirosis: A Spatial Analysis in Semarang City

NASA Astrophysics Data System (ADS)

Nur Fajriyah, Silviana; Udiyono, Ari; Saraswati, Lintang Dian

2017-02-01

Leptospirosis is zoonotic potentially epidemic with clinical manifestations from mild to severe and can cause death. The incidence of leptospirosis in Indonesia tends to increase by the year. The case fatality rate in Semarang was greater than the national’s (9.38%). The purpose of this study was to describe the environmental risk factors of leptospirosis in Semarang spatially. The study design was descriptive observational with cross sectional approach. The population and samples in this study were confirmed leptospirosis in Semarang from January 2014 until May 2015, 88 respondents in 61 villages of 15 sub-districts in Semarang. The variables were environmental conditions, the presence of rats, wastewater disposal, waste disposal facilities, the presence of pets, the presence of rivers, flood’s profile, tidal inundation profile, vegetation, contact with rats, and Protected Personal Equipment/PPE utilization. Based on the spatial analysis, variables that found in the big half area of Semarang are environmental conditions, the presence of rats, wastewater disposal, waste disposal facilities, contact with rats, and PPE utilization. The presence of pets at risk, the presence of rivers, flood’s profile, inundation profile, and vegetation were found only in small half of Semarang area. People are expected to maintain their personal and environmental hygiene to prevent the transmission.

Differences in coagulation among Asians and Caucasians and the implication for reconstructive microsurgery.

PubMed

Singhal, Dhruv; Smorodinsky, Emmanuil; Guo, Lifei

2011-01-01

Microvascular reconstructive surgery has seen a revival with the introduction of muscle-sparing perforator flaps. Recognition of potential ethnic differences in coagulation profiles would be important to a microvascular surgeon. Based on clinical observations, we hypothesize that Asian patients have a less thrombogenic coagulation profile than Caucasians. An extensive retrospective review was performed. The annual incidence of venous thromboembolism in the United States is generally accepted to range from 70 to 120 events per 100,000 people versus 16 to 17 events per 100,000 persons in Asia. Autopsy analysis of pulmonary embolism incidence was noted to be 15% in North Americans and less than 1% in Asian populations. Thromboelastography analysis of Asian and Caucasian patients undergoing cholecystectomy revealed different hemostatic mechanisms. Comparison of Asians and Caucasians undergoing the Fontan procedure revealed significantly lower postoperative factor levels in Asians than Caucasians. Baseline comparison of factor and serum levels revealed Asians with the least thrombogenic profiles compared with other ethnic groups. Asians and Caucasians demonstrate different baseline rates of deep vein thrombosis and pulmonary embolism, different hemostatic responses to surgery, and different baseline levels of clotting factors. Further study may lead to better pre-, intra-, and postoperative care of the free flap patient based on their ethnic coagulation profile. © Thieme Medical Publishers.

Country Profiles, Malaysia.

ERIC Educational Resources Information Center

Marzuki, Ariffin Bin; Peng, J. Y.

A profile of Malaysia is sketched in this paper. Emphasis is placed on the nature, scope, and accomplishments of population activities in the country. Topics and sub-topics include: location and description of the country; population (size, growth patterns, age structure, urban/rural distribution, ethnic and religious composition, migration,…

Country Profiles, Jamaica.

ERIC Educational Resources Information Center

Population Council, New York, NY.

A profile of Jamaica is sketched in this paper. Emphasis is placed on the nature, scope, and accomplishments of population activities in the country. Topics and sub-topics include: location and description of the island; population - size, growth patterns, age structure, rural/urban distribution, ethnic and religious composition, literacy, future…

Country Profiles, Indonesia.

ERIC Educational Resources Information Center

Population Council, New York, NY.

A profile of Indonesia is sketched in this paper. Emphasis is placed on the nature, scope, and accomplishments of population activities in the country. Topics and sub-topics include: location and description of the country; population - size, growth patterns, age structure, urban/rural distribution, ethnic and religious composition, migration,…

Country Profiles, Taiwan.

ERIC Educational Resources Information Center

Keeny, S. M.; And Others

A profile of Taiwan is sketched in this paper. Emphasis is placed on the nature, scope, and accomplishments of population activities in the country. Topics and sub-topics include: location and description of the country; population (size, growth patterns, age structure, urban/rural distribution, ethnic and religious composition, migration,…

Taxonomic structure and monitoring of the dominant population of lactic acid bacteria during wheat flour sourdough type I propagation using Lactobacillus sanfranciscensis starters.

PubMed

Siragusa, Sonya; Di Cagno, Raffaella; Ercolini, Danilo; Minervini, Fabio; Gobbetti, Marco; De Angelis, Maria

2009-02-01

The structure and stability of the dominant lactic acid bacterium population were assessed during wheat flour sourdough type I propagation by using singly nine strains of Lactobacillus sanfranciscensis. Under back-slopping propagation with wheat flour type 0 F114, cell numbers of presumptive lactic acid bacteria varied slightly between and within starters. As determined by randomly amplified polymorphic DNA-PCR and restriction endonuclease analysis-pulsed-field gel electrophoresis analyses, only three (LS8, LS14, and LS44) starters dominated throughout 10 days of propagation. The others progressively decreased to less than 3 log CFU g(-1). Partial sequence analysis of the 16S rRNA and recA genes and PCR-denaturating gradient gel electrophoresis analysis using the rpoB gene allowed identification of Weissella confusa, Lactobacillus sanfranciscensis, Lactobacillus plantarum, Lactobacillus rossiae, Lactobacillus brevis, Lactococcus lactis subsp. lactis, Pediococcus pentosaceus, and Lactobacillus spp. as the dominant species of the raw wheat flour. At the end of propagation, one autochthonous strain of L. sanfranciscensis was found in all the sourdoughs. Except for L. brevis, strains of the above species were variously found in the mature sourdoughs. Persistent starters were found in association with other biotypes of L. sanfranciscensis and with W. confusa or L. plantarum. Sourdoughs were characterized for acidification, quotient of fermentation, free amino acids, and community-level catabolic profiles by USING Biolog 96-well Eco microplates. In particular, catabolic profiles of sourdoughs containing persistent starters behaved similarly and were clearly differentiated from the others. The three persistent starters were further used for the production of sourdoughs and propagated by using another wheat flour whose lactic acid bacterium population in part differed from the previous one. Also, in this case all three starter strains persisted during propagation.

Differential Gene Expression Profiling of Functionally and Developmentally Distinct Human Prostate Epithelial Populations

PubMed Central

Liu, Haibo; Cadaneanu, Radu M; Lai, Kevin; Zhang, Baohui; Huo, Lihong; An, Dong Sun; Li, Xinmin; Lewis, Michael S; Garraway, Isla P

2015-01-01

BACKGROUND Human fetal prostate buds appear in the 10th gestational week as solid cords, which branch and form lumens in response to androgen 1. Previous in vivo analysis of prostate epithelia isolated from benign prostatectomy specimens indicated that Epcam+CD44−CD49fHi basal cells possess efficient tubule initiation capability relative to other subpopulations 2. Stromal interactions and branching morphogenesis displayed by adult tubule-initiating cells (TIC) are reminiscent of fetal prostate development. In the current study, we evaluated in vivo tubule initiation by human fetal prostate cells and determined expression profiles of fetal and adult epithelial subpopulations in an effort to identify pathways used by TIC. METHODS Immunostaining and FACS analysis based on Epcam, CD44, and CD49f expression demonstrated the majority (99.9%) of fetal prostate epithelial cells (FC) were Epcam+CD44− with variable levels of CD49f expression. Fetal populations isolated via cell sorting were implanted into immunocompromised mice. Total RNA isolation from Epcam+CD44−CD49fHi FC, adult Epcam+CD44−CD49fHi TIC, Epcam+CD44+CD49fHi basal cells (BC), and Epcam+CD44−CD49fLo luminal cells (LC) was performed, followed by microarray analysis of 19 samples using the Affymetrix Gene Chip Human U133 Plus 2.0 Array. Data was analyzed using Partek Genomics Suite Version 6.4. Genes selected showed >2-fold difference in expression and P < 5.00E-2. Results were validated with RT-PCR. RESULTS Grafts retrieved from Epcam+CD44− fetal cell implants displayed tubule formation with differentiation into basal and luminal compartments, while only stromal outgrowths were recovered from Epcam- fetal cell implants. Hierarchical clustering revealed four distinct groups determined by antigenic profile (TIC, BC, LC) and developmental stage (FC). TIC and BC displayed basal gene expression profiles, while LC expressed secretory genes. FC had a unique profile with the most similarities to adult TIC. Functional, network, and canonical pathway identification using Ingenuity Pathway Analysis Version 7.6 compiled genes with the highest differential expression (TIC relative to BC or LC). Many of these genes were found to be significantly associated with prostate tumorigenesis. CONCLUSIONS Our results demonstrate clustering gene expression profiles of FC and adult TIC. Pathways associated with TIC are known to be deregulated in cancer, suggesting a cell-of-origin role for TIC versus re-emergence of pathways common to these cells in tumorigenesis. Prostate 75: 764–776, 2015. © The Authors. The Prostate, published by Wiley Periodicals, Inc. PMID:25663004

Differential gene expression profiling of functionally and developmentally distinct human prostate epithelial populations.

PubMed

Liu, Haibo; Cadaneanu, Radu M; Lai, Kevin; Zhang, Baohui; Huo, Lihong; An, Dong Sun; Li, Xinmin; Lewis, Michael S; Garraway, Isla P

2015-05-01

Human fetal prostate buds appear in the 10th gestational week as solid cords, which branch and form lumens in response to androgen 1. Previous in vivo analysis of prostate epithelia isolated from benign prostatectomy specimens indicated that Epcam⁺ CD44⁻ CD49f(Hi) basal cells possess efficient tubule initiation capability relative to other subpopulations 2. Stromal interactions and branching morphogenesis displayed by adult tubule-initiating cells (TIC) are reminiscent of fetal prostate development. In the current study, we evaluated in vivo tubule initiation by human fetal prostate cells and determined expression profiles of fetal and adult epithelial subpopulations in an effort to identify pathways used by TIC. Immunostaining and FACS analysis based on Epcam, CD44, and CD49f expression demonstrated the majority (99.9%) of fetal prostate epithelial cells (FC) were Epcam⁺ CD44⁻ with variable levels of CD49f expression. Fetal populations isolated via cell sorting were implanted into immunocompromised mice. Total RNA isolation from Epcam⁺ CD44⁻ CD49f(Hi) FC, adult Epcam⁺ CD44⁻ CD49f(Hi) TIC, Epcam⁺ CD44⁺ CD49f(Hi) basal cells (BC), and Epcam⁺ CD44⁻ CD49f(Lo) luminal cells (LC) was performed, followed by microarray analysis of 19 samples using the Affymetrix Gene Chip Human U133 Plus 2.0 Array. Data was analyzed using Partek Genomics Suite Version 6.4. Genes selected showed >2-fold difference in expression and P < 5.00E-2. Results were validated with RT-PCR. Grafts retrieved from Epcam⁺ CD44⁻ fetal cell implants displayed tubule formation with differentiation into basal and luminal compartments, while only stromal outgrowths were recovered from Epcam- fetal cell implants. Hierarchical clustering revealed four distinct groups determined by antigenic profile (TIC, BC, LC) and developmental stage (FC). TIC and BC displayed basal gene expression profiles, while LC expressed secretory genes. FC had a unique profile with the most similarities to adult TIC. Functional, network, and canonical pathway identification using Ingenuity Pathway Analysis Version 7.6 compiled genes with the highest differential expression (TIC relative to BC or LC). Many of these genes were found to be significantly associated with prostate tumorigenesis. Our results demonstrate clustering gene expression profiles of FC and adult TIC. Pathways associated with TIC are known to be deregulated in cancer, suggesting a cell-of-origin role for TIC versus re-emergence of pathways common to these cells in tumorigenesis. © 2015 The Authors. The Prostate, published by Wiley Periodicals, Inc.

LA-ICP-MS depth profile analysis of apatite: Protocol and implications for (U-Th)/He thermochronometry

NASA Astrophysics Data System (ADS)

Johnstone, Samuel; Hourigan, Jeremy; Gallagher, Christopher

2013-05-01

Heterogeneous concentrations of α-producing nuclides in apatite have been recognized through a variety of methods. The presence of zonation in apatite complicates both traditional α-ejection corrections and diffusive models, both of which operate under the assumption of homogeneous concentrations. In this work we develop a method for measuring radial concentration profiles of 238U and 232Th in apatite by laser ablation ICP-MS depth profiling. We then focus on one application of this method, removing bias introduced by applying inappropriate α-ejection corrections. Formal treatment of laser ablation ICP-MS depth profile calibration for apatite includes construction and calibration of matrix-matched standards and quantification of rates of elemental fractionation. From this we conclude that matrix-matched standards provide more robust monitors of fractionation rate and concentrations than doped silicate glass standards. We apply laser ablation ICP-MS depth profiling to apatites from three unknown populations and small, intact crystals of Durango fluorapatite. Accurate and reproducible Durango apatite dates suggest that prolonged exposure to laser drilling does not impact cooling ages. Intracrystalline concentrations vary by at least a factor of 2 in the majority of the samples analyzed, but concentration variation only exceeds 5x in 5 grains and 10x in 1 out of the 63 grains analyzed. Modeling of synthetic concentration profiles suggests that for concentration variations of 2x and 10x individual homogeneous versus zonation dependent α-ejection corrections could lead to age bias of >5% and >20%, respectively. However, models based on measured concentration profiles only generated biases exceeding 5% in 13 of the 63 cases modeled. Application of zonation dependent α-ejection corrections did not significantly reduce the age dispersion present in any of the populations studied. This suggests that factors beyond homogeneous α-ejection corrections are the dominant source of overdispersion in apatite (U-Th)/He cooling ages.

Physiology of Pseudomonas aeruginosa in biofilms as revealed by transcriptome analysis

PubMed Central

2010-01-01

Background Transcriptome analysis was applied to characterize the physiological activities of Pseudomonas aeruginosa grown for three days in drip-flow biofilm reactors. Conventional applications of transcriptional profiling often compare two paired data sets that differ in a single experimentally controlled variable. In contrast this study obtained the transcriptome of a single biofilm state, ranked transcript signals to make the priorities of the population manifest, and compared ranki ngs for a priori identified physiological marker genes between the biofilm and published data sets. Results Biofilms tolerated exposure to antibiotics, harbored steep oxygen concentration gradients, and exhibited stratified and heterogeneous spatial patterns of protein synthetic activity. Transcriptional profiling was performed and the signal intensity of each transcript was ranked to gain insight into the physiological state of the biofilm population. Similar rankings were obtained from data sets published in the GEO database http://www.ncbi.nlm.nih.gov/geo. By comparing the rank of genes selected as markers for particular physiological activities between the biofilm and comparator data sets, it was possible to infer qualitative features of the physiological state of the biofilm bacteria. These biofilms appeared, from their transcriptome, to be glucose nourished, iron replete, oxygen limited, and growing slowly or exhibiting stationary phase character. Genes associated with elaboration of type IV pili were strongly expressed in the biofilm. The biofilm population did not indicate oxidative stress, homoserine lactone mediated quorum sensing, or activation of efflux pumps. Using correlations with transcript ranks, the average specific growth rate of biofilm cells was estimated to be 0.08 h-1. Conclusions Collectively these data underscore the oxygen-limited, slow-growing nature of the biofilm population and are consistent with antimicrobial tolerance due to low metabolic activity. PMID:21083928

Exploratory analysis of ERCC2 DNA methylation in survival among pediatric medulloblastoma patients.

PubMed

Banfield, Emilyn; Brown, Austin L; Peckham, Erin C; Rednam, Surya P; Murray, Jeffrey; Okcu, M Fatih; Mitchell, Laura E; Chintagumpala, Murali M; Lau, Ching C; Scheurer, Michael E; Lupo, Philip J

2016-10-01

Medulloblastoma is the most frequent malignant pediatric brain tumor. While survival rates have improved due to multimodal treatment including cisplatin-based chemotherapy, there are few prognostic factors for adverse treatment outcomes. Notably, genes involved in the nucleotide excision repair pathway, including ERCC2, have been implicated in cisplatin sensitivity in other cancers. Therefore, this study evaluated the role of ERCC2 DNA methylation profiles on pediatric medulloblastoma survival. The study population included 71 medulloblastoma patients (age <18years at diagnosis) and recruited from Texas Children's Cancer Center between 2004 and 2009. DNA methylation profiles were generated from peripheral blood samples using the Illumina Infinium Human Methylation 450 Beadchip. Sixteen ERCC2-associated CpG sites were evaluated in this analysis. Multivariable regression models were used to determine the adjusted association between DNA methylation and survival. Cox regression and Kaplan-Meier curves were used to compare 5-year overall survival between hyper- and hypo-methylation at each CpG site. In total, 12.7% (n=9) of the patient population died within five years of diagnosis. In our population, methylation of the cg02257300 probe (Hazard Ratio=9.33; 95% Confidence Interval: 1.17-74.64) was associated with death (log-rank p=0.01). This association remained suggestive after correcting for multiple comparisons (FDR p<0.2). No other ERCC2-associated CpG site was associated with survival in this population of pediatric medulloblastoma patients. These findings provide the first evidence that DNA methylation within the promoter region of the ERCC2 gene may be associated with survival in pediatric medulloblastoma. If confirmed in future studies, this information may lead to improved risk stratification or promote the development of novel, targeted therapeutics. Copyright © 2016 Elsevier Ltd. All rights reserved.

Tracing the assembly history of NGC 1395 through its Globular Cluster System

NASA Astrophysics Data System (ADS)

Escudero, Carlos G.; Faifer, Favio R.; Smith Castelli, Analía V.; Forte, Juan C.; Sesto, Leandro A.; González, Nélida M.; Scalia, María C.

2018-03-01

We used deep Gemini-South/GMOS g΄r΄i΄z΄ images to study the globular cluster (GC) system of the massive elliptical galaxy NGC 1395, located in the Eridanus supergroup. The photometric analysis of the GC candidates reveals a clear colour bimodality distribution, indicating the presence of `blue' and `red' GC subpopulations. While a negative radial colour gradient is detected in the projected spatial distribution of the red GCs, the blue GCs display a shallow colour gradient. The blue GCs also display a remarkable shallow and extended surface density profile, suggesting a significant accretion of low-mass satellites in the outer halo of the galaxy. In addition, the slope of the projected spatial distribution of the blue GCs in the outer regions of the galaxy, is similar to that of the X-ray halo emission. Integrating up to 165 kpc the profile of the projected spatial distribution of the GCs, we estimated a total GC population and specific frequency of 6000 ± 1100 and SN = 7.4 ± 1.4, respectively. Regarding NGC 1395 itself, the analysis of the deep Gemini/GMOS images shows a low surface brightness umbrella-like structure indicating, at least, one recent merger event. Through relations recently published in the literature, we obtained global parameters, such as Mstellar = 9.32 × 1011 M⊙ and Mh = 6.46 × 1013 M⊙. Using public spectroscopic data, we derive stellar population parameters of the central region of the galaxy by the full spectral fitting technique. We have found that this region seems to be dominated for an old stellar population, in contrast to findings of young stellar populations from the literature.

Who are the people in your neighborhood? A descriptive analysis of individuals on public sex offender registries.

PubMed

Ackerman, Alissa R; Harris, Andrew J; Levenson, Jill S; Zgoba, Kristen

2011-01-01

Despite growing focus on registration and notification systems as central elements of national sex offender management practice, there has been remarkably little systematic analysis of the content of these registries and the diversity of individuals contained within them. Specifically, little research attention has been paid to examining the heterogeneity of the population of registered sex offenders - a circumstance that may obscure important distinctions within the population and, in turn, may undermine the ostensible purpose of SORN to prevent sexual victimization. Addressing this significant gap in our current knowledge, this article sets forth a national profile of the registered sex offender (RSO) population, drawn from an analysis of data on 445,127 RSOs obtained from the public registries of 49 states, Washington, DC, Puerto Rico and Guam. In contrast with the homogenized perception about registered sex offenders that permeates much public discourse, the analysis illuminates the wide diversity of registrants across a range of demographic, offense-related, registry status, and risk-oriented variables. Policy and practice implications concerning risk, prevention, and the public safety utility of sex offender registries are discussed. Copyright © 2011 Elsevier Ltd. All rights reserved.

Cognitive Profiles on the Severe Impairment Battery Are Similar in Alzheimer Disease and Down Syndrome With Dementia.

PubMed

Dick, Malcolm B; Doran, Eric; Phelan, Michael; Lott, Ira T

2016-01-01

Previous research has revealed similarities in the neuropathology, clinical presentation, and risk factors between persons with Alzheimer disease from the general population (GP-AD) and those with Down syndrome (DS-AD). Less is known, however, about the extent of similarities and differences in the cognitive profiles of these 2 populations. Fifty-one moderate to severely demented GP-AD and 59 DS-AD individuals participated in this study which compared the cognitive profiles of these 2 populations on the Severe Impairment Battery (SIB), controlling for sex as well as level of functional ability using a modified version of the Bristol Activities of Daily Living Scale. Overall, the neuropsychological profiles of the higher-functioning individuals within the DS-AD and advanced GP-AD groups, as represented by mean difference scores on the SIB as a whole and across the 9 separate cognitive domains, were very similar to one another after adjusting for sex and functional impairment. To our knowledge, this is the first study to directly compare the cognitive profiles of these 2 populations on the SIB. Findings suggest that the underlying dementia in GP-AD and DS-AD may have corresponding and parallel effects on cognition.

Characterization of the core rumen microbiome in cattle during transition from forage to concentrate as well as during and after an acidotic challenge.

PubMed

Petri, Renee M; Schwaiger, Tyler; Penner, Greg B; Beauchemin, Karen A; Forster, Robert J; McKinnon, John J; McAllister, Tim A

2013-01-01

This study investigated the effect of diet and host on the rumen bacterial microbiome and the impact of an acidotic challenge on its composition. Using parallel pyrosequencing of the V3 hypervariable region of 16S rRNA gene, solid and liquid associated bacterial communities of 8 heifers were profiled. Heifers were exclusively fed forage, before being transitioned to a concentrate diet, subjected to an acidotic challenge and allowed to recover. Samples of rumen digesta were collected when heifers were fed forage, mixed forage, high grain, during challenge (4 h and 12 h) and recovery. A total of 560,994 high-quality bacterial sequences were obtained from the solid and liquid digesta. Using cluster analysis, prominent bacterial populations differed (P≤0.10) in solid and liquid fractions between forage and grain diets. Differences among hosts and diets were not revealed by DGGE, but real time qPCR showed that several bacteria taxon were impacted by changes in diet, with the exception of Streptococcus bovis. Analysis of the core rumen microbiome identified 32 OTU's representing 10 distinct bacterial taxa including Bacteroidetes (32.8%), Firmicutes (43.2%) and Proteobacteria (14.3%). Diversity of OTUs was highest with forage with 38 unique OTUs identified as compared to only 11 with the high grain diet. Comparison of the microbial profiles of clincial vs. subclinical acidotic heifers found a increases in the relative abundances of Acetitomaculum, Lactobacillus, Prevotella, and Streptococcus. Increases in Streptococcus and Lactobacillus likely reflect the tolerance of these species to low pH and their ability to proliferate on surplus fermentable carbohydrate. The acetogen, Acetitomaculum may thereforeplay a role in the conversion of lactate to acetate in acidotic animals. Further profiling of the bacterial populations associated with subclinical and clinical acidosis could establish a microbial fingerprint for these disorders and provide insight into whether there are causative microbial populations that could potentially be therapeutically manipulated.

Characterization of the Core Rumen Microbiome in Cattle during Transition from Forage to Concentrate as Well as during and after an Acidotic Challenge

PubMed Central

Petri, Renee M.; Schwaiger, Tyler; Penner, Greg B.; Beauchemin, Karen A.; Forster, Robert J.; McKinnon, John J.; McAllister, Tim A.

2013-01-01

This study investigated the effect of diet and host on the rumen bacterial microbiome and the impact of an acidotic challenge on its composition. Using parallel pyrosequencing of the V3 hypervariable region of 16S rRNA gene, solid and liquid associated bacterial communities of 8 heifers were profiled. Heifers were exclusively fed forage, before being transitioned to a concentrate diet, subjected to an acidotic challenge and allowed to recover. Samples of rumen digesta were collected when heifers were fed forage, mixed forage, high grain, during challenge (4 h and 12 h) and recovery. A total of 560,994 high-quality bacterial sequences were obtained from the solid and liquid digesta. Using cluster analysis, prominent bacterial populations differed (P≤0.10) in solid and liquid fractions between forage and grain diets. Differences among hosts and diets were not revealed by DGGE, but real time qPCR showed that several bacteria taxon were impacted by changes in diet, with the exception of Streptococcus bovis. Analysis of the core rumen microbiome identified 32 OTU's representing 10 distinct bacterial taxa including Bacteroidetes (32.8%), Firmicutes (43.2%) and Proteobacteria (14.3%). Diversity of OTUs was highest with forage with 38 unique OTUs identified as compared to only 11 with the high grain diet. Comparison of the microbial profiles of clincial vs. subclinical acidotic heifers found a increases in the relative abundances of Acetitomaculum, Lactobacillus, Prevotella, and Streptococcus. Increases in Streptococcus and Lactobacillus likely reflect the tolerance of these species to low pH and their ability to proliferate on surplus fermentable carbohydrate. The acetogen, Acetitomaculum may thereforeplay a role in the conversion of lactate to acetate in acidotic animals. Further profiling of the bacterial populations associated with subclinical and clinical acidosis could establish a microbial fingerprint for these disorders and provide insight into whether there are causative microbial populations that could potentially be therapeutically manipulated. PMID:24391765

Differential Protein Expression Profiles in Glaucomatous Trabecular Meshwork: An Evaluation Study on a Small Primary Open Angle Glaucoma Population.

PubMed

Micera, Alessandra; Quaranta, Luciano; Esposito, Graziana; Floriani, Irene; Pocobelli, Augusto; Saccà, Sergio Claudio; Riva, Ivano; Manni, Gianluca; Oddone, Francesco

2016-02-01

Primary open angle glaucoma (POAG) is a progressive optic neuropathy characterized by impaired aqueous outflow and extensive remodeling in the trabecular meshwork (TM). The aim of this study was to characterize and compare the expression patterns of selected proteins belonging to the tissue remodeling, inflammation and growth factor pathways in ex vivo glaucomatous and post-mortem TMs using protein-array analysis. TM specimens were collected from 63 white subjects, including 40 patients with glaucoma and 23 controls. Forty POAG TMs were collected at the time of surgery and 23 post-mortem specimens were from non-glaucomatous donor sclerocorneal tissues. Protein profiles were evaluated using a chip-based array consisting of 60 literature-selected antibodies. A different expression of some factors was observed in POAG TMs with respect to post-mortem specimens, either in abundance (interleukin [IL]10, IL6, IL5, IL7, IL12, IL3, macrophage inflammatory protein [MIP]1δ/α, vascular endothelial growth factor [VEGF], transforming growth factor beta 1 [TGFβ1], soluble tumor necrosis factor receptor I [sTNFRI]) or in scarcity (IL16, IL18, intercellular adhesion molecule 3 [ICAM3], matrix metalloproteinase-7 [MMP7], tissue inhibitor of metalloproteinase 1 [TIMP1]). MMP2, MMP7, TGFβ1, and VEGF expressions were confirmed by Western blot, zymography, and polymerase chain reaction. No difference in protein profile expression was detected between glaucomatous subtypes. The analysis of this small TM population highlighted some proteins linked to POAG, some previously reported and others of new detection (IL7, MIPs, sTNFαRI). A larger POAG population is required to select promising disease-associated biomarker candidates. This study was partially supported by the Fondazione Roma, the Italian Ministry of Health and the "National 5xMille 2010 tax donation to IRCCS-G.B. Bietti Foundation".

Evaluation of serum levels of C-reactive protein and lipid profiles in patients with chronic periodontitis and/or coronary heart disease in an ethnic Han population.

PubMed

Liu, Juan; Wu, Yafei; Ding, Yi; Meng, Sui; Ge, Song; Deng, Hui

2010-03-01

To investigate the relationship of coronary heart disease (CHD)-associated factors-C-reactive protein (CRP) and lipid profiles-with periodontitis in an ethnic Han population. Forty healthy individuals as control, 40 patients with chronic periodontitis (CP), 28 patients with CHD, and 47 patients with both CP and CHD were included in the study. Serum CRP levels, lipid profile concentrations, and three periodontal clinical parameters (probing depth, clinical attachment level, and bleeding on probing) were measured and analyzed. The chi-square test, Student-Newman-Keuls test, analysis of covariance, and a logistic regression analysis were used in this study. The mean CRP level of patients with CP alone was 2.4 +/- 1.5 mg/L. There were significant differences in mean serum CRP levels among groups after confounders were adjusted, with CP+CHD patients having the highest level (7.3 +/- 5.7 mg/L) and the controls the lowest (1.0 +/- 0.6 mg/L) (P < .001). Mean HDL cholesterol level of CP patients (1.1 +/- 0.7 mmol/L) was significantly lower than that of controls (1.4 +/- 0.6 mmol/L) (P < .05), although it was significantly higher than that of the other two groups with CHD (0.8 +/- 0.5 mmol/L and 0.7 +/- 0.4 mmol/L) (P < .001). Significant correlations of CRP and HDL cholesterol with the three clinical periodontal parameters were apparent (P < .05). CRP and HDL cholesterol were found to be significantly associated with an increased frequency of CHD in this regression model (OR = 3.7 and OR = 1.9, respectively, P < .05). In an ethnic Han population with a low normal range of serum CRP levels, chronic periodontitis is associated with increased CRP levels and decreased HDL cholesterol concentrations, which suggests that there may be some relationship between periodontal inflammation and CHD.

Profile and Risk Factor Analysis of Unintentional Injuries in Children.

PubMed

Bhamkar, Rahul; Seth, Bageshree; Setia, Maninder Singh

2016-10-01

To study the profile and various risk factors associated with unintentional injuries in children. The study is a cross sectional analysis of data collected from 351 children presenting with unintentional injury to a tertiary care hospital in Navi Mumbai, India. Data were collected about variables based on Haddon Phase Factor Matrix - host, environment and agent factors. Proportions for categorical variables across various groups were compared using Chi square test or Fisher's exact test. Logistic regression model was used to evaluate the factors. Falls (36 %) were the most common injuries followed by bites (23 %). Majority of children were school going children (38 %) followed by preschool children (29 %). Forty-seven percent were from lower socioeconomic class. Commonest place of injury was home (48 %) and the commonest time was evening (49 %). Though there was male predominance in injuries, the difference across gender did not vary significantly (p = 0.15). Poisonings were significantly more common in infants and toddlers and in rural population (p < 0.001); kerosene being the commonest agent. Rural population is at more risk of bites compared to urban (p < 0.001); dog bites being the commonest followed by scorpion bites. Foreign bodies were significantly more common in upper and middle socioeconomic class and bites, in lower socioeconomic class (p < 0.005). Injuries from rural area and lower socioeconomic class were more serious, requiring hospitalization; they were also more likely to present late to the hospital (p < 0.05). Profile of injuries varies widely as per the variations in agent, host and environmental factors. Socio-environmental, economic conditions and infancy-toddler age groups are predisposing risk factors for bites and poisoning. Although rural areas and lower socioeconomic class population are more vulnerable to serious types of injuries, they still lack essential basic medical care.

Motivational Profiles in Physical Education and Their Relation to the Theory of Planned Behavior

PubMed Central

Moreno-Murcia, Juan Antonio; Cervelló Gimeno, Eduardo; Hernández, Elisa Huéscar; Pedreño, Noelia Belan-do; Rodríguez Marín, Jesús Jesus

2013-01-01

The aim of this study was to establish motivational profiles for doing physical activity according to the variables from the theory of planned action in a sample of 698 students aged 14 to 16. The instruments used were the Questionnaire of Behavioral Regulation in Sport (BRQ-R) and the Questionnaire of the Theory of Planned Behavior (TCP). Cluster analysis revealed two motivational profiles: a “self-determined ”profile with high scores in intrinsic motivation and low scores in extrinsic motivation and amotivation, and a “non self- determined ”profile with low scores in intrinsic motivation and high scores in extrinsic motivation and amotivation. Positive significant differences in attitudes, norms, and intent to control were found for the self-determined profile related to “non self-determined ”profile. Key Points A “self-determined ”profile was found with higher scores for the four types of intrinsic motivations (general, knowledge, stimulation and achievement) and identified regulation than for introjected and external regulation. A “non self-determined ”profile was found with higher scores for external, introjected regulation and amotivation than for the four types of intrinsic motivation (general, knowledge, stimulation and achievement). In the context of the “non self-determined profile ”we could encourage programs that adapt to these needs in such a way that they contribute to increasing the rates of doing physical activity in the population. PMID:24149164

Seasonal changes in antioxidative/oxidative profile of mining and non-mining populations of Syrian beancaper as determined by soil conditions.

PubMed

López-Orenes, Antonio; Bueso, María C; Conesa, Héctor M; Calderón, Antonio A; Ferrer, María A

2017-01-01

Soil pollution by heavy metals/metalloids (HMMs) is a problem worldwide. To prevent dispersion of contaminated particles by erosion, the maintenance of a vegetative cover is needed. Successful plant establishment in multi-polluted soils can be hampered not only by HMM toxicities, but also by soil nutrient deficiencies and the co-occurrence of abiotic stresses. Some plant species are able to thrive under these multi-stress scenarios often linked to marked fluctuations in environmental factors. This study aimed to investigate the metabolic adjustments involved in Zygophyllum fabago acclimative responses to conditions prevailing in HMM-enriched mine-tailings piles, during Mediterranean spring and summer. To this end, fully expanded leaves, and rhizosphere soil, of three contrasting mining and non-mining populations of Z. fabago grown spontaneously in south-eastern Spain were sampled in two consecutive years. Approximately 50 biochemical, physiological and edaphic parameters were examined, including leaf redox components, primary and secondary metabolites, endogenous levels of salicylic acid, and physicochemical properties of soil (fertility parameters and total concentration of HMMs). Multivariate data analysis showed a clear distinction in antioxidative/oxidative profiles between and within the populations studied. Levels of chlorophylls, proteins and proline characterized control plants whereas antioxidant capacity and C- and S-based antioxidant compounds were biomarkers of mining plants. Seasonal variations were characterized by higher levels of alkaloids and PAL and soluble peroxidase activities in summer, and by soluble sugars and hydroxycinnamic acids in spring irrespective of the population considered. Although the antioxidant systems are subjected to seasonal variations, the way and the intensity with which every population changes its antioxidative/oxidative profile seem to be determined by soil conditions. In short, Z. fabago displays a high physiological plasticity that allow it to successfully shift its metabolism to withstand the multiple stresses that plants must cope with in mine tailings piles under Mediterranean climatic conditions. Copyright © 2016 Elsevier B.V. All rights reserved.

Population Pharmacokinetics of Atazanavir in Patients with Human Immunodeficiency Virus Infection▿

PubMed Central

Colombo, Sara ; Buclin, Thierry; Cavassini, Matthias; Décosterd, Laurent A.; Telenti, Amalio; Biollaz, Jérôme; Csajka, Chantal

2006-01-01

Atazanavir (ATV) is a new azapeptide protease inhibitor recently approved and currently used at a fixed dose of either 300 mg once per day (q.d.) in combination with 100 mg ritonavir (RTV) or 400 mg q.d. without boosting. ATV is highly bound to plasma proteins and extensively metabolized by CYP3A4. Since ATV plasma levels are highly variable and seem to be correlated with both viral response and toxicity, dosage individualization based on plasma concentration monitoring might be indicated. This study aimed to assess the ATV pharmacokinetic profile in a target population of HIV patients, to characterize interpatient and intrapatient variability, and to identify covariates that might influence ATV disposition. A population analysis was performed with NONMEM with 574 plasma samples from a cohort of 214 randomly selected patients receiving ATV. A total of 346 randomly collected ATV plasma levels and 19 full concentration-time profiles at steady state were available. The pharmacokinetic parameter estimates were an oral clearance (CL) of 12.9 liters/h (coefficient of variation [CV], 26%), a volume of distribution of 88.3 liters (CV, 29%), an absorption rate constant of 0.405 h−1 (CV, 122%), and a lag time of 0.88 h. A relative bioavailability value was introduced to account for undercompliance due to infrequent follow-ups (0.81; CV, 45%). Among the covariates tested, only RTV significantly reduced CL by 46%, thereby increasing the ATV elimination half-life from 4.6 h to 8.8 h. The pharmacokinetic parameters of ATV were adequately described by a one-compartment population model. The concomitant use of RTV improved the pharmacokinetic profile. However, the remaining high interpatient variability suggests the possibility of an impact of unmeasured covariates, such as genetic traits or environmental influences. This population pharmacokinetic model, together with therapeutic drug monitoring and Bayesian dosage adaptation, can be helpful in the selection and adaptation of ATV doses. PMID:16940065

Latent classes of emotional and behavioural problems in epidemiological and referred samples and their relations to DSM-IV diagnoses.

PubMed

Bianchi, Valentina; Brambilla, Paolo; Garzitto, Marco; Colombo, Paola; Fornasari, Livia; Bellina, Monica; Bonivento, Carolina; Tesei, Alessandra; Piccin, Sara; Conte, Stefania; Perna, Giampaolo; Frigerio, Alessandra; Castiglioni, Isabella; Fabbro, Franco; Molteni, Massimo; Nobile, Maria

2017-05-01

Researchers' interest have recently moved toward the identification of recurrent psychopathological profiles characterized by concurrent elevations on different behavioural and emotional traits. This new strategy turned to be useful in terms of diagnosis and outcome prediction. We used a person-centred statistical approach to examine whether different groups could be identified in a referred sample and in a general-population sample of children and adolescents, and we investigated their relation to DSM-IV diagnoses. A latent class analysis (LCA) was performed on the Child Behaviour Checklist (CBCL) syndrome scales of the referred sample (N = 1225), of the general-population sample (N = 3418), and of the total sample. Models estimating 1-class through 5-class solutions were compared and agreement in the classification of subjects was evaluated. Chi square analyses, a logistic regression, and a multinomial logistic regression analysis were used to investigate the relations between classes and diagnoses. In the two samples and in the total sample, the best-fitting models were 4-class solutions. The identified classes were Internalizing Problems (15.68%), Severe Dysregulated (7.82%), Attention/Hyperactivity (10.19%), and Low Problems (66.32%). Subsequent analyses indicated a significant relationship between diagnoses and classes as well as a main association between the severe dysregulated class and comorbidity. Our data suggested the presence of four different psychopathological profiles related to different outcomes in terms of psychopathological diagnoses. In particular, our results underline the presence of a profile characterized by severe emotional and behavioural dysregulation that is mostly associated with the presence of multiple diagnosis.

Hydrostratigraphic analysis of the MADE site with full-resolution GPR and direct-push hydraulic profiling

USGS Publications Warehouse

Dogan, M.; Van Dam, R. L.; Bohling, Geoffrey C.; Butler, J.J.; Hyndman, D.W.

2011-01-01

Full-resolution 3D Ground-Penetrating Radar (GPR) data were combined with high-resolution hydraulic conductivity (K) data from vertical Direct-Push (DP) profiles to characterize a portion of the highly heterogeneous MAcro Dispersion Experiment (MADE) site. This is an important first step to better understand the influence of aquifer heterogeneities on observed anomalous transport. Statistical evaluation of DP data indicates non-normal distributions that have much higher similarity within each GPR facies than between facies. The analysis of GPR and DP data provides high-resolution estimates of the 3D geometry of hydrostratigraphic zones, which can then be populated with stochastic K fields. The lack of such estimates has been a significant limitation for testing and parameterizing a range of novel transport theories at sites where the traditional advection-dispersion model has proven inadequate. ?? 2011 by the American Geophysical Union.

Clinical and investigative profile of biopsy-proven sarcoid uveitis in India.

PubMed

Ganesh, Sudha K; Agarwal, Manisha

2008-01-01

Retrospective analysis of the clinical features, investigative profile, response to treatment, and final visual outcome in histopathologically confirmed cases of sarcoid uveitis. Retrospective case series analysis was done of 15 eyes of 9 patients seen between July 1999 and August 2003 with biopsy-proven sarcoid uveitis. There were 3 were males and 6 females. The mean age at presentation was 44.1 years (range 11-62 years), The mean follow-up was 28.4 months. Six patients had bilateral ocular involvement and 3 had unilateral involvement. Five out of 9 patients had primarily ocular involvement. The most common presentation was intermediate uveitis and granulomatous anterior uveitis in 7 patients. Eight of 9 patients responded well to the medical treatment with systemic and periocular steroids. Ocular lesions can be the primary manifestation of systemic sarcoidosis. Sarcoid uveitis in the Asian Indian population often presents an intermediate uveitis with granulomatous anterior uveitis.

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.

Come one, come all.

PubMed

Lee, Siu Sylvia

2004-05-05

Aging is a complex process that involves the gradual functional decline of many different tissues and cells. Gene expression microarray analysis provides a comprehensive view of the gene expression signature associated with age and is particularly valuable for understanding the molecular mechanisms that contribute to the aging process. However, because of the stochastic nature of the aging process, animals of the same chronological age often manifest great physiological differences. Therefore, profiling the gene expression pattern of a large population of aging animals risks either exaggerating or masking the changes in gene expression that correspond to physiological aging. In a recent paper, Golden and Melov surveyed the gene expression profiles of individual aging Caenorhabditis elegans, hoping to circumvent the problem of variability among worms of the same chronological age. This initial analysis of age-dependent gene expression in individual aging worms is an important step toward deciphering the molecular basis of physiological aging.

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.

Global analysis of population stratification using a smart panel of 27 continental ancestry-informative SNPs.

PubMed

Jiang, Li; Wei, Yi-Liang; Zhao, Lei; Li, Na; Liu, Tao; Liu, Hai-Bo; Ren, Li-Jie; Li, Jiu-Ling; Hao, Hui-Fang; Li, Qing; Li, Cai-Xia

2018-07-01

Over the last decade, several panels of ancestry-informative markers have been proposed for the analysis of population genetic structure. The differentiation efficiency depends on the discriminatory ability of the included markers and the reference population coverage. We previously developed a small set of 27 autosomal single nucleotide polymorphisms (SNPs) for analyzing African, European, and East Asian ancestries. In the current study, we gathered a high-coverage reference database of 110 populations (10,350 individuals) from across the globe. The discrimination power of the panel was re-evaluated using four continental ancestry groups (as well as Indigenous Americans). We observed that all the 27 SNPs demonstrated stratified population specificity leading to a striking ancestral discrimination. Five markers (rs728404, rs7170869, rs2470102, rs1448485, and rs4789193) showed differences (δ > 0.3) in the frequency profiles between East Asian and Indigenous American populations. Ancestry components of all involved populations were accurately accessed compared with those from previous genome-wide analyses, thereafter achieved broadly population separation. Thus, our ancestral inference panel of a small number of highly informative SNPs in combination with a large-scale reference database provides a high-resolution in estimating ancestry compositions and distinguishing individual origins. We propose extensive usage in biomedical studies and forensics. Copyright © 2018 Elsevier B.V. All rights reserved.

High-resolution mass spectrometry to evaluate the influence of cross-breeding segregating populations on the phenolic profile of virgin olive oils.

PubMed

Sánchez de Medina, Verónica; Calderón-Santiago, Mónica; El Riachy, Milad; Priego-Capote, Feliciano; Luque de Castro, María Dolores

2014-12-01

The growing demand for high-quality virgin olive oils (VOOs) has increased the interest in olive breeding programs. Cross-breeding is considered, within these programs, the best strategy to generate new cultivars as an attempt to improve the present cultivars. In this research, the phenolic profile of VOOs from target crosses (Arbequina × Arbosana, Picual × Koroneiki and Sikitita × Arbosana) and their corresponding genitors (Arbequina, Arbosana, Koroneiki, Picual and Sikitita) has been evaluated using a targeted metabolomics approach. The phenolic profiles were obtained by liquid chromatographic-hybrid quadrupole time-of-flight mass spectrometric targeted analysis of 37 phenols or compounds involved in the main pathways for their biosynthesis. Statistical multivariate analysis by principal component analysis was applied to study the influence of genotype on phenol composition. Phenolic compounds with the highest contribution to explain the observed variability associated to genotype were identified through fold change algorithms (cut-off > 2.0) and t-test analysis. A total of nine phenols (viz. quercetin, ligstroside aglycon (p-HPEA-EA), demethyl oleuropein aglycon, oleuropein aglycon (3,4-DHPEA-EA), hydroxypinoresinol, hydroxytyrosol and phenolic acids such as p-coumaric acid, ferulic acid and protocatechuic acid) contributed to explain the observed variability with 99% confidence (P<0.01). © 2014 Society of Chemical Industry.

Adult males with haemophilia have a different macrovascular and microvascular endothelial function profile compared with healthy controls.

PubMed

Sun, H; Yang, M; Fung, M; Chan, S; Jawi, M; Anderson, T; Poon, M-C; Jackson, S

2017-09-01

Endothelial function has been identified as an independent predictor of cardiovascular risk in the general population. It is unclear if the haemophilia population has a different endothelial function profile compared to the healthy population. This prospective study aims to assess if there is a difference in endothelial function between haemophilia patients and healthy controls, and the impact of endothelial function on vascular outcomes in the haemophilia population. Baseline cardiovascular risk factors and endothelial function were presented. Adult males with haemophilia A or B recruited from the British Columbia and Southern Alberta haemophilia treatment centres were matched to healthy male controls by age and cardiovascular risk factors. Macrovascular endothelial function was assessed by brachial artery flow-mediated dilation (FMD) and nitroglycerin-mediated dilation (NMD), and microvascular endothelial function was assessed by hyperaemic velocity time integral (VTI). Multivariable linear regression was used to assess the association between haemophilia and endothelial function. A total of 81 patients with haemophilia and 243 controls were included. Patients with haemophilia had a similar FMD and NMD compared to controls, although haemophilia was associated with higher FMD on multivariable analysis. Haemophilia was associated with significantly lower VTI on univariate and multivariable analyses, regardless of haemophilia type and severity. Adult males with haemophilia appear to have lower microvascular endothelial function compared to healthy controls. Future studies to assess the impact of endothelial dysfunction on cardiovascular events in the haemophilia population are needed. © 2017 John Wiley & Sons Ltd.

Impact of APOE gene polymorphisms on the lipid profile in an Algerian population

PubMed Central

2013-01-01

Background The importance of apolipoprotein E (APOE) in lipid and lipoprotein metabolism is well established. However, the impact of APOE polymorphisms has never been investigated in an Algerian population. This study assessed, for the fist time, the relationships between three APOE polymorphisms (epsilon, rs439401, rs4420638) and plasma lipid concentrations in a general population sample from Algeria. Methods The association analysis was performed in the ISOR study, a representative sample of the population living in Oran (787 subjects aged between 30 and 64). Polymorphisms were considered both individually and as haplotypes. Results In the ISOR sample, APOE ϵ4 allele carriers had higher plasma triglyceride (p=0.0002), total cholesterol (p=0.009) and LDL-cholesterol (p=0.003) levels than ϵ3 allele carriers. No significant associations were detected for the rs4420638 and rs439401 SNPs. Linkage disequilibrium and haplotype analyses confirmed the respectively deleterious and protective impacts of the ϵ4 and ϵ2 alleles on LDL-cholesterol levels and showed that the G allele of the rs4420638 polymorphism may exert a protective effect on LDL-cholesterol levels in subjects bearing the APOE epsilon 4 allele. Conclusion Our results showed that (i) the APOE epsilon polymorphism has the expected impact on the plasma lipid profile and (ii) the rs4420638 G allele may counterbalance the deleterious effect of the ϵ4 allele on LDL-cholesterol levels in an Algerian population. PMID:24160669

Premating isolation is determined by larval rearing substrates in cactophilic Drosophila mojavensis. IX. Host plant and population specific epicuticular hydrocarbon expression influences mate choice and sexual selection.

PubMed

Havens, J A; Etges, W J

2013-03-01

Sexual signals in cactophilic Drosophila mojavensis include cuticular hydrocarbons (CHCs), contact pheromones that mediate female discrimination of males during courtship. CHCs, along with male courtship songs, cause premating isolation between diverged populations, and are influenced by genotype × environment interactions caused by different host cacti. CHC profiles of mated and unmated adult flies from a Baja California and a mainland Mexico population of D. mojavensis reared on two host cacti were assayed to test the hypothesis that male CHCs mediate within-population female discrimination of males. In multiple choice courtship trials, mated and unmated males differed in CHC profiles, indicating that females prefer males with particular blends of CHCs. Mated and unmated females significantly differed in CHC profiles as well. Adults in the choice trials had CHC profiles that were significantly different from those in pair-mated adults from no-choice trials revealing an influence of sexual selection. Females preferred different male CHC blends in each population, but the influence of host cactus on CHC variation was significant only in the mainland population indicating population-specific plasticity in CHCs. Different groups of CHCs mediated female choice-based sexual selection in each population suggesting that geographical and ecological divergence has the potential to promote divergence in mate communication systems. © 2012 The Authors. Journal of Evolutionary Biology © 2012 European Society For Evolutionary Biology.

Specific Safety Profile of Bevacizumab in Asian Patients With Advanced NSCLC

PubMed Central

Chen, Zhenguang; Zhong, Beilong; Lun, Xueping; Lai, Yingrong; Bella, Amos Ela; Yang, Weilin; Wu, Jiabin

2015-01-01

Abstract Randomized studies have obtained varying findings regarding the benefits and toxicities of bevacizumab in the treatment of nonsmall cell lung cancer (NSCLC). It is unclear whether the discrepancies among trials are due to ethnic/racial differences. We therefore performed a meta-analysis of all published, randomized, controlled clinical trials involving bevacizumab in patients with NSCLC to assess its effectiveness and safety in Asian and non-Asian populations. Results from the phase II JO19907 trial, the phase III AVAiL and ECOG 4599 trials, and the phase IV SAiL trials were used to calculate the benefits and toxicities of bevacizumab in Asian and non-Asian patients. Combined statistical estimates, including hazard ratios and odds ratios, were calculated using fixed-effects and random-effects models. A total of 4308 patients were evaluated. Combining bevacizumab with different chemotherapy regimens resulted in similar objective response rates, overall survival, and progression-free survival in Asian and non-Asian populations. Disease control rates, however, were only reported in Asian populations. The rates of severe bleeding (relative risk [RR], 2.17; P = 0.02) and thromboembolism (RR, 3.65; P < 0.0001) were significantly higher, while the rate of severe proteinuria was significantly lower (RR, 0.43; P < 0.0001), in non-Asian than in Asian populations. The rates of severe hypertension (P = 0.71) and hemoptysis (P = 0.66) were similar in Asian and non-Asian populations. Bevacizumab combined with chemotherapy for first-line NSCLC treatment showed similar benefits in Asian and non-Asian populations, but had specific safety profiles in each. PMID:26091469

Association Studies of Specific Cholesterol Related Genes (APOE, LPL, and CETP) with Lipid Profile and Memory Function: A Correlative Study Among Rural and Tribal Population of Dharmapuri District, India.

PubMed

Periyasamy, Sabapathy; Sathya, Mohan; Karthick, Chennakesavan; Kandasamy, Mahesh; Shanmugaapriya, Sellathamby; Tamilselvan, Jeyavelu; Jayachandran, Kesavan Swaminathan; Anusuyadevi, Muthuswamy

2017-01-01

 Epidemiological studies state that dementia has multiple etiologies including genetic mutation, genetic variation, and environmental factors. Accumulating evidence suggests that dysregulation of cholesterol homeostasis is the major etiological factor in initiating neurodegeneration. Apolipoprotein E (APOE) polymorphic alleles and associated polymorphism of lipoprotein lipase (LPL) and cholesteryl ester transfer protein (CETP) that are important components in regulating cholesterol metabolism are implicated in neurodegenerative diseases. Therefore, the current study focused on identifying the association between several common polymorphism (viz., APOE, CETP, and LPL) to that of change in serum lipid levels and memory symptoms. Volunteer subjects aged 50 and above from rural and tribal areas of the Dharmapuri district, Tamilnadu, India were chosen for the current study and polymorphism was analyzed using PCR-RFLP. Fasting lipid profile and memory function using simplified version of Global Clinical Dementia rating were assessed. Significant difference in the major lipid profile parameters were observed (TC, TGL, LDL, VLDL) among rural and tribal populations that were associated with significant genotypic variation of APOE, CETP, and LPL. Regression analysis revealed significant risk for memory loss that are dependent on age and genetic variants like CETP. These data predict positive correlation between cholesterol-associated genes and their relationship to altered lipid profile and memory symptoms, which possibly link gene-polymorphism and susceptibility ratio for aging and dementia.

A New Method for Rapid Screening of End-Point PCR Products: Application to Single Genome Amplified HIV and SIV Envelope Amplicons

PubMed Central

Houzet, Laurent; Deleage, Claire; Satie, Anne-Pascale; Merlande, Laetitia; Mahe, Dominique; Dejucq-Rainsford, Nathalie

2015-01-01

PCR is the most widely applied technique for large scale screening of bacterial clones, mouse genotypes, virus genomes etc. A drawback of large PCR screening is that amplicon analysis is usually performed using gel electrophoresis, a step that is very labor intensive, tedious and chemical waste generating. Single genome amplification (SGA) is used to characterize the diversity and evolutionary dynamics of virus populations within infected hosts. SGA is based on the isolation of single template molecule using limiting dilution followed by nested PCR amplification and requires the analysis of hundreds of reactions per sample, making large scale SGA studies very challenging. Here we present a novel approach entitled Long Amplicon Melt Profiling (LAMP) based on the analysis of the melting profile of the PCR reactions using SYBR Green and/or EvaGreen fluorescent dyes. The LAMP method represents an attractive alternative to gel electrophoresis and enables the quick discrimination of positive reactions. We validate LAMP for SIV and HIV env-SGA, in 96- and 384-well plate formats. Because the melt profiling allows the screening of several thousands of PCR reactions in a cost-effective, rapid and robust way, we believe it will greatly facilitate any large scale PCR screening. PMID:26053379

Transgenerational cell fate profiling

PubMed Central

Jemaà, Mohamed; Galluzzi, Lorenzo; Kepp, Oliver; Castedo, Maria; Rello-Varona, Santiago; Vitale, Ilio; Kroemer, Guido

2013-01-01

The illicit generation of tetraploid cells constitutes a prominent driver of oncogenesis, as it often precedes the development of aneuploidy and genomic instability. In addition, tetraploid (pre-)malignant cells display an elevated resistance against radio- and chemotherapy. Here, we report a strategy to preferentially kill tetraploid tumor cells based on the broad-spectrum kinase inhibitor SP600125. Live videomicroscopy revealed that SP600125 affects the execution of mitosis, impedes proper cell division and/or activates apoptosis in near-to-tetraploid, though less so in parental, cancer cells. We propose a novel graphical model to quantify the differential response of diploid and tetraploid cells to mitotic perturbators, including SP600125, which we baptized “transgenerational cell fate profiling.” We speculate that this representation constitutes a valid alternative to classical “single-cell fate” and “genealogical” profiling and, hence, may facilitate the analysis of cell fate within a heterogeneous population as well as the visual examination of cell cycle alterations. PMID:23255111

Andromeda's dwarf spheroidals and the universal mass profile

NASA Astrophysics Data System (ADS)

Collins, Michelle; Rich, R. M.; Martin, N.; Ibata, R.; Chapman, S. C.; McConnachie, A. W.; PAndAS

2014-01-01

As the faintest, least massive galaxies we are able to observe, dwarf spheroidal galaxies represent the fundamental galactic unit. Their study in the Milky Way has led to several interesting findings and are helping us to better understand the behaviour of dark matter on the smallest scales. In this talk, I will present work from the ongoing PAndAS spectroscopic follow up survey of Andromeda, focusing on our results for its dwarf galaxy population. I will show that by including the masses measured for these objects in our analysis of the mass profiles of all dwarf galaxies, we are able to demonstrate that the notion of a universal mass profile for these most minute of galaxies is false. I will also identify several interesting objects whose properties defy our expectations, and discuss what these mean for our understanding of the physics governing galactic evolution.

A Study of the Microbial Spatial Heterogeneity of Bahamian Thrombolites Using Molecular, Biochemical, and Stable Isotope Analyses

NASA Astrophysics Data System (ADS)

Louyakis, Artemis S.; Mobberley, Jennifer M.; Vitek, Brooke E.; Visscher, Pieter T.; Hagan, Paul D.; Reid, R. Pamela; Kozdon, Reinhard; Orland, Ian J.; Valley, John W.; Planavsky, Noah J.; Casaburi, Giorgio; Foster, Jamie S.

2017-05-01

Thrombolites are buildups of carbonate that exhibit a clotted internal structure formed through the interactions of microbial mats and their environment. Despite recent advances, we are only beginning to understand the microbial and molecular processes associated with their formation. In this study, a spatial profile of the microbial and metabolic diversity of thrombolite-forming mats of Highborne Cay, The Bahamas, was generated by using 16S rRNA gene sequencing and predictive metagenomic analyses. These molecular-based approaches were complemented with microelectrode profiling and in situ stable isotope analysis to examine the dominant taxa and metabolic activities within the thrombolite-forming communities. Analyses revealed three distinctive zones within the thrombolite-forming mats that exhibited stratified populations of bacteria and archaea. Predictive metagenomics also revealed vertical profiles of metabolic capabilities, such as photosynthesis and carboxylic and fatty acid synthesis within the mats that had not been previously observed. The carbonate precipitates within the thrombolite-forming mats exhibited isotopic geochemical signatures suggesting that the precipitation within the Bahamian thrombolites is photosynthetically induced. Together, this study provides the first look at the spatial organization of the microbial populations within Bahamian thrombolites and enables the distribution of microbes to be correlated with their activities within modern thrombolite systems.

Biological and behavioral modifiers of urinary arsenic metabolic profiles in a U.S. population

EPA Science Inventory

Biological and behavioral modifiers of urinary arsenic metabolic profiles in a U.S. population David J. Thomas – ISTD, NHEERL Edward F. Hudgens – EHPD, NHEERL John Rogers - Westat Relations between intensity of arsenic exposure from home tap water and levels of inorganic As ...

Increased prevalence of metabolic syndrome in non-obese asian Indian-an urban-rural comparison.

PubMed

Mahadik, S R; Deo, S S; Mehtalia, S D

2007-06-01

In the present study we evaluated the association of insulin resistance (IR) with different components of Metabolic Syndrome (MS) in an Asian Indian population, and performed a comparative study between urban and rural populations of India. A Total of 267 urban men and women aged 25-70 years participated in this study. RESULTS were compared with rural data from a previously published study. Fasting serum insulin, uric acid, and lipid profile were measured along with fasting and 2 hour plasma glucose. Association of MS and IR was studied by using univariate regression analysis. Prevalence of MS was significantly higher in the urban population compared to that of the rural population (35.2% vs 20.6%, chi(2) = 23.2, p < 0.001). Calculated insulin resistence (HOMA-IR) was common in MS group of both populations. Percentage prevalence of IR was high and almost the same in both population (42%). Percentage prevalence of abdominal obesity and hypertriglyceridemia was significantly higher in the urban population compared to the rural population. Linear regression analysis of IR significantly correlated with different components of MS of both the population. The significant finding of the present study was that the rural population exhibited a high prevalence of MS and IR, though nonobese. IR correlated with components of MS not only in the urban but also in the rural population. To reduce the incidence of Type 2 Diabetes (T2DM) and cardiovascular disease (CVD) in our populations, early identification of populations at risk based on prevalence of MS and IR will become of prime importance.

The role of East Asian monsoon system in shaping population divergence and dynamics of a constructive desert shrub Reaumuria soongarica

PubMed Central

Yin, Hengxia; Yan, Xia; Shi, Yong; Qian, Chaoju; Li, Zhonghu; Zhang, Wen; Wang, Lirong; Li, Yi; Li, Xiaoze; Chen, Guoxiong; Li, Xinrong; Nevo, Eviatar; Ma, Xiao-Fei

2015-01-01

Both of the uplift of Qinghai-Tibet Plateau (QTP) and the development of East Asian monsoon system (EAMS) could have comprehensively impacted the formation and evolution of Arid Central Asia (ACA). To understand how desert plants endemic to ACA responded to these two factors, we profiled the historical population dynamics and distribution range shift of a constructive desert shrub Reaumuria soongarica (Tamaricaceae) based on species wide investigation of sequence variation of chloroplast DNA and nuclear ribosomal ITS. Phylogenetic analysis uncovered a deep divergence occurring at ca. 2.96 Mya between the western and eastern lineages of R. soongarica, and ecological niche modeling analysis strongly supported that the monsoonal climate could have fragmented its habitats in both glacial and interglacial periods and impelled its intraspecific divergence. Additionally, the population from the east monsoonal zone expanded rapidly, suggesting that the local monsoonal climate significantly impacted its population dynamics. The isolation by distance tests supported strong maternal gene flow along the direction of the East Asian winter monsoon, whose intensification induced the genetic admixture along the latitudinal populations of R. soongarica. Our results presented a new case that the development of EAMS had prominently impacted the intraspecific divergence and population dynamics of this desert plant. PMID:26510579

Metabolic Profiles Predict Adverse Events Following Coronary Artery Bypass Grafting

PubMed Central

Shah, Asad A.; Craig, Damian M.; Sebek, Jacqueline K.; Haynes, Carol; Stevens, Robert C.; Muehlbauer, Michael J.; Granger, Christopher B.; Hauser, Elizabeth R.; Newby, L. Kristin; Newgard, Christopher B.; Kraus, William E.; Hughes, G. Chad; Shah, Svati H.

2012-01-01

Objectives Clinical models incompletely predict outcomes following coronary artery bypass grafting. Novel molecular technologies may identify biomarkers to improve risk stratification. We examined whether metabolic profiles can predict adverse events in patients undergoing coronary artery bypass grafting. Methods The study population comprised 478 subjects from the CATHGEN biorepository of patients referred for cardiac catheterization who underwent coronary artery bypass grafting after enrollment. Targeted mass spectrometry-based profiling of 69 metabolites was performed in frozen, fasting plasma samples collected prior to surgery. Principal-components analysis and Cox proportional hazards regression modeling were used to assess the relation between metabolite factor levels and a composite outcome of post-coronary artery bypass grafting myocardial infarction, need for percutaneous coronary intervention, repeat coronary artery bypass grafting, or death. Results Over a mean follow-up of 4.3 ± 2.4 years, 126 subjects (26.4%) suffered an adverse event. Three principal-components analysis-derived factors were significantly associated with adverse outcome in univariable analysis: short-chain dicarboxylacylcarnitines (factor 2, P=0.001); ketone-related metabolites (factor 5, P=0.02); and short-chain acylcarnitines (factor 6, P=0.004). These three factors remained independently predictive of adverse outcome after multivariable adjustment: factor 2 (adjusted hazard ratio 1.23; 95% confidence interval [1.10-1.38]; P<0.001), factor 5 (1.17 [1.01-1.37], P=0.04), and factor 6 (1.14 [1.02-1.27], P=0.03). Conclusions Metabolic profiles are independently associated with adverse outcomes following coronary artery bypass grafting. These profiles may represent novel biomarkers of risk that augment existing tools for risk stratification of coronary artery bypass grafting patients and may elucidate novel biochemical pathways that mediate risk. PMID:22306227

IsomiR expression profiles in human lymphoblastoid cell lines exhibit population and gender dependencies

PubMed Central

Loher, Phillipe; Londin, Eric R.; Rigoutsos, Isidore

2014-01-01

For many years it was believed that each mature microRNA (miRNA) existed as a single entity with fixed endpoints and a ‘static’ and unchangeable primary sequence. However, recent evidence suggests that mature miRNAs are more ‘dynamic’ and that each miRNA precursor arm gives rise to multiple isoforms, the isomiRs. Here we report on our identification of numerous and abundant isomiRs in the lymphoblastoid cell lines (LCLs) of 452 men and women from five different population groups. Unexpectedly, we find that these isomiRs exhibit an expression profile that is population-dependent and gender-dependent. This is important as it indicates that the LCLs of each gender/population combination have their own unique collection of mature miRNA transcripts. Moreover, each identified isomiR has its own characteristic abundance that remains consistent across biological replicates indicating that these are not degradation products. The primary sequences of identified isomiRs differ from the known miRBase miRNA either at their 5´-endpoint (leads to a different ‘seed’ sequence and suggests a different targetome), their 3´-endpoint, or both simultaneously. Our analysis of Argonaute PAR-CLIP data from LCLs supports the association of many of these newly identified isomiRs with the Argonaute silencing complex and thus their functional roles through participation in the RNA interference pathway. PMID:25229428

IsomiR expression profiles in human lymphoblastoid cell lines exhibit population and gender dependencies.

PubMed

Loher, Phillipe; Londin, Eric R; Rigoutsos, Isidore

2014-09-30

For many years it was believed that each mature microRNA (miRNA) existed as a single entity with fixed endpoints and a 'static' and unchangeable primary sequence. However, recent evidence suggests that mature miRNAs are more 'dynamic' and that each miRNA precursor arm gives rise to multiple isoforms, the isomiRs. Here we report on our identification of numerous and abundant isomiRs in the lymphoblastoid cell lines (LCLs) of 452 men and women from five different population groups. Unexpectedly, we find that these isomiRs exhibit an expression profile that is population-dependent and gender-dependent. This is important as it indicates that the LCLs of each gender/population combination have their own unique collection of mature miRNA transcripts. Moreover, each identified isomiR has its own characteristic abundance that remains consistent across biological replicates indicating that these are not degradation products. The primary sequences of identified isomiRs differ from the known miRBase miRNA either at their 5´-endpoint (leads to a different 'seed' sequence and suggests a different targetome), their 3´-endpoint, or both simultaneously. Our analysis of Argonaute PAR-CLIP data from LCLs supports the association of many of these newly identified isomiRs with the Argonaute silencing complex and thus their functional roles through participation in the RNA interference pathway.

National profile of foot orthotic provision in the United Kingdom, part 2: podiatrist, orthotist and physiotherapy practices.

PubMed

Nester, C J; Graham, A; Martinez-Santos, A; Williams, A E; McAdam, J; Newton, V; Sweeney, D; Walker, D

2018-01-01

A national survey recently provided the first description of foot orthotic provision in the United Kingdom. This article aims to profile and compare the foot orthoses practice of podiatrists, orthotists and physiotherapists within the current provision. Quantitative data were collected from podiatrists, orthotists and physiotherapists via an online questionnaire. The topics, questions and answers were developed through a series of pilot phases. The professions were targeted through electronic and printed materials advertising the survey. Data were captured over a 10 month period in 2016. Differences between professions were investigated using Chi squared and Fischer's exact tests, and regression analysis was used to predict the likelihood of each aspect of practice in each of the three professions. Responses from 357 podiatrists, 93 orthotists and 49 physiotherapists were included in the analysis. The results reveal statistically significant differences in employment and clinical arrangements, the clinical populations treated, and the nature and volume of foot orthoses caseload. Podiatrists, orthotists and physiotherapists provide foot orthoses to important clinical populations in both a prevention and treatment capacity. Their working context, scope of practice and mix of clinical caseload differs significantly, although there are areas of overlap. Addressing variations in practice could align this collective workforce to national allied health policy.

Attitudes toward organ donation in rural areas of southeastern Spain.

PubMed

Conesa, C; Ríos, A; Ramírez, P; Cantéras, M; Rodríguez, M M; Parrilla, P

2006-04-01

Rural areas present a worse attitude toward organ donation. However, the factors conditioning this attitude are not well known. Our aim was to determine the profile of the population opposed to donation in rural areas. A random sample stratified by age and sex was obtained from municipalities with less than 10,000 inhabitants. Attitudes toward donation were assessed by a questionnaire which evaluated variables that may influence these attitudes. A descriptive statistical study used the Student t test and chi-square test as well as a logistic regression analysis. Among 181 respondents, 63% were in favor of donation and 37% against or undecided. Among the reasons to be against donation were rejection of body mutilation (43%) and fear of apparent death (41%). The psychosocial variables against donation were age >or=44 years, primary education or below, no previous experience with donation, no prosocial activities, an unfavorable opinion of the partner, and fear of corpse mutilation. The variables persisting in the multivariate analysis were level of education, previous experience, prosocial activities, and fear of corpse manipulation. Among the rural population the profile of a person opposed to donation was someone older than 44 years, with a low level of education and no previous experience with donation, who does not participate in prosocial activities and is opposed to corpse manipulation.

[Methods of use and behavior of cocaine addicts consulting medical-legal emergency units in Paris. Clinical aspects and urinary toxicology profile].

PubMed

Bécour, Bertrand; Menet, Marie-Claude; Questel, Frank; Guyon, François; Diamant-Berger, Odile

2003-03-01

Establish the epidemiological characteristics and urinary toxicological profiles of a population of cocaine addicts under police custody. A series of 60 cocaine addicts consulting the medico-legal emergency unit of the Hôtel-Dieu hospital in Paris was studied prospectively on the following elements: clinical characteristics, method of cocaine administration and association with other licit or illicit substances. Urinary toxicological analysis, using immuno-chemistry and chromatography linked to a mass spectrometer was systematically proposed to each patient. Half of the 17 to 26 year-old patients declared having consumed cocaine for the past 2 to 5 years. Inhalation of the vapours and the intravenous route were used more than the cigarette or nasal route. The majority of 26 to 35 year-olds were multi-drug addicted, generally associating cocaine, heroine and tobacco. Analysis of the urine provided an objective assessment of the cocaine consumption of these persons under police custody in Paris. Screening for urinary toxicity gives better knowledge on the consumption of addictive products by the person in whom urine was sampled. This study was conducted in cocaine addicts under police custody, and for the majority were social misfits. In this population, the consumption of crack by inhalation predominated.

Toward Exploring the Synergy Between Cloud Radar Polarimetry and Doppler Spectral Analysis in Deep Cold Precipitating Systems in the Arctic

NASA Astrophysics Data System (ADS)

Oue, Mariko; Kollias, Pavlos; Ryzhkov, Alexander; Luke, Edward P.

2018-03-01

The study of Arctic ice and mixed-phase clouds, which are characterized by a variety of ice particle types in the same cloudy volume, is challenging research. This study illustrates a new approach to qualitative and quantitative analysis of the complexity of ice and mixed-phase microphysical processes in Arctic deep precipitating systems using the combination of Ka-band zenith-pointing radar Doppler spectra and quasi-vertical profiles of polarimetric radar variables measured by a Ka/W-band scanning radar. The results illustrate the frequent occurrence of multimodal Doppler spectra in the dendritic/planar growth layer, where locally generated, slower-falling particle populations are well separated from faster-falling populations in terms of Doppler velocity. The slower-falling particle populations contribute to an increase of differential reflectivity (ZDR), while an enhanced specific differential phase (KDP) in this dendritic growth temperature range is caused by both the slower and faster-falling particle populations. Another area with frequent occurrence of multimodal Doppler spectra is in mixed-phase layers, where both populations produce ZDR and KDP values close to 0, suggesting the occurrence of a riming process. Joint analysis of the Doppler spectra and the polarimetric radar variables provides important insight into the microphysics of snow formation and allows the separation of the contributions of ice of different habits to the values of reflectivity and ZDR.

Prescreening of microbial populations for the assessment of sequencing potential.

PubMed

Hanning, Irene B; Ricke, Steven C

2011-01-01

Next-generation sequencing (NGS) is a powerful tool that can be utilized to profile and compare microbial populations. By amplifying a target gene present in all bacteria and subsequently sequencing amplicons, the bacteria genera present in the populations can be identified and compared. In some scenarios, little to no difference may exist among microbial populations being compared in which case a prescreening method would be practical to determine which microbial populations would be suitable for further analysis by NGS. Denaturing density-gradient electrophoresis (DGGE) is relatively cheaper than NGS and the data comparing microbial populations are ready to be viewed immediately after electrophoresis. DGGE follows essentially the same initial methodology as NGS by targeting and amplifying the 16S rRNA gene. However, as opposed to sequencing amplicons, DGGE amplicons are analyzed by electrophoresis. By prescreening microbial populations with DGGE, more efficient use of NGS methods can be accomplished. In this chapter, we outline the protocol for DGGE targeting the same gene (16S rRNA) that would be targeted for NGS to compare and determine differences in microbial populations from a wide range of ecosystems.

Transition to an aging Japan: public pension, savings, and capital taxation.

PubMed

Kato, R

1998-09-01

This study examined options for compensating for the shortages of money for public pensions due to population aging in Japan: increases in pension contributions, consumption pension taxes, interest income pension taxes, and inheritance pension taxes. The analysis relied on simulation in an expanded life cycle growth model. Data were obtained from 1992 estimations of population by the Institute of Population Problems of the Ministry of Health and Welfare. This study is unique in its use of real population data for the simulations and in its use of transition states. The analysis begins with a description of the altered Overlapping Generations Model by Auerback and Kotlikoff (1983). The model accounts for the inaccuracy of lifetime and liquidity constraints and ordinary budget constraints and reproduces the consumption-savings profiles of older people and incorporates wage income taxation and other forms of taxation. Income includes wage and interest income. The analysis includes a description of the method of simulation, assumptions, and evaluation of the effects of population aging. It is assumed that narrower government sector spending on general expenditures per worker will increase by 1% every year. It is concluded that national saving rates will probably decrease due to population aging. The lowest levels of capital stock and savings will result from higher pension contributions. The highest level of capital stock will result from higher consumption pension taxes during 1990-2015. Preferred policies should focus on increasing interest income rates.

Qualifications and Competencies for Population Health Management Positions: A Content Analysis of Job Postings.

PubMed

Meyer, Melanie

2017-12-01

The need for population health management expertise has increased as the health care industry shifts toward value-based care. However, many organizations report hiring gaps as they seek to fill positions. The purpose of this study was to analyze the types of population health management positions for which health care organizations are hiring, including qualifications and competencies required for these positions. A content analysis was conducted on 271 job postings collected during a 2-month period. A typology of qualifications and competencies was developed based on the content analysis. Profiles were generated for the top 5 job title classifications: directors, coordinators, care managers, analysts, and specialists. This study highlights the investment health care organizations are making in population health management and the prominent role these positions are playing in the health care environment today. Many organizations are building out population health management teams resulting in multiple positions at different levels being added. As the market demands competent candidates who are equipped with specialized population health expertise as well as practical experience in program development, technology applications, care management, and analytics, professional education programs will need to adapt curricula to address the required areas. Competencies for specific job title classifications may need further evaluation and refinement over time. Study results can be used by organizations for strategic planning, by educators to target needed qualifications and competencies, and by researchers and policy advisors to assess progress toward value-based care.

Characterization of the genetic variation present in CYP3A4 in three South African populations.

PubMed

Drögemöller, Britt; Plummer, Marieth; Korkie, Lundi; Agenbag, Gloudi; Dunaiski, Anke; Niehaus, Dana; Koen, Liezl; Gebhardt, Stefan; Schneider, Nicol; Olckers, Antonel; Wright, Galen; Warnich, Louise

2013-01-01

The CYP3A4 enzyme is the most abundant human cytochrome P450 (CYP) and is regarded as the most important enzyme involved in drug metabolism. Inter-individual and inter-population variability in gene expression and enzyme activity are thought to be influenced, in part, by genetic variation. Although Southern African individuals have been shown to exhibit the highest levels of genetic diversity, they have been under-represented in pharmacogenetic research to date. Therefore, the aim of this study was to identify genetic variation within CYP3A4 in three South African population groups comprising of 29 Khoisan, 65 Xhosa and 65 Mixed Ancestry (MA) individuals. To identify known and novel CYP3A4 variants, 15 individuals were randomly selected from each of the population groups for bi-directional Sanger sequencing of ~600 bp of the 5'-upstream region and all thirteen exons including flanking intronic regions. Genetic variants detected were genotyped in the rest of the cohort. In total, 24 SNPs were detected, including CYP3A4(*)12, CYP3A4(*)15, and the reportedly functional CYP3A4(*)1B promoter polymorphism, as well as two novel non-synonymous variants. These putatively functional variants, p.R162W and p.Q200H, were present in two of the three populations and all three populations, respectively, and in silico analysis predicted that the former would damage the protein product. Furthermore, the three populations were shown to exhibit distinct genetic profiles. These results confirm that South African populations show unique patterns of variation in the genes encoding xenobiotic metabolizing enzymes. This research suggests that population-specific genetic profiles for CYP3A4 and other drug metabolizing genes would be essential to make full use of pharmacogenetics in Southern Africa. Further investigation is needed to determine if the identified genetic variants influence CYP3A4 metabolism phenotype in these populations.

Gene Expression Profiling of Peripheral Blood From Kidney Transplant Recipients for the Early Detection of Digestive System Cancer.

PubMed

Kusaka, M; Okamoto, M; Takenaka, M; Sasaki, H; Fukami, N; Kataoka, K; Ito, T; Kenmochi, T; Hoshinaga, K; Shiroki, R

2017-06-01

Kidney transplant recipients are at increased risk of developing cancer in comparison with the general population. To effectively manage post-transplantation malignancies, it is essential to proactively monitor patients. A long-term intensive screening program was associated with a reduced incidence of cancer after transplantation. This study evaluated the usefulness of the gene expression profiling of peripheral blood samples obtained from kidney transplant patients and adopted a screening test for detecting cancer of the digestive system (gastric, colon, pancreas, and biliary tract). Nineteen patients were included in this study and a total of 53 gene expression screening tests were performed. The gene expression profiles of blood-delivered total RNA and whole genome human gene expression profiles were obtained. We investigated the expression levels of 2665 genes associated with digestive cancers and counted the number of genes in which expression was altered. A hierarchical clustering analysis was also performed. The final prediction of the cancer possibility was determined according to an algorithm. The number of genes in which expression was altered was significantly increased in the kidney transplant recipients in comparison with the general population (1091 ± 63 vs 823 ± 94; P = .0024). The number of genes with altered expression decreased after the induction of mechanistic target of rapamycin (mTOR) inhibitor (1484 ± 227 vs 883 ± 154; P = .0439). No cases of possible digestive cancer were detected in this study period. The gene expression profiling of peripheral blood samples may be a useful and noninvasive diagnostic tool that allows for the early detection of cancer of the digestive system. Copyright © 2017 Elsevier Inc. All rights reserved.

Analysis of cellular autofluorescence in touch samples by flow cytometry: implications for front end separation of trace mixture evidence.

PubMed

Katherine Philpott, M; Stanciu, Cristina E; Kwon, Ye Jin; Bustamante, Eduardo E; Greenspoon, Susan A; Ehrhardt, Christopher J

2017-07-01

The goal of this study was to survey optical and biochemical variation in cell populations deposited onto a surface through touch or contact and identify specific features that may be used to distinguish and then sort cell populations from separate contributors in a trace biological mixture. Although we were not able to detect meaningful biochemical variation in touch samples deposited by different contributors through preliminary antibody surveys, we did observe distinct differences in red autofluorescence emissions (650-670 nm), with as much as a tenfold difference in mean fluorescence intensities observed between certain pairs of donors. Results indicate that the level of red autofluorescence in touch samples can be influenced by a donor's contact with specific material prior to handling the substrate from which cells were collected. In particular, we observed increased red autofluorescence in cells deposited subsequent to handling laboratory gloves, plant material, and certain types of marker ink, which could be easily visualized microscopically or using flow cytometry, and persisted after hand washing. To test whether these observed optical differences could potentially be used as the basis for a cell separation workflow, a controlled two-person touch mixture was separated into two fractions via fluorescence-activated cell sorting (FACS) using gating criteria based on intensity of 650-670 nm emissions and then subjected to DNA analysis. Genetic analysis of the sorted fractions provided partial DNA profiles that were consistent with separation of individual contributors from the mixture suggesting that variation in autofluorescence signatures, even if driven by extrinsic factors, may nonetheless be a useful means of isolating contributors to some touch mixtures. Graphical Abstract Conceptual workflow diagram. Trace biological mixtures containing cells from multiple individuals are analyzed by flow cytometry. Cells are then physically separated into two populations based on intensity of red autofluorescence using Fluorescence Activated Cell Sorting. Each isolated cell fraction is subjected to DNA analysis resulting in a DNA profile for each contributor.

Two different approaches to the affective profiles model: median splits (variable-oriented) and cluster analysis (person-oriented).

PubMed

Garcia, Danilo; MacDonald, Shane; Archer, Trevor

2015-01-01

Background. The notion of the affective system as being composed of two dimensions led Archer and colleagues to the development of the affective profiles model. The model consists of four different profiles based on combinations of individuals' experience of high/low positive and negative affect: self-fulfilling, low affective, high affective, and self-destructive. During the past 10 years, an increasing number of studies have used this person-centered model as the backdrop for the investigation of between and within individual differences in ill-being and well-being. The most common approach to this profiling is by dividing individuals' scores of self-reported affect using the median of the population as reference for high/low splits. However, scores just-above and just-below the median might become high and low by arbitrariness, not by reality. Thus, it is plausible to criticize the validity of this variable-oriented approach. Our aim was to compare the median splits approach with a person-oriented approach, namely, cluster analysis. Method. The participants (N = 2, 225) were recruited through Amazons' Mechanical Turk and asked to self-report affect using the Positive Affect Negative Affect Schedule. We compared the profiles' homogeneity and Silhouette coefficients to discern differences in homogeneity and heterogeneity between approaches. We also conducted exact cell-wise analyses matching the profiles from both approaches and matching profiles and gender to investigate profiling agreement with respect to affectivity levels and affectivity and gender. All analyses were conducted using the ROPstat software. Results. The cluster approach (weighted average of cluster homogeneity coefficients = 0.62, Silhouette coefficients = 0.68) generated profiles with greater homogeneity and more distinctive from each other compared to the median splits approach (weighted average of cluster homogeneity coefficients = 0.75, Silhouette coefficients = 0.59). Most of the participants (n = 1,736, 78.0%) were allocated to the same profile (Rand Index = .83), however, 489 (21.98%) were allocated to different profiles depending on the approach. Both approaches allocated females and males similarly in three of the four profiles. Only the cluster analysis approach classified men significantly more often than chance to a self-fulfilling profile (type) and females less often than chance to this very same profile (antitype). Conclusions. Although the question whether one approach is more appropriate than the other is still without answer, the cluster method allocated individuals to profiles that are more in accordance with the conceptual basis of the model and also to expected gender differences. More importantly, regardless of the approach, our findings suggest that the model mirrors a complex and dynamic adaptive system.

Evolution and Determinants of Health-Related Quality-of-Life in Kidney Transplant Patients Over the First 3 Years After Transplantation.

PubMed

Villeneuve, Claire; Laroche, Marie-Laure; Essig, Marie; Merville, Pierre; Kamar, Nassim; Coubret, Anne; Lacroix, Isabelle; Bouchet, Stéphane; Fruit, Dorothée; Marquet, Pierre; Rousseau, Annick

2016-03-01

Health-related quality of life (HRQOL) usually improved after kidney transplantation; however, a non-negligible number of patients did not benefit from transplantation in HRQOL. The aims of this cohort study were to describe the evolution of HRQOL in kidney transplant recipients to search for subgroups with distinct time profiles and to investigate these determinants. Three hundred thirty-seven adult patients were followed up from 1 to 36 months after kidney transplantation. Each patient completed repeated HRQOL assessments (median, 5; range, 2-9). K-means for longitudinal data was used to identify homogeneous clusters of HRQOL time profiles obtained for the mental and physical composite scores (MCS and PCS) and for the 8 dimensions of the short-form 36 scale. Covariates associated with these clusters were investigated using random forest analysis. Magnitude and shape of the HRQOL variations over time were investigated using linear regression mixed models. Two longitudinal clusters were identified for the time profiles of PCS and MCS. Patients classified in the higher cluster (ie, 60% of the population) exhibited a steady-state HRQOL, similar on average to the general population, whereas in the lower cluster, PCS and MCS scores were significantly lower than in the general population. Muscular weakness in the first year after transplantation explained 19% of the interpatient variability of PCS 3 months after transplantation, whereas associated with anxiety, it explained 24% of interpatient MCS variability. This work suggests to promote (i) physical rehabilitation programs after transplantation to curb the muscular loss and (ii) systematic attention to the patient's anxiety.

No association of apolipoprotein B gene polymorphism and blood lipids in obese Egyptian subjects.

PubMed

Bogari, Neda M; Abdel-Latif, Azza M; Hassan, Maha A; Ramadan, Abeer; Fawzy, Ahmed

2015-03-18

Several environmental and genetic factors are associated with high levels of lipids in obese patients. Apolipoprotein B (ApoB) is the major protein component of low-density lipoproteins (LDL), very-low density lipoproteins (VLDL) and chylomicrons and plays a central role in lipid metabolism. Several apoB restriction fragment length polymorphisms (XbaI, EcoRI, MspI) have been reported to be associated with variation in lipid levels and obesity. To date, no data are available on the relationship between XbaI polymorphism and lipid levels in Egyptian populations. Following clinical profiling, 178 obese (body mass index [BMI] >25 kg/m(2)) and 178 age-matched non-obese (BMI ≤ 25 kg/m(2)) subjects were included in this case-control study. All samples were analysed for total cholesterol, triglycerides and HDL-cholesterol. Genetic analysis of apoB XbaI (X) was performed using Polymerase Chain Reaction-Restriction Fragment Length polymorphism (PCR-RFLP). The aim of this study was to assess the association of apoB XbaI gene polymorphism (X) and lipid profiles in obese and non-obese Egyptian populations. Obese subjects demonstrated significantly higher values of waist-to-hip ratio, blood pressure, and total lipid. However, in our sample we did not find significant differences in apoB XbaI gene polymorphism (X) genotype or allele frequencies. Moreover, none of the studied lipid parameters showed any association with the gene polymorphism. This study reveals no significant association of apoB XbaI gene polymorphism (X) with obesity or lipid profiles in an Egyptian population.

Characterisation of the chemical profiles of Brazilian and Andean morphotypes belonging to the Anastrepha fraterculus complex (Diptera, Tephritidae)

PubMed Central

Vaníčková, Lucie; Břízová, Radka; Pompeiano, Antonio; Ferreira, Luana Lima; de Aquino, Nathaly Costa; Tavares, Raphael de Farias; Rodriguez, Laura D.; Mendonça, Adriana de Lima; Canal, Nelson Augusto; do Nascimento, Ruth Rufino

2015-01-01

Abstract Fruit fly sexual behaviour is directly influenced by chemical and non-chemical cues that play important roles in reproductive isolation. The chemical profiles of pheromones and cuticular hydrocarbons (CHs) of eight fruit fly populations of the Andean, Brazilian-1 and Brazilian-3 morphotypes of the Anastrepha fraterculus cryptic species complex originating from Colombia (four populations) and Brazil (four populations) were analysed using two-dimensional gas chromatography with mass spectrometric detection. The resulting chemical diversity data were studied using principal component analyses. Andean morphotypes could be discriminated from the Brazilian-1 and Brazilian-3 morphotypes by means of male-borne pheromones and/or male and female CH profiles. The Brazilian-1 and Brazilian-3 morphotypes were found to be monophyletic. The use of chemical profiles as species- and sex-specific signatures for cryptic species separations is discussed. PMID:26798260

Single cell gene expression profiling of cortical osteoblast lineage cells.

PubMed

Flynn, James M; Spusta, Steven C; Rosen, Clifford J; Melov, Simon

2013-03-01

In tissues with complex architectures such as bone, it is often difficult to purify and characterize specific cell types via molecular profiling. Single cell gene expression profiling is an emerging technology useful for characterizing transcriptional profiles of individual cells isolated from heterogeneous populations. In this study we describe a novel procedure for the isolation and characterization of gene expression profiles of single osteoblast lineage cells derived from cortical bone. Mixed populations of different cell types were isolated from adult long bones of C57BL/6J mice by enzymatic digestion, and subsequently subjected to FACS to purify and characterize osteoblast lineage cells via a selection strategy using antibodies against CD31, CD45, and alkaline phosphatase (AP), specific for mature osteoblasts. The purified individual osteoblast lineage cells were then profiled at the single cell level via nanofluidic PCR. This method permits robust gene expression profiling on single osteoblast lineage cells derived from mature bone, potentially from anatomically distinct sites. In conjunction with this technique, we have also shown that it is possible to carry out single cell profiling on cells purified from fixed and frozen bone samples without compromising the gene expression signal. The latter finding means the technique can be extended to biopsies of bone from diseased individuals. Our approach for single cell expression profiling provides a new dimension to the transcriptional profile of the primary osteoblast lineage population in vivo, and has the capacity to greatly expand our understanding of how these cells may function in vivo under normal and diseased states. Copyright © 2012 Elsevier Inc. All rights reserved.

Population genetics of Enterocytozoon bieneusi in captive giant pandas of China.

PubMed

Li, Wei; Song, Yuan; Zhong, Zhijun; Huang, Xiangming; Wang, Chengdong; Li, Caiwu; Yang, Haidi; Liu, Haifeng; Ren, Zhihua; Lan, Jingchao; Wu, Kongju; Peng, Guangneng

2017-10-18

Most studies on Enterocytozoon bieneusi are conducted based on the internal transcribed spacer (ITS) region of the rRNA gene, whereas some have examined E. bieneusi population structures. Currently, the population genetics of this pathogen in giant panda remains unknown. The objective of this study was to determine the E. bieneusi population in captive giant pandas in China. We examined 69 E. bieneusi-positive specimens from captive giant pandas in China using five loci (ITS, MS1, MS3, MS4 and MS7) to infer E. bieneusi population genetics. For multilocus genotype (MLG) analysis of E. bieneusi-positive isolates, the MS1, MS3, MS4, and MS7 microsatellite and minisatellite loci were amplified and sequenced in 48, 45, 50 and 47 specimens, respectively, generating ten, eight, nine and five types. We successfully amplified 36 specimens and sequenced all five loci, forming 24 MLGs. Multilocus sequence analysis revealed a strong and significant linkage disequilibrium (LD), indicating a clonal population. This result was further supported by measurements of pairwise intergenic LD and a standardized index of association (I S A ) from allelic profile data. The analysis in STRUCTURE suggested three subpopulations in E. bieneusi, further confirmed using right's fixation index (F ST ). Subpopulations 1 and 2 exhibited an epidemic structure, whereas subpopulation 3 had a clonal structure. Our results describe E. bieneusi population genetics in giant pandas for the first time, improving the current understanding E. bieneusi epidemiology in the studied region. These data also benefit future studies exploring potential transmission risks from pandas to other animals, including humans.

Gut bacterial diversity of the tribes of India and comparison with the worldwide data

PubMed Central

Dehingia, Madhusmita; Thangjam devi, Kanchal; Talukdar, Narayan C.; Talukdar, Rupjyoti; Reddy, Nageshwar; Mande, Sharmila S.; Deka, Manab; Khan, Mojibur R.

2015-01-01

The gut bacteria exert phenotypic traits to the host but the factors which determine the gut bacterial profile (GBP) is poorly understood. This study aimed to understand the effect of ethnicity and geography on GBP of Mongoloid and Proto-Australoid tribes of India. Fecal bacterial diversity was studied in fifteen tribal populations representing four geographic regions (Assam, Telangana, Manipur and Sikkim) by DGGE followed by NGS analysis on Illumina MiSeq platform. Geography and diet had significant effect on GBP of the Indian tribes which was dominated by Prevotella. The effects were more prominent with lower taxonomic levels, indicating probable functional redundancy of the core GBP. A comparison with the worldwide data revealed that GBP of the Indian population was similar to the Mongolian population (Mongolia). The bacterial genera Faecalibacterium, Eubacterium, Clostridium, Blautia, Ruminococcus and Roseburia were found to be core genera in the representative populations of the world. PMID:26689136

Tailoring sub-micron PLGA particle release profiles via centrifugal fractioning

PubMed Central

Dutta, Dipankar; Salifu, Mariama; Sirianni, Rachael W.; Stabenfeldt, Sarah E.

2016-01-01

Poly(D,L-lactic-co-glycolic) acid (PLGA)-based submicron particles are uniquely posed to overcome limitations of conventional drug delivery systems. However, tailoring cargo/payload release profiles from PLGA micro/nanoparticles typically requires optimization of the multi-parameter formulation, where small changes may cause drastic shifts in the resulting release profiles. In this study, we aimed to establish whether refining the average diameter of submicron particle populations after formulation alters protein release profiles. PLGA particles were first produced via double emulsion-solvent evaporation method to encapsulate bovine serum albumin. Particles were then subjected to centrifugal fractioning protocols varying in both spin time and force to determine encapsulation efficiency and release profile of differently sized populations that originated from a single batch. We found the average particle diameter was related to marked alterations in encapsulation efficiencies (range: 36.4–49.4%), burst release (range: 15.8–49.1%), and time for total cargo release (range: 38–78 days). Our data corroborate previous reports relating PLGA particle size with such release characteristics, however, this is the first study, to our knowledge, to directly compare particle population size while holding all formulation parameters constant. In summary, centrifugal fractioning to selectively control the population distribution of sub-micron PLGA particles represents a feasible tool to tailor release characteristics. PMID:26517011

The role of personality in aggressive behaviour among individuals with intellectual disabilities.

PubMed

Chaïb, L S; Crocker, A G

2014-11-01

Aggressive behaviour is associated with certain personality traits in both the general population and among individuals with mental health problems, but little attention has been paid to the relationship between aggressive behaviour and personality among individuals with intellectual disabilities (ID). The aim of this study was to circumscribe personality profiles associated with aggressive behaviour among individuals with ID. In this cross-sectional study of 296 adults with mild or moderate ID, information on mental health, personality and aggressive behaviour was gathered through structured interviews with the ID participants and their case manager, and a review of client files. The results of the Reiss Profile were submitted to hierarchical cluster analysis method. Subsequently, the distribution of aggressive behaviour, sociodemographic characteristics and clinical characteristics across personality profiles was analysed. The analyses yielded seven distinct personality profiles in relation to patterns of aggressive behaviour: Pacifists, Socials, Confidents, Altruists, Conformists, Emotionals and Asocials. The identification of distinct personality profiles sheds light on the risk factors for aggressive behaviour, and suggests new approaches to improving diagnostic and intervention strategies. © 2013 The Authors. Journal of Intellectual Disability Research © 2013 John Wiley & Sons Ltd, MENCAP & IASSIDD.

Dietary patterns among a national random sample of British adults

PubMed Central

Pryer, J; Nichols, R; Elliott, P; Thakrar, B; Brunner, E; Marmot, M

2001-01-01

STUDY OBJECTIVES—To identify groups within the UK male and female population who report similar patterns of diet.
DESIGN—National representative dietary survey, using seven day weighed dietary records, of men and women aged 16-64 years living in private households in Great Britain in 1986-7. Cluster analysis was used to aggregate participants into diet groups.
SETTING—Great Britain.
PARTICIPANTS—1087 men and 1110 women.
RESULTS—93% of men and 86% of women fell into one of four distinct diet groups. Among men the most prevalent diet group was "beer and convenience food" (34% of the male population); second was "traditional British diet" (18%); third was "healthier but sweet diet" (17.5%) and fourth was "healthier diet " (17%). Among women, the most prevalent diet group was " traditional British diet" (32%); second, was "healthy cosmopolitan diet" (25%); third was a "convenience food diet" (21%); and fourth was "healthier but sweet diet" (15%). There were important differences in nutrient profile, sociodemographic and behavioural characteristics between diet groups.
CONCLUSIONS—Cluster analysis identified four diet groups among men and four among women, which differed not only in terms of reported dietary intakes, but also with respect to nutrient, social and behavioural profiles. The groups identified could provide a useful basis for development, monitoring and targeting of public health nutrition policy in the UK.


Keywords: diet; cluster analysis; sociodemographic variables PMID:11112948

Relation of four nontraditional lipid profiles to diabetes in rural Chinese H-type hypertension population.

PubMed

Wang, Haoyu; Guo, Xiaofan; Chen, Yintao; Li, Zhao; Xu, Jiaqi; Sun, Yingxian

2017-10-11

Mounting evidence suggested that nontraditional lipid profiles have been recognized as a reliable indicator for unfavorable cardiovascular events. The purpose of this study was to explore the role of nontraditional lipid profiles as potential clinical indices for the assessment of prevalent diabetes in rural Chinese H-type hypertension population. During 2012 to 2013, we conducted a large cross-sectional study of 2944 H-type hypertension participants (≥35 years of age) from rural areas in northeast China. Subjects underwent accurate assessment of lipid profiles, fasting plasma glucose (FPG), homocysteine (Hcy) according to standard protocols. The proportion of diabetes showed a graded and linear increase across the quartiles for all four nontraditional lipid parameters. Nontraditional lipid variables were independent determinants of FPG, and its correlation for TG/HDL-C was strongest, whether potential confounders were adjusted or not. Multivariable logistic regression analysis established that the highest triglycerides (TG)/ high-density lipoprotein cholesterol (HDL-C) quartile manifested the largest ORs of prevalent diabetes (OR: 3.275, 95%CI: 2.109-5.087) compared with the lowest quartile. The fully adjusted ORs (95%CI) were 2.753 (1.783-4.252), 2.178 (1.415-2.351), 1.648 (1.097-2.478) for the top quartile of total cholesterol (TC)/HDL-C, low-density lipoprotein cholesterol (LDL-C)/HDL-C, and non-high-density lipoprotein cholesterol (non-HDL-C), respectively. On the basis of the area under receiver-operating characteristic curve (AUC), TG/HDL-C showed the optimal discriminating power for diabetes (AUC: 0.684, 95% CI: 0.650-0.718). Nontraditional lipid profiles (TG/HDL-C, TC/HDL-C, LDL-C/HDL-C and non-HDL-C) were all consistently and independently correlated with prevalent diabetes among the H-type hypertension population in rural China. TG/HDL-C was prone to be more profitable in assessing the risk of prevalent diabetes and should be encouraged as an effective clinical tool for monitoring and targeted intervention of diabetes in H-type hypertension adults.

Data-driven approach to detect common copy-number variations and frequency profiles in a population-based Korean cohort.

PubMed

Moon, Sanghoon; Kim, Young Jin; Hong, Chang Bum; Kim, Dong-Joon; Lee, Jong-Young; Kim, Bong-Jo

2011-11-01

To date, hundreds of thousands of copy-number variation (CNV) data have been reported using various platforms. The proportion of Asians in these data is, however, relatively small as compared with that of other ethnic groups, such as Caucasians and Yorubas. Because of limitations in platform resolution and the high noise level in signal intensity, in most CNV studies (particularly those using single nucleotide polymorphism arrays), the average number of CNVs in an individual is less than the number of known CNVs. In this study, we ascertained reliable, common CNV regions (CNVRs) and identified actual frequency rates in the Korean population to provide more CNV information. We performed two-stage analyses for detecting structural variations with two platforms. We discovered 576 common CNVRs (88 CNV segments on average in an individual), and 87% (501 of 576) of these CNVRs overlapped by ≥1 bp with previously validated CNV events. Interestingly, from the frequency analysis of CNV profiles, 52 of 576 CNVRs had a frequency rate of <1% in the 8842 individuals. Compared with other common CNV studies, this study found six common CNVRs that were not reported in previous CNV studies. In conclusion, we propose the data-driven detection approach to discover common CNVRs including those of unreported in the previous Korean CNV study while minimizing false positives. Through our approach, we successfully discovered more common CNVRs than previous Korean CNV study and conducted frequency analysis. These results will be a valuable resource for the effective level of CNVs in the Korean population.

Epidural Abscess: A Propensity Analysis of Surgical Treatment Strategies.

PubMed

Chaker, Anisse N; Bhimani, Abhiraj D; Esfahani, Darian R; Rosinski, Clayton L; Geever, Brett W; Patel, Akash S; Hobbs, Jonathan G; Burch, Taylor G; Patel, Saavan; Mehta, Ankit I

2018-06-18

Observational analysis of retrospectively collected data. A retrospective study was performed in order to compare the surgical profile of risk factors and perioperative complications for laminectomy and laminectomy with fusion procedures in the treatment of SEA. Spinal epidural abscess (SEA) is a highly morbid condition typically presenting with back pain, fever, and neurologic deficits. Posterior fusion has been used to supplement traditional laminectomy of SEA to improve spinal stability. At present, the ideal surgical strategy - laminectomy with or without fusion - remains elusive. 30-day outcomes such as reoperation and readmission following laminectomy and laminectomy with fusion in patients with SEA were investigated utilizing the American College of Surgeons National Quality Improvement Program database. Demographics and clinical risk factors were collected, and propensity matching was performed to account for differences in risk profiles between the groups. 738 patients were studied (608 laminectomy alone, 130 fusion). The fusion population was in worse health. The fusion population experienced significantly greater rate of return to the operating room (odds ratio (OR) 1.892), with the difference primarily accounted for by cervical spine operations. Additionally, fusion patients had significantly greater rates of blood transfusion. Infection was the most common reason for reoperation in both populations. Both laminectomy and laminectomy with fusion effectively treat SEA, but addition of fusion is associated with significantly higher rates of transfusion and perioperative return to the operating room. In operative situations where either procedure is reasonable, surgeons should consider that fusion nearly doubles the odds of reoperation in the short-term, and weigh this risk against the benefit of added stability. 3.

Heterogeneous resistance to vancomycin in Staphylococcus epidermidis, Staphylococcus haemolyticus and Staphylococcus warneri clinical strains: characterisation of glycopeptide susceptibility profiles and cell wall thickening.

PubMed

Nunes, Ana Paula Ferreira; Teixeira, Lúcia Martins; Iorio, Natália Lopes Pontes; Bastos, Carla Callegário Reis; de Sousa Fonseca, Leila; Souto-Padrón, Thaís; dos Santos, Kátia Regina Netto

2006-04-01

The population analysis profile (PAP) method as well as analysis of autolytic activity and cellular ultrastructure by transmission electron microscopy (TEM) were used to characterise Staphylococcus epidermidis, Staphylococcus haemolyticus and Staphylococcus warneri clinical strains with reduced susceptibility to glycopeptides. All strains showed heterogeneous profiles to vancomycin and teicoplanin by the PAP method. Subpopulations that grew in the presence of high concentrations of each drug were selected from the PAP as derivative strains. Their glycopeptide minimal inhibitory concentrations (MICs) were determined and subsequently all parental and derivative strains were grown in one-half of the MIC of vancomycin or teicoplanin. An increase in cell wall thickness of all derivative strains was seen by TEM, with statistically significant values (P<0.01) compared with their respective parental strains. In general, variable rates of autolysis among the strains were observed. Cell wall thickness is an important factor involved in glycopeptide resistance and, in association with PAP results, confirmed the Brazilian coagulase-negative staphylococci clinical isolates as being heteroresistant to glycopeptides. Detection of these heteroresistant organisms is important in order to achieve more judicious use of vancomycin and teicoplanin in hospitals.

A MAYAN FOUNDER MUTATION IS A COMMON CAUSE OF DEAFNESS IN GUATEMALA

PubMed Central

Carranza, Claudia; Menendez, Ibis; Herrera, Mariana; Castellanos, Patricia; Amado, Carlos; Maldonado, Fabiola; Rosales, Luisa; Escobar, Nancy; Guerra, Mariela; Alvarez, Darwin; Foster, Joseph; Guo, Shengru; Blanton, Susan H.; Bademci, Guney; Tekin, Mustafa

2017-01-01

SUMMARY Over 5% of the world population have varying degrees of hearing loss. Mutations in GJB2 are the most common cause of autosomal recessive non-syndromic hearing loss (NSHL) in many populations. The frequency and type of mutations are influenced by ethnicity. Guatemala is a multi-ethnic country with four major populations: Maya, Ladino, Xinca, and Garifuna. To determine the mutation profile of GJB2 in a NSHL population from Guatemala, we sequenced both exons of GJB2 in 133 unrelated families. A total of six pathogenic variants were detected. The most frequent pathogenic variant is c.131G>A (p.Trp44*) detected in 21 of 266 alleles. We show that c.131G>A is associated with a conserved haplotype in Guatemala suggesting a single founder. The majority of Mayan population lives in the west region of the country from where all c.131G>A carriers originated. Further analysis of genome-wide variation of individuals carrying the c.131G>A mutation compared to those of Native American, European, and African populations shows a close match with the Mayan population. PMID:26346709

Safety of Tofacitinib in the Treatment of Rheumatoid Arthritis in Latin America Compared With the Rest of the World Population.

PubMed

Castañeda, Oswaldo M; Romero, Felix J; Salinas, Ariel; Citera, Gustavo; Mysler, Eduardo; Rillo, Oscar; Radominski, Sebastiao C; Cardiel, Mario H; Jaller, Juan J; Alvarez-Moreno, Carlos; Ponce de Leon, Dario; Castelli, Graciela; García, Erika G; Kwok, Kenneth; Rojo, Ricardo

2017-06-01

Rheumatoid arthritis (RA) is a chronic, autoimmune disease characterized by joint destruction. Tofacitinib is an oral Janus kinase inhibitor for the treatment of RA. This post hoc analysis assessed the safety of tofacitinib in Latin American (LA) patients with RA versus the Rest of World (RoW) population. Data were pooled from 14 clinical studies of tofacitinib: six Phase 2, six Phase 3 and two long-term extension studies. Incidence rates (IRs; patients with events/100 patient-years of treatment exposure) were calculated for safety events of special interest combined across tofacitinib doses. 95% confidence intervals (CI) for IRs were calculated using the maximum likelihood method. Descriptive comparisons were made between LA and RoW (excluding LA) populations. This analysis included data from 984 LA patients and 4687 RoW patients. IRs for safety events of special interest were generally similar between LA and RoW populations, with overlapping 95% CIs. IRs for discontinuation due to adverse events, serious infections, tuberculosis, all herpes zoster (HZ), serious HZ, malignancies (excluding non-melanoma skin cancer) and major adverse cardiovascular events were numerically lower for LA versus RoW patients; IR for mortality was numerically higher. No lymphoma was reported in the LA population versus eight cases in the RoW population. Exposure (extent and length) was lower in the LA population (2148.33 patient-years [mean = 2.18 years]) versus RoW (10515.68 patient-years [mean = 2.24 years]). This analysis of pooled data from clinical studies of tofacitinib in patients with RA demonstrates that tofacitinib has a consistent safety profile across LA and RoW patient populations.

Gene expression profiling of single cells on large-scale oligonucleotide arrays

PubMed Central

Hartmann, Claudia H.; Klein, Christoph A.

2006-01-01

Over the last decade, important insights into the regulation of cellular responses to various stimuli were gained by global gene expression analyses of cell populations. More recently, specific cell functions and underlying regulatory networks of rare cells isolated from their natural environment moved to the center of attention. However, low cell numbers still hinder gene expression profiling of rare ex vivo material in biomedical research. Therefore, we developed a robust method for gene expression profiling of single cells on high-density oligonucleotide arrays with excellent coverage of low abundance transcripts. The protocol was extensively tested with freshly isolated single cells of very low mRNA content including single epithelial, mature and immature dendritic cells and hematopoietic stem cells. Quantitative PCR confirmed that the PCR-based global amplification method did not change the relative ratios of transcript abundance and unsupervised hierarchical cluster analysis revealed that the histogenetic origin of an individual cell is correctly reflected by the gene expression profile. Moreover, the gene expression data from dendritic cells demonstrate that cellular differentiation and pathway activation can be monitored in individual cells. PMID:17071717

Analysis of Chromobacterium sp. natural isolates from different Brazilian ecosystems

PubMed Central

Lima-Bittencourt, Cláudia I; Astolfi-Filho, Spartaco; Chartone-Souza, Edmar; Santos, Fabrício R; Nascimento, Andréa MA

2007-01-01

Background Chromobacterium violaceum is a free-living bacterium able to survive under diverse environmental conditions. In this study we evaluate the genetic and physiological diversity of Chromobacterium sp. isolates from three Brazilian ecosystems: Brazilian Savannah (Cerrado), Atlantic Rain Forest and Amazon Rain Forest. We have analyzed the diversity with molecular approaches (16S rRNA gene sequences and amplified ribosomal DNA restriction analysis) and phenotypic surveys of antibiotic resistance and biochemistry profiles. Results In general, the clusters based on physiological profiles included isolates from two or more geographical locations indicating that they are not restricted to a single ecosystem. The isolates from Brazilian Savannah presented greater physiologic diversity and their biochemical profile was the most variable of all groupings. The isolates recovered from Amazon and Atlantic Rain Forests presented the most similar biochemical characteristics to the Chromobacterium violaceum ATCC 12472 strain. Clusters based on biochemical profiles were congruent with clusters obtained by the 16S rRNA gene tree. According to the phylogenetic analyses, isolates from the Amazon Rain Forest and Savannah displayed a closer relationship to the Chromobacterium violaceum ATCC 12472. Furthermore, 16S rRNA gene tree revealed a good correlation between phylogenetic clustering and geographic origin. Conclusion The physiological analyses clearly demonstrate the high biochemical versatility found in the C. violaceum genome and molecular methods allowed to detect the intra and inter-population diversity of isolates from three Brazilian ecosystems. PMID:17584942

Genetic diversity and antimicrobial resistance of Flavobacterium psychrophilum isolated from cultured rainbow trout, Onchorynchus mykiss (Walbaum), in Spain.

PubMed

Del Cerro, A; Márquez, I; Prieto, J M

2010-04-01

Flavobacterium psychrophilum is the causative agent of bacterial cold-water disease (CWD) and rainbow trout fry syndrome (RTFS) in salmonids. These diseases are a major problem in the aquaculture industry in Spain, and a better understanding of the epidemiology of F. psychrophilum isolates is necessary to improve management strategies. In this study, to investigate genetic variability of this bacterium, pulsed-field gel electrophoresis after DNA digestion with endonuclease StuI, plasmid profiling analysis and antimicrobial susceptibility testing were undertaken with 25 isolates of F. psychrophilum from Spain. These isolates were classified into 17 patterns by PFGE analysis, which were grouped into four clusters and seven independent branches. Twenty isolates (80%) possessed plasmids of 3.5 kb (n = 13) or 5.5 kb (n = 7). No plasmids were associated with antibiotic resistance to oxytetracycline (OTC) or florfenicol (FLO). Twenty isolates (80%) had minimum inhibitory concentrations (MICs) to OTC of between 2.4 and 9.7 microg mL(-1), and all isolates were susceptible to FLO. A relationship between the origin of the isolates and PFGE genotypes was found. Plasmid profile typing correlated with PFGE profile typing, whereas no correlation was found between antimicrobial susceptibility testing and PFGE profiles. These results suggest that the population of F. psychrophilum with pathogenic potential in northern Spain is quite heterogeneous.

Differences in lipid profiles in two Hispanic ischemic stroke populations.

PubMed

Arauz, A; Romano, J G; Ruiz-Franco, A; Shang, T; Dong, C; Rundek, T; Koch, S; Hernández-Curiel, B; Pacheco, J; Rojas, P; Ruiz-Navarro, F; Katsnelson, M; Sacco, R L

2014-06-01

The study aims to compare lipid profiles among ischemic stroke patients in a predominantly Caribbean-Hispanic population in Miami and a Mestizo Hispanic population in Mexico City. We analyzed ischemic stroke Hispanic patients with complete baseline fasting lipid profile enrolled contemporaneously in the prospective registries of two tertiary care teaching hospitals in Mexico City and Miami. Demographic characteristics, risk factors, medications, ischemic stroke subtype, and first fasting lipid profile were compared. Vascular risk factor definitions were standardized. Multiple linear regression analysis was performed to compare lipid fractions. A total of 324 patients from Mexico and 236 from Miami were analyzed. Mexicans were significantly younger (58 · 1 vs. 67 · 4 years), had a lower frequency of hypertension (53 · 4% vs. 79 · 7%), and lower body mass index (27 vs. 28 · 5). There was a trend toward greater prevalence of diabetes in Mexicans (31 · 5 vs. 24 · 6%, P = 0 · 07). Statin use at the time of ischemic stroke was more common in Miami Hispanics (18 · 6 vs. 9 · 4%). Mexicans had lower total cholesterol levels (169 · 9 ± 46 · 1 vs. 179 · 9 ± 48 · 4 mg/dl), lower low-density lipoprotein (92 · 3 ± 37 · 1 vs. 108 · 2 ± 40 · 8 mg/dl), and higher triglyceride levels (166 · 9 ± 123 · 9 vs. 149 · 2 ± 115 · 2 mg/dl). These differences remained significant after adjusting for age, gender, hypertension, diabetes, body mass index, smoking, ischemic stroke subtype, and statin use. We found significant differences in lipid fractions in Hispanic ischemic stroke patients, with lower total cholesterol and low-density lipoprotein, and higher triglyceride levels in Mexicans. These findings highlight the heterogeneity of dyslipidemia among the Hispanic race-ethnic group and may lead to different secondary prevention strategies. © 2013 The Authors. International Journal of Stroke © 2013 World Stroke Organization.

Combined Volatolomics for Monitoring of Human Body Chemistry

PubMed Central

Broza, Yoav Y.; Zuri, Liat; Haick, Hossam

2014-01-01

Analysis of volatile organic compounds (VOCs) is a promising approach for non-invasive, fast and potentially inexpensive diagnostics. Here, we present a new methodology for profiling the body chemistry by using the volatile fraction of molecules in various body fluids. Using mass spectrometry and cross-reactive nanomaterial-based sensors array, we demonstrate that simultaneous VOC detection from breath and skin would provide complementary, non-correlated information of the body's volatile metabolites profile. Eventually with further wide population validation studies, such a methodology could provide more accurate monitoring of pathological changes compared to the information provided by a single body fluid. The qualitative and quantitative methods presented here offers a variety of options for novel mapping of the metabolic properties of complex organisms, including humans. PMID:24714440

Combined volatolomics for monitoring of human body chemistry.

PubMed

Broza, Yoav Y; Zuri, Liat; Haick, Hossam

2014-04-09

Analysis of volatile organic compounds (VOCs) is a promising approach for non-invasive, fast and potentially inexpensive diagnostics. Here, we present a new methodology for profiling the body chemistry by using the volatile fraction of molecules in various body fluids. Using mass spectrometry and cross-reactive nanomaterial-based sensors array, we demonstrate that simultaneous VOC detection from breath and skin would provide complementary, non-correlated information of the body's volatile metabolites profile. Eventually with further wide population validation studies, such a methodology could provide more accurate monitoring of pathological changes compared to the information provided by a single body fluid. The qualitative and quantitative methods presented here offers a variety of options for novel mapping of the metabolic properties of complex organisms, including humans.

Sandfly saliva of Lutzomyia ovallesi (Diptera: Psychodidae) as a possible marker for the transmission of Leishmania in Venezuela Andes region.

PubMed

Nieves, E; Sánchez, Y; Sánchez, H; Rondón, M; González, N; Carrero, J

2012-03-01

The saliva of the Phlebotominae is highly immunogenic to the vertebrate host and is a determining factor in the Leishmania infection. The aim of this work was to study the saliva of Lutzomyia ovallesi as a possible risk marker for the transmission of Leishmania. Two populations of L. ovallesi from different geographical areas and subjected to different environmental conditions were compared by geometric morphometry of the wings, by protein profile analysis of salivary glands and by assessing the presence of anti-saliva protein in human sera confronted with laboratory L. ovallesi saliva. The results showed differences in the isometric size and structure of the wings but no allometric effects. Protein profiles of salivary glands of both the L. ovallesi populations studied were found to be similar, based on 11 protein bands with molecular weights ranging from 16 to 99 kDa. Anti-saliva antibodies were present in human sera, but human sera infected and uninfected with leishmaniasis could not be differentiated. We conclude that the saliva of laboratory-reared L. ovallesi is representative of that of the wild population. It is suggested to study the presence of anti-saliva antibodies in other species of sandflies and mosquitoes.

Epidemiological Profile and Risk Factors for Acquiring HBV and/or HCV in HIV-Infected Population Groups in Nepal.

PubMed

Bhattarai, Manjula; Baniya, Jagat Bahadur; Aryal, Nirmal; Shrestha, Bimal; Rauniyar, Ramanuj; Adhikari, Anurag; Koirala, Pratik; Oli, Pardip Kumar; Pandit, Ram Deo; Stein, David A; Gupta, Birendra Prasad

2018-01-01

HBV and HCV infections are widespread among the HIV-infected individuals in Nepal. The goals of this study were to investigate the epidemiological profile and risk factors for acquiring HBV and/or HCV coinfection in disadvantaged HIV-positive population groups in Nepal. We conducted a retrospective study on blood samples from HIV-positive patients from the National Public Health Laboratory at Kathmandu to assay for HBsAg, HBeAg, and anti-HCV antibodies, HIV viral load, and CD4+ T cell count. Among 579 subjects, the prevalence of HIV-HBV, HIV-HCV, and HIV-HBV-HCV coinfections was 3.62%, 2.93%, and 0.34%, respectively. Multivariate regression analysis indicated that spouses of HIV-positive migrant labourers were at significant risk for coinfection with HBV infection, and an age of >40 years in HIV-infected individuals was identified as a significant risk factor for HCV coinfection. Overall our study indicates that disadvantaged population groups such as intravenous drug users, migrant workers and their spouses, female sex workers, and men who have sex with HIV-infected men are at a high and persistent risk of acquiring viral hepatitis. We conclude that Nepalese HIV patients should receive HBV and HCV diagnostic screening on a regular basis.

The disease profile of poverty: morbidity and mortality in northern Uganda in the context of war, population displacement and HIV/AIDS.

PubMed

Accorsi, S; Fabiani, M; Nattabi, B; Corrado, B; Iriso, R; Ayella, E O; Pido, B; Onek, P A; Ogwang, M; Declich, S

2005-03-01

The population of Gulu District (northern Uganda) has been severely incapacitated by war, epidemics and social disruption. This study is aimed at describing disease patterns and trends in this area through a retrospective analysis of discharge records for 155205 in-patients of Lacor Hospital in the period 1992-2002. The burden of infectious diseases in childhood is overwhelming, with malaria accounting for the steepest increase in admissions. Admissions for war-related injuries and malnutrition fluctuated with the intensity of the war and the severity of famine. Emerging and re-emerging infections, such as HIV/AIDS, tuberculosis and Ebola, accounted for a heavy disease burden; however, there has been a trend for admissions related to HIV/AIDS and tuberculosis to decrease since the implementation of community-based services. Vulnerable groups (infants, children and women) accounted for 79.8% of admissions. Long-term war, population displacement, the collapse of social structures and the breakdown of the health system place people at a much greater risk of persistent, emerging and re-emerging infectious diseases, malnutrition and war-related injuries, shaping the 'disease profile of poverty'. Most of the disease burden results from infectious diseases of childhood, whose occurrence could be dramatically reduced by low-cost and effective preventive and curative interventions.

Developmental validation of an X-Insertion/Deletion polymorphism panel and application in HAN population of China.

PubMed

Zhang, Suhua; Sun, Kuan; Bian, Yingnan; Zhao, Qi; Wang, Zheng; Ji, Chaoneng; Li, Chengtao

2015-12-14

InDels are short-length polymorphisms characterized by low mutation rates, high inter-population diversity, short amplicon strategy and simplicity of laboratory analysis. This work describes the developmental validation of an X-InDels panel amplifying 18 bi-allelic markers and Amelogenin in one single PCR system. Developmental validation indicated that this novel panel was reproducible, accurate, sensitive and robust for forensic application. Sensitivity testing of the panel was such that a full profile was obtainable even with 125 pg of human DNA with intra-locus balance above 70%. Specificity testing was demonstrated by the lack of cross-reactivity with a variety of commonly encountered animal species and microorganisms. For the stability testing in cases of PCR inhibition, full profiles have been obtained with hematin (≤1000 μM) and humic acid (≤150 ng/μL). For the forensic investigation of the 18 X-InDels in the HAN population of China, no locus deviated from the Hardy-Weinberg equilibrium and linkage disequilibrium. Since they are independent from each other, the CDPfemale was 0.999999726 and CDPmale was 0.999934223. The forensic parameters suggested that this X-Indel panel is polymorphic and informative, which provides valuable X-linked information for deficient relationship cases where autosomal markers are uninformative.

Developmental validation of an X-Insertion/Deletion polymorphism panel and application in HAN population of China

PubMed Central

Zhang, Suhua; Sun, Kuan; Bian, Yingnan; Zhao, Qi; Wang, Zheng; Ji, Chaoneng; Li, Chengtao

2015-01-01

InDels are short-length polymorphisms characterized by low mutation rates, high inter-population diversity, short amplicon strategy and simplicity of laboratory analysis. This work describes the developmental validation of an X-InDels panel amplifying 18 bi-allelic markers and Amelogenin in one single PCR system. Developmental validation indicated that this novel panel was reproducible, accurate, sensitive and robust for forensic application. Sensitivity testing of the panel was such that a full profile was obtainable even with 125 pg of human DNA with intra-locus balance above 70%. Specificity testing was demonstrated by the lack of cross-reactivity with a variety of commonly encountered animal species and microorganisms. For the stability testing in cases of PCR inhibition, full profiles have been obtained with hematin (≤1000 μM) and humic acid (≤150 ng/μL). For the forensic investigation of the 18 X-InDels in the HAN population of China, no locus deviated from the Hardy–Weinberg equilibrium and linkage disequilibrium. Since they are independent from each other, the CDPfemale was 0.999999726 and CDPmale was 0.999934223. The forensic parameters suggested that this X-Indel panel is polymorphic and informative, which provides valuable X-linked information for deficient relationship cases where autosomal markers are uninformative. PMID:26655948

Impact of Bioreactor Environment and Recovery Method on the Profile of Bacterial Populations from Water Distribution Systems.

PubMed

Luo, Xia; Jellison, Kristen L; Huynh, Kevin; Widmer, Giovanni

2015-01-01

Multiple rotating annular reactors were seeded with biofilms flushed from water distribution systems to assess (1) whether biofilms grown in bioreactors are representative of biofilms flushed from the water distribution system in terms of bacterial composition and diversity, and (2) whether the biofilm sampling method affects the population profile of the attached bacterial community. Biofilms were grown in bioreactors until thickness stabilized (9 to 11 weeks) and harvested from reactor coupons by sonication, stomaching, bead-beating, and manual scraping. High-throughput sequencing of 16S rRNA amplicons was used to profile bacterial populations from flushed biofilms seeded into bioreactors as well as biofilms recovered from bioreactor coupons by different methods. β diversity between flushed and reactor biofilms was compared to β diversity between (i) biofilms harvested from different reactors and (ii) biofilms harvested by different methods from the same reactor. These analyses showed that average diversity between flushed and bioreactor biofilms was double the diversity between biofilms from different reactors operated in parallel. The diversity between bioreactors was larger than the diversity associated with different biofilm recovery methods. Compared to other experimental variables, the method used to recover biofilms had a negligible impact on the outcome of water biofilm analyses based on 16S amplicon sequencing. Results from this study show that biofilms grown in reactors over 9 to 11 weeks are not representative models of the microbial populations flushed from a distribution system. Furthermore, the bacterial population profile of biofilms grown in replicate reactors from the same flushed water are likely to diverge. However, four common sampling protocols, which differ with respect to disruption of bacterial cells, provide similar information with respect to the 16S rRNA population profile of the biofilm community.

Regional analysis of social characteristics for evacuation resource planning: ARkStorm scenario

USGS Publications Warehouse

Wein, Anne; Ratliff, Jamie L.; Allan Baez,; Sleeter, Rachel

2016-01-01

Local planning is insufficient for regional catastrophes; regional exercises are needed to test emergency plans and decision-making structures. The ARkStorm scenario would trigger a mass evacuation that would be complicated by the social characteristics of populations [e.g., vehicle ownership, age, poverty, English language limitation (ELL), and shelter needs]. Land cover data and dasymetric mapping improves the allocation of residential populations and their social characteristics to the ARkStorm flood zone in 21 counties in California. Numbers and concentrations of county, urban, and rural residents exposed to flooding as well as populations in and out of the scenario flood zone are profiled. The results inform mass evacuation planning by providing a means to (1) examine the sufficiency of mutual aid agreements, (2) underscore planning for carless populations, and (3) tailor multilingual communication strategies. The various geographical distinctions emphasize different challenges throughout the region. It will be important to investigate behavioral responses to warnings, identify evacuation constraints (e.g., shelter capacity versus need), and obtain comparable data on transient populations.

A Content Analysis of Displayed Alcohol References on a Social Networking Web Site

PubMed Central

Moreno, Megan A; Briner, Leslie R; Williams, Amanda; Brockman, Libby; Walker, Leslie; Christakis, Dimitri A

2010-01-01

Purpose Exposure to alcohol use in media is associated with adolescent alcohol use. Adolescents frequently display alcohol references on Internet media such as social networking websites (SNSs). The purpose of this study was to conduct a theoretically-based content analysis of older adolescents’ displayed alcohol references on a SNS. Methods We evaluated 400 randomly selected public MySpace profiles of self-reported 17 to 20-year-olds from zip codes representing urban, suburban and rural communities in one Washington county. Content was evaluated for alcohol references suggesting: 1) explicit versus figurative alcohol use, 2) alcohol-related motivations, associations and consequences, including references that met CRAFFT problem drinking criteria. We compared profiles from four target zip codes for prevalence and frequency of alcohol display. Results Of 400 profiles, 225 profiles (56.3%) contained 341 references to alcohol. Profile owners who displayed alcohol references were mostly male (54.2%) and White (70.7%). The most frequent reference category was explicit use (49.3%), the most commonly displayed alcohol use motivation was peer pressure (4.7%). Few references met CRAFFT problem drinking criteria (3.2%). There were no differences in prevalence or frequency of alcohol display among the four sociodemographic communities. Conclusions Despite alcohol use being illegal and potentially stigmatizing in this population, explicit alcohol use is frequently referenced on adolescents’ MySpace profiles across several sociodemographic communities. Motivations, associations and consequences regarding alcohol use referenced on MySpace appear consistent with previous studies of adolescent alcohol use. These references may be a potent source of influence on adolescents, particularly given that they are created and displayed by peers. PMID:20638009

Comparative Gene Expression Profiles Induced by PPARγ and PPARα/γ Agonists in Human Hepatocytes

PubMed Central

Rogue, Alexandra; Lambert, Carine; Jossé, Rozenn; Antherieu, Sebastien; Spire, Catherine; Claude, Nancy; Guillouzo, André

2011-01-01

Background Several glitazones (PPARγ agonists) and glitazars (dual PPARα/γ agonists) have been developed to treat hyperglycemia and, simultaneously, hyperglycemia and dyslipidemia, respectively. However, most have caused idiosyncratic hepatic or extrahepatic toxicities through mechanisms that remain largely unknown. Since the liver plays a key role in lipid metabolism, we analyzed changes in gene expression profiles induced by these two types of PPAR agonists in human hepatocytes. Methodology/Principal Findings Primary human hepatocytes and the well-differentiated human hepatoma HepaRG cells were exposed to different concentrations of two PPARγ (troglitazone and rosiglitazone) and two PPARα/γ (muraglitazar and tesaglitazar) agonists for 24 h and their transcriptomes were analyzed using human pangenomic Agilent microarrays. Principal Component Analysis, hierarchical clustering and Ingenuity Pathway Analysis® revealed large inter-individual variability in the response of the human hepatocyte populations to the different compounds. Many genes involved in lipid, carbohydrate, xenobiotic and cholesterol metabolism, as well as inflammation and immunity, were regulated by both PPARγ and PPARα/γ agonists in at least a number of human hepatocyte populations and/or HepaRG cells. Only a few genes were selectively deregulated by glitazars when compared to glitazones, indicating that PPARγ and PPARα/γ agonists share most of their target genes. Moreover, some target genes thought to be regulated only in mouse or to be expressed in Kupffer cells were also found to be responsive in human hepatocytes and HepaRG cells. Conclusions/Significance This first comprehensive analysis of gene regulation by PPARγ and PPARα/γ agonists favor the conclusion that glitazones and glitazars share most of their target genes and induce large differential changes in gene profiles in human hepatocytes depending on hepatocyte donor, the compound class and/or individual compound, thereby supporting the occurrence of idiosyncratic toxicity in some patients. PMID:21533120

Plasma Lipidomic Profiling in a Military Population of Mild Traumatic Brain Injury and Post-Traumatic Stress Disorder with Apolipoprotein E ɛ4-Dependent Effect.

PubMed

Emmerich, Tanja; Abdullah, Laila; Crynen, Gogce; Dretsch, Michael; Evans, James; Ait-Ghezala, Ghania; Reed, Jon; Montague, Hannah; Chaytow, Helena; Mathura, Venkatarajan; Martin, Justin; Pelot, Robert; Ferguson, Scott; Bishop, Alex; Phillips, John; Mullan, Michael; Crawford, Fiona

2016-07-15

In the military population, there is high comorbidity between mild traumatic brain injury (mTBI) and post-traumatic stress disorder (PTSD) due to the inherent risk of psychological trauma associated with combat. These disorders present with long-term neurological dysfunction and remain difficult to diagnose due to their comorbidity and overlapping clinical presentation. Therefore, we performed cross-sectional analysis of blood samples from demographically matched soldiers (total, n = 120) with mTBI, PTSD, and mTBI+PTSD and those who were considered cognitively and psychologically normal. Soldiers were genotyped for apolipoprotein E (APOE) ɛ4, and phospholipids (PL) were examined using liquid chromatography/mass spectrometry analysis. We observed significantly lower levels of several major PL classes in TBI, PTSD, and TBI+PTSD, compared with controls. PTSD severity analysis revealed that significant PL decreases were primarily restricted to the moderate-to-severe PTSD group. An examination of the degree of unsaturation showed that monounsaturated fatty acid-containing phosphatidylcholine (PC) and phosphatidylinositol (PI) species were lower in the TBI and TBI+PTSD groups. However, these PLs were unaltered among PTSD subjects, compared with controls. Similarly, ether PC (ePC) levels were lower in PTSD and TBI+PTSD subjects, relative to controls. Ratios of arachidonic acid (AA) to docosahexaenoic acid (DHA)-containing species were significantly decreased within PC and phosphatidylethanolamine (PE) classes. APOE ɛ4 (+) subjects exhibited higher PL levels than their APOE ɛ4 (-) counterparts within the same diagnostic groups. These findings suggest that PL profiles, together with APOE genotyping, could potentially aid to differentiate diagnosis of mTBI and PTSD and warrant further validation. In conclusion, PL profiling may facilitate clinical diagnosis of mTBI and PTSD currently hindered by comorbid pathology and overlapping symptomology of these two conditions.

Safety and pharmacokinetic profile of rufinamide in pediatric patients aged less than 4 years with Lennox-Gastaut syndrome: An interim analysis from a multicenter, randomized, active-controlled, open-label study.

PubMed

Arzimanoglou, Alexis; Ferreira, Jose A; Satlin, Andrew; Mendes, Shannon; Williams, Betsy; Critchley, David; Schuck, Edgar; Hussein, Ziad; Kumar, Dinesh; Dhadda, Shobha; Bibbiani, Francesco

2016-05-01

A good knowledge of safety and age group-specific pharmacokinetics (PK) of antiepileptic drugs (AEDs) in young pediatric patients is of great importance in clinical practice. This paper presents 6-month interim safety and PK from an ongoing 2-year open-label study (Study 303) of adjunctive rufinamide treatment in pediatric subjects ≥ 1 to < 4 years with inadequately controlled epilepsies of the Lennox-Gastaut syndrome (LGS) spectrum. Subjects (N = 37) were randomized to either rufinamide or any other approved AED chosen by the investigator as adjunctive therapy to the subject's existing regimen of 1-3 AEDs. Interim safety results showed that treatment-emergent adverse events (TEAEs) were similar between the rufinamide (22 [88.0%]) and any-other-AED group (9 [81.8%]), with most events considered mild or moderate. A population PK analysis was conducted including plasma rufinamide concentrations from Study 303 and two other study populations of LGS subjects ≥ 4 years. The rufinamide PK profile was dose independent. The apparent clearance (CL/F) estimated from the PK model was 2.19 L/h; it was found to increase significantly as a function of body weight. Coadministration of valproic acid significantly decreased rufinamide CL/F. CL/F was not significantly affected by other concomitant AEDs, age, gender, race, hepatic function, or renal function. No adjustments to body weight-based rufinamide dosing in subjects ≥ 1 to < 4 years are necessary. Rufinamide was safe and well tolerated in these pediatric subjects. Results from the interim analysis demonstrate that rufinamide's safety and PK profile is comparable in subjects ≥ 1 to < 4 and ≥ 4 years with LGS. Study 303 (clinicaltrials.gov: NCT01405053). Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

Non-thermal O/1D/ produced by dissociative recombination of O2/+/ - A theoretical model and observational results. [in earth atmosphere

NASA Technical Reports Server (NTRS)

Schmitt, G. A.; Abreu, V. J.; Hays, P. B.

1981-01-01

Thermal and nonthermal O(1D) number density profiles are calculated. The two populations are assumed to be coupled by a thermalization cross-section which determines the loss and production in the nonthermal and thermal populations, respectively. The sources, sinks and transport of the two populations are used to model volume emission rate profiles at 6300 A. The 6300 A brightness measured by the Visible Airglow Experiment is then used to establish the presence of the nonthermal population and to determine the thermalization cross-section.

Exploring the effects of population change on the costs of physician services.

PubMed

Denton, Frank T; Gafni, Amiram; Spencer, Byron G

2002-09-01

The effects of population aging on future health care costs are an important public policy concern in many countries. We focus in this paper on physician services and investigate how changes in the size and age distribution of a population can affect the aggregate and per capita costs of such services. The principal data set (unpublished, for Ontario) provides information about payments to physicians, by age and sex of patients. Using it, we derive age/cost profiles for 19 categories of physicians. Adopting an index-theoretic framework, we then use the profiles to analyse the "pure" effects of population change (historical and projected) on physician costs, and to decompose the effects into population growth effects and population aging effects. We present calculations for Ontario, for the population of 15 industrialized countries, and for four theoretical populations.

Pressure profiles of plasmas confined in the field of a dipole magnet

NASA Astrophysics Data System (ADS)

Davis, Matthew Stiles

Understanding the maintenance and stability of plasma pressure confined by a strong magnetic field is a fundamental challenge in both laboratory and space plasma physics. Using magnetic and X-ray measurements on the Levitated Dipole Experiment (LDX), the equilibrium plasma pressure has been reconstructed, and variations of the plasma pressure for different plasma conditions have been examined. The relationship of these profiles to the magnetohydrodynamic (MHD) stability limit, and to the enhanced stability limit that results from a fraction of energetic trapped electrons, has been analyzed. In each case, the measured pressure profiles and the estimated fractional densities of energetic electrons were qualitatively consistent with expectations of plasma stability. LDX confines high temperature and high pressure plasma in the field of a superconducting dipole magnet. The strong dipole magnet can be either mechanically supported or magnetically levitated. When the dipole was mechanically supported, the plasma density profile was generally uniform while the plasma pressure was highly peaked. The uniform density was attributed to the thermal plasma being rapidly lost along the field to the mechanical supports. In contrast, the strongly peaked plasma pressure resulted from a fraction of energetic, mirror trapped electrons created by microwave heating at the electron cyclotron resonance (ECRH). These hot electrons are known to be gyrokinetically stabilized by the background plasma and can adopt pressure profiles steeper than the MHD limit. X-ray measurements indicated that this hot electron population could be described by an energy distribution in the range 50-100 keV. Combining information from the magnetic reconstruction of the pressure profile, multi-chord interferometer measurements of the electron density profile, and X-ray measurements of the hot electron energy distribution, the fraction of energetic electrons at the pressure peak was estimated to be ˜ 35% of the total electron population. When the dipole was magnetically levitated the plasma density increased substantially because particle losses to the mechanical supports were eliminated so particles could only be lost via slower cross-field transport processes. The pressure profile was observed to be broader during levitated operation than it was during supported operation, and the pressure appeared to be contained in both a thermal population and an energetic electron population. X-ray spectra indicated that the X-rays came from a similar hot electron population during levitated and supported operation; however, the hot electron fraction was an order of magnitude smaller during levitated operation (<3% of the total electron population). Pressure gradients for both supported and levitated plasmas were compared to the MHD limit. Levitated plasmas had pressure profiles that were (i) steeper than, (ii) shallower than, or (iii) near the MHD limit dependent on plasma conditions. However, those profiles that exceeded the MHD limit were observed to have larger fractions of energetic electrons. When the dipole magnet was supported, high pressure plasmas always had profiles that exceeded the MHD interchange stability limit, but the high pressure in these plasmas appeared to arise entirely from a population of energetic trapped electrons.

Profiles of the Adult Education Target Population: Information from the 2000 Census. Revised

ERIC Educational Resources Information Center

Lasater, Beth; Elliott, Barbara

2005-01-01

This report presents national, regional, and state profiles of the target population for adult education, that is, those individuals aged 16 years and over, who have not attained a high school diploma or equivalent and are not currently enrolled in school. The tables contained in this report describe the following characteristics of the target…

Enantiospecific Pheromone Production and Response Profiles for Populations of Pine Engraver, Ips pini (SAY) (Coleoptera: Scolytidae), in British Columbia

Treesearch

D.R. Miller; J.H. Borden; K.N. Slessor

1996-01-01

Analyses of the enantiomeric composition of ipsdienol produced by individual male pine engravers, Ips pini (Say), from six populations in British Columbia, support the hypothesis that New York and Idaho races of this species hybridize in southeastern British Columbia. Production profiles, expressed as frequency distributions of (+):(-) ipsdienol...

Measurements of the talus in the assessment of population affinity.

PubMed

Bidmos, Mubarak A; Dayal, Manisha R; Adegboye, Oyelola A

2018-06-01

As part of their routine work, forensic anthropologists are expected to report population affinity as part of the biological profile of an individual. The skull is the most widely used bone for the estimation of population affinity but it is not always present in a forensic case. Thus, other bones that preserve well have been shown to give a good indication of either the sex or population affinity of an individual. In this study, the potential of measurements of the talus was investigated for the purpose of estimating population affinity in South Africans. Nine measurements from two hundred and twenty tali of South African Africans (SAA) and South African Whites (SAW) from the Raymond A. Dart Collection of Human Skeletons were used. Direct and step-wise discriminant function and logistic regression analyses were carried out using SPSS and SAS. Talar length was the best single variable for discriminating between these two groups for males while in females the head height was the best single predictor. Average accuracies for correct population affinity classification using logistic regression analysis were higher than those obtained from discriminant function analysis. This study was the first of its type to employ discriminant function analyses and logistic regression analyses to estimate the population affinity of an individual from the talus. Thus these equations can now be used by South African anthropologists when estimating the population affinity of dismembered or damaged or incomplete skeletal remains of SAA and SAW. Copyright © 2018 Elsevier B.V. All rights reserved.

Potential Role of Gut Microbiota in ALS Pathogenesis and Possible Novel Therapeutic Strategies.

PubMed

Mazzini, Letizia; Mogna, Luca; De Marchi, Fabiola; Amoruso, Angela; Pane, Marco; Aloisio, Irene; Cionci, Nicole Bozzi; Gaggìa, Francesca; Lucenti, Ausiliatrice; Bersano, Enrica; Cantello, Roberto; Di Gioia, Diana; Mogna, Giovanni

2018-05-18

Recent preclinical studies suggest that dysfunction of gastrointestinal tract may play a role in amyotrophic lateral sclerosis (ALS) pathogenesis through a modification of the gut microbiota brain axis. Our study is the first focused on microbiota analysis in ALS patients. Our aim was to study the main human gut microbial groups and the overall microbial diversity in ALS and healthy subjects. Moreover we have examined the influence of a treatment with a specific bacteriotherapy composed of Lactobacillus strains (Lactobacillus fermentum, Lactobacillus delbrueckii, Lactobacillus plantarum, Lactobacillus salivarius) acting on the gastrointestinal barrier. We enrolled 50 ALS patients and 50 healthy controls, matched for sex, age, and origin. Fecal samples were used for total genomic DNA extraction. Enterobacteria, Bifidobacterium spp., Lactobacillus spp., Clostridium sensu stricto, Escherichia coli and yeast were quantified using quantitative polymerase chain reaction approach. Denaturing gradient gel electrophoresis analyses were performed to investigate total eubacteria and yeasts populations. Patients were randomized to double-blind treatment either with microorganisms or placebo for 6 months and monitored for clinical progression and microbiota composition. The comparison between ALS subjects and healthy group revealed a variation in the intestinal microbial composition with a higher abundance of E. coli and enterobacteria and a low abundance of total yeast in patients. Polymerase chain reaction denaturing gradient gel electrophoresis analysis showed a cluster distinction between the bacterial profiles of ALS patients and the healthy subjects. The complexity of the profiles in both cases may indicate that a real dysbiosis status is not evident in the ALS patients although differences between healthy and patients exist. The effects of the progression of the disease and of the bacteriotherapy on the bacterial and yeast populations are currently in progress. Our preliminary results confirm that there is a difference in the microbiota profile in ALS patients.

Magnitude of dyslipedemia and its association with micro and macro vascular complications in type 2 diabetes: a hospital based study from Bikaner (Northwest India).

PubMed

Agrawal, R P; Sharma, Poornima; Pal, Mahender; Kochar, A; Kochar, D K

2006-08-01

Type 2 diabetes is not only associated with hyperglycemia but also with disorders of lipid metabolism. The aim of this study was to investigate the association of dyslipedemia with micro and macro vascular complications of diabetes. Population based cross sectional study included 4067 diabetic patients who visited hospital during January 2000 to December 2002. Lipid profile was estimated by semi autoanalyser, Retinopathy was assessed by fundoscopy, Nephropathy by microalbuminurea, coronary artery disease (CAD) by electro cardiogram (ECG) changes, peripheral vascular disease (PVD) by doppler study and neuropathy by clinical examinations. The association of dyslipedemia with micro and macro vascular complications was assessed by regression analysis. The prevalence of dyslipedemia is high in diabetic population with high serum cholesterol >240mg/dl was seen in 15%, serum triglycerides >160mg/dl was seen in 42.41%, raised LDL >130mg/dl in 45.26%, VLDL >40mg/dl in 24.09% and low levels of HDL-C <40mg/dl were seen in 52.27%. On regression analysis, CAD had strong correlation with high levels of VLDL (0.76), triglycerides (0.82), LDL (0.23) and low HDL (-0.81). Similar association was seen with PVD. Diabetic retinopathy and nephropathy were found to have significant correlation with low HDL (-0.43) and raised LDL (0.37), respectively. Neuropathy was not found to have any significant correlation with lipid profile abnormalities. Lipid profile abnormalities are very common in type 2 diabetes and it has great influence on CAD and PVD. Hence, appropriate preventive and treatment strategies should be considered timely.

Differential gene expression in dentate granule cells in mesial temporal lobe epilepsy with and without hippocampal sclerosis.

PubMed

Griffin, Nicole G; Wang, Yu; Hulette, Christine M; Halvorsen, Matt; Cronin, Kenneth D; Walley, Nicole M; Haglund, Michael M; Radtke, Rodney A; Skene, J H Pate; Sinha, Saurabh R; Heinzen, Erin L

2016-03-01

Hippocampal sclerosis is the most common neuropathologic finding in cases of medically intractable mesial temporal lobe epilepsy. In this study, we analyzed the gene expression profiles of dentate granule cells of patients with mesial temporal lobe epilepsy with and without hippocampal sclerosis to show that next-generation sequencing methods can produce interpretable genomic data from RNA collected from small homogenous cell populations, and to shed light on the transcriptional changes associated with hippocampal sclerosis. RNA was extracted, and complementary DNA (cDNA) was prepared and amplified from dentate granule cells that had been harvested by laser capture microdissection from surgically resected hippocampi from patients with mesial temporal lobe epilepsy with and without hippocampal sclerosis. Sequencing libraries were sequenced, and the resulting sequencing reads were aligned to the reference genome. Differential expression analysis was used to ascertain expression differences between patients with and without hippocampal sclerosis. Greater than 90% of the RNA-Seq reads aligned to the reference. There was high concordance between transcriptional profiles obtained for duplicate samples. Principal component analysis revealed that the presence or absence of hippocampal sclerosis was the main determinant of the variance within the data. Among the genes up-regulated in the hippocampal sclerosis samples, there was significant enrichment for genes involved in oxidative phosphorylation. By analyzing the gene expression profiles of dentate granule cells from surgically resected hippocampal specimens from patients with mesial temporal lobe epilepsy with and without hippocampal sclerosis, we have demonstrated the utility of next-generation sequencing methods for producing biologically relevant results from small populations of homogeneous cells, and have provided insight on the transcriptional changes associated with this pathology. Wiley Periodicals, Inc. © 2016 International League Against Epilepsy.

Ultrahigh-resolution spectroscopy with atomic or molecular dark resonances: Exact steady-state line shapes and asymptotic profiles in the adiabatic pulsed regime

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

Zanon-Willette, Thomas; Clercq, Emeric de; Arimondo, Ennio

2011-12-15

Exact and asymptotic line shape expressions are derived from the semiclassical density matrix representation describing a set of closed three-level {Lambda} atomic or molecular states including decoherences, relaxation rates, and light shifts. An accurate analysis of the exact steady-state dark-resonance profile describing the Autler-Townes doublet, the electromagnetically induced transparency or coherent population trapping resonance, and the Fano-Feshbach line shape leads to the linewidth expression of the two-photon Raman transition and frequency shifts associated to the clock transition. From an adiabatic analysis of the dynamical optical Bloch equations in the weak field limit, a pumping time required to efficiently trap amore » large number of atoms into a coherent superposition of long-lived states is established. For a highly asymmetrical configuration with different decay channels, a strong two-photon resonance based on a lower states population inversion is established when the driving continuous-wave laser fields are greatly unbalanced. When time separated resonant two-photon pulses are applied in the adiabatic pulsed regime for atomic or molecular clock engineering, where the first pulse is long enough to reach a coherent steady-state preparation and the second pulse is very short to avoid repumping into a new dark state, dark-resonance fringes mixing continuous-wave line shape properties and coherent Ramsey oscillations are created. Those fringes allow interrogation schemes bypassing the power broadening effect. Frequency shifts affecting the central clock fringe computed from asymptotic profiles and related to the Raman decoherence process exhibit nonlinear shapes with the three-level observable used for quantum measurement. We point out that different observables experience different shifts on the lower-state clock transition.« less

[Demography and donation frequencies of blood and plasma donor populations in Germany].

PubMed

Ritter, Sabine; Willand, L; Reinhard, B; Offergeld, R; Hamouda, O

2008-08-01

According to Article 22 of the Transfusion Act, the Robert Koch Institute collects and evaluates nationwide data on the prevalence and incidence of transfusion-relevant infections among blood and plasma donors in Germany. Due to revision of the Transfusion Act in 2005 not only the number of donations but also the number of donors has become available for analysis. Here we give a detailed account on the demographic profile and donation frequencies of German whole blood, plasma and platelet donors in 2006. Overall, 4 % of the German population eligible to donate were active as repeat whole blood donors in 2006; 0.3 % repeatedly donated plasma or platelets. Irrespective of the type of donation, the percentage of donors among the general population was highest among the youngest age group (18 to 24 years). While the age distribution of whole blood repeat donors roughly resembled that of the general population, with the greatest number among those aged 35 to 44, younger age groups were overrepresented among repeat plasma donors. Donation frequency varied depending on donor age and sex, with an average of 1.9 per year for whole blood donations, 11.9 for plasmapheresis and 4.0 for plateletpheresis. With the exception of the latter, men donated more frequently than women. For both sexes, donation frequency increased with age. Detailed knowledge of the demographic profile and changes in the composition of donor populations are essential for planning adequate blood supply. The data presented may serve as reference for assessing the consequences of measures that affect the number of donors and/or donations (for example changing deferral criteria) in Germany.

Essential oils and chemical diversity of southeast European populations of Salvia officinalis L.

PubMed

Cvetkovikj, Ivana; Stefkov, Gjoshe; Karapandzova, Marija; Kulevanova, Svetlana; Satović, Zlatko

2015-07-01

The essential oils of 25 populations of Dalmatian sage (Salvia officinalis L.) from nine Balkan countries, including 17 indigenous populations (representing almost the entire native distribution area) and eight non-indigenous (cultivated or naturalized) populations were analyzed. Their essential-oil yield ranged from 0.25 to 3.48%. Within the total of 80 detected compounds, ten (β-pinene, 1,8-cineole, cis-thujone, trans-thujone, camphor, borneol, trans-caryophyllene, α-humulene, viridiflorol, and manool) represented 42.60 to 85.70% of the components in the analyzed essential oils. Strong positive correlations were observed between the contents of trans-caryophyllene and α-humulene, α-humulene and viridiflorol, and viridiflorol and manool. Principal component analysis (PCA) on the basis of the contents of the ten main compounds showed that four principal components had an eigenvalue greater than 1 and explained 79.87% of the total variation. Performing cluster analysis (CA), the sage populations could be grouped into four distinct chemotypes (A-D). The essential oils of 14 out of the 25 populations of Dalmatian sage belonged to Chemotype A and were rich in cis-thujone and camphor, with low contents of trans-thujone. The correlation between the essential-oil composition and geographic variables of the indigenous populations was not significant; hence, the similarities in the essential-oil profile among populations could not be explained by the physical proximity of the populations. Additionally, the southeastern populations tended to have higher EO yields than the northwestern ones. Copyright © 2015 Verlag Helvetica Chimica Acta AG, Zürich.

Tobacco, Marijuana, and Alcohol Use in University Students: A Cluster Analysis

PubMed Central

Primack, Brian A.; Kim, Kevin H.; Shensa, Ariel; Sidani, Jaime E.; Barnett, Tracey E.; Switzer, Galen E.

2012-01-01

Objective Segmentation of populations may facilitate development of targeted substance abuse prevention programs. We aimed to partition a national sample of university students according to profiles based on substance use. Participants We used 2008–2009 data from the National College Health Assessment from the American College Health Association. Our sample consisted of 111,245 individuals from 158 institutions. Method We partitioned the sample using cluster analysis according to current substance use behaviors. We examined the association of cluster membership with individual and institutional characteristics. Results Cluster analysis yielded six distinct clusters. Three individual factors—gender, year in school, and fraternity/sorority membership—were the most strongly associated with cluster membership. Conclusions In a large sample of university students, we were able to identify six distinct patterns of substance abuse. It may be valuable to target specific populations of college-aged substance users based on individual factors. However, comprehensive intervention will require a multifaceted approach. PMID:22686360

Fractal-like Distributions over the Rational Numbers in High-throughput Biological and Clinical Data

NASA Astrophysics Data System (ADS)

Trifonov, Vladimir; Pasqualucci, Laura; Dalla-Favera, Riccardo; Rabadan, Raul

2011-12-01

Recent developments in extracting and processing biological and clinical data are allowing quantitative approaches to studying living systems. High-throughput sequencing (HTS), expression profiles, proteomics, and electronic health records (EHR) are some examples of such technologies. Extracting meaningful information from those technologies requires careful analysis of the large volumes of data they produce. In this note, we present a set of fractal-like distributions that commonly appear in the analysis of such data. The first set of examples are drawn from a HTS experiment. Here, the distributions appear as part of the evaluation of the error rate of the sequencing and the identification of tumorogenic genomic alterations. The other examples are obtained from risk factor evaluation and analysis of relative disease prevalence and co-mordbidity as these appear in EHR. The distributions are also relevant to identification of subclonal populations in tumors and the study of quasi-species and intrahost diversity of viral populations.

Clonal architecture of secondary acute myeloid leukemia defined by single-cell sequencing.

PubMed

Hughes, Andrew E O; Magrini, Vincent; Demeter, Ryan; Miller, Christopher A; Fulton, Robert; Fulton, Lucinda L; Eades, William C; Elliott, Kevin; Heath, Sharon; Westervelt, Peter; Ding, Li; Conrad, Donald F; White, Brian S; Shao, Jin; Link, Daniel C; DiPersio, John F; Mardis, Elaine R; Wilson, Richard K; Ley, Timothy J; Walter, Matthew J; Graubert, Timothy A

2014-07-01

Next-generation sequencing has been used to infer the clonality of heterogeneous tumor samples. These analyses yield specific predictions-the population frequency of individual clones, their genetic composition, and their evolutionary relationships-which we set out to test by sequencing individual cells from three subjects diagnosed with secondary acute myeloid leukemia, each of whom had been previously characterized by whole genome sequencing of unfractionated tumor samples. Single-cell mutation profiling strongly supported the clonal architecture implied by the analysis of bulk material. In addition, it resolved the clonal assignment of single nucleotide variants that had been initially ambiguous and identified areas of previously unappreciated complexity. Accordingly, we find that many of the key assumptions underlying the analysis of tumor clonality by deep sequencing of unfractionated material are valid. Furthermore, we illustrate a single-cell sequencing strategy for interrogating the clonal relationships among known variants that is cost-effective, scalable, and adaptable to the analysis of both hematopoietic and solid tumors, or any heterogeneous population of cells.

Injury profiles related to mortality in patients with a low Injury Severity Score: a case-mix issue?

PubMed

Joosse, Pieter; Schep, Niels W L; Goslings, J Carel

2012-07-01

Outcome prediction models are widely used to evaluate trauma care. External benchmarking provides individual institutions with a tool to compare survival with a reference dataset. However, these models do have limitations. In this study, the hypothesis was tested whether specific injuries are associated with increased mortality and whether differences in case-mix of these injuries influence outcome comparison. A retrospective study was conducted in a Dutch trauma region. Injury profiles, based on injuries most frequently endured by unexpected death, were determined. The association between these injury profiles and mortality was studied in patients with a low Injury Severity Score by logistic regression. The standardized survival of our population (Ws statistic) was compared with North-American and British reference databases, with and without patients suffering from previously defined injury profiles. In total, 14,811 patients were included. Hip fractures, minor pelvic fractures, femur fractures, and minor thoracic injuries were significantly associated with mortality corrected for age, sex, and physiologic derangement in patients with a low injury severity. Odds ratios ranged from 2.42 to 2.92. The Ws statistic for comparison with North-American databases significantly improved after exclusion of patients with these injuries. The Ws statistic for comparison with a British reference database remained unchanged. Hip fractures, minor pelvic fractures, femur fractures, and minor thoracic wall injuries are associated with increased mortality. Comparative outcome analysis of a population with a reference database that differs in case-mix with respect to these injuries should be interpreted cautiously. Prognostic study, level II.

DNA methylation profiling reveals the presence of population-specific signatures correlating with phenotypic characteristics.

PubMed

Giri, Anil K; Bharadwaj, Soham; Banerjee, Priyanka; Chakraborty, Shraddha; Parekatt, Vaisak; Rajashekar, Donaka; Tomar, Abhishek; Ravindran, Aarthi; Basu, Analabha; Tandon, Nikhil; Bharadwaj, Dwaipayan

2017-06-01

Phenotypic characteristics are known to vary substantially among different ethnicities around the globe. These variations are mediated by number of stochastic events and cannot be attributed to genetic architecture alone. DNA methylation is a well-established mechanism that sculpts our epigenome influencing phenotypic variation including disease manifestation. Since DNA methylation is an important determinant for health issues of a population, it demands a thorough investigation of the natural differences in genome wide DNA methylation patterns across different ethnic groups. This study is based on comparative analyses of methylome from five different ethnicities with major focus on Indian subjects. The current study uses hierarchical clustering approaches, principal component analysis and locus specific differential methylation analysis on Illumina 450K methylation data to compare methylome of different ethnic subjects. Our data indicates that the variations in DNA methylation patterns of Indians are less among themselves compared to other global population. It empirically correlated with dietary, cultural and demographical divergences across different ethnic groups. Our work further suggests that Indians included in this study, despite their genetic similarity with the Caucasian population, are in close proximity with Japanese in terms of their methylation signatures.

Study of electronic structure and Compton profiles of transition metal diborides

NASA Astrophysics Data System (ADS)

Bhatt, Samir; Heda, N. L.; Kumar, Kishor; Ahuja, B. L.

2017-08-01

We report Compton profiles (CPs) of transition metal diborides (MB2; M= Ti and Zr) using a 740 GBq 137Cs Compton spectrometer measured at an intermediate resolution of 0.34 a.u. To validate the experimental momentum densities, we have employed the linear combination of atomic orbitals (LCAO) method to compute the theoretical CPs along with the energy bands, density of states (DOS) and Mulliken's population response. The LCAO computations have been performed in the frame work of density functional theory (DFT) and hybridization of Hartree-Fock and DFT (namely B3LYP and PBE0). For both the diborides, the CPs based on revised Perdew-Burke-Ernzerhof exchange and correlation functions (DFT-PBESol) lead to a better agreement with the experimental momentum densities than other reported approximations. Energy bands, DOS and real space analysis of CPs confirm a metallic-like character of both the borides. Further, a comparison of DFT-PBESol and experimental data on equal-valence-electron-density scale shows more ionicity in ZrB2 than that in TiB2, which is also supported by the Mulliken's population based charge transfer data.

Categorizing Cells on the Basis of their Chemical Profiles: Progress in Single-Cell Mass Spectrometry.

PubMed

Comi, Troy J; Do, Thanh D; Rubakhin, Stanislav S; Sweedler, Jonathan V

2017-03-22

The chemical differences between individual cells within large cellular populations provide unique information on organisms' homeostasis and the development of diseased states. Even genetically identical cell lineages diverge due to local microenvironments and stochastic processes. The minute sample volumes and low abundance of some constituents in cells hinder our understanding of cellular heterogeneity. Although amplification methods facilitate single-cell genomics and transcriptomics, the characterization of metabolites and proteins remains challenging both because of the lack of effective amplification approaches and the wide diversity in cellular constituents. Mass spectrometry has become an enabling technology for the investigation of individual cellular metabolite profiles with its exquisite sensitivity, large dynamic range, and ability to characterize hundreds to thousands of compounds. While advances in instrumentation have improved figures of merit, acquiring measurements at high throughput and sampling from large populations of cells are still not routine. In this Perspective, we highlight the current trends and progress in mass-spectrometry-based analysis of single cells, with a focus on the technologies that will enable the next generation of single-cell measurements.

In vitro ovine articular chondrocyte proliferation: experiments and modelling.

PubMed

Mancuso, L; Liuzzo, M I; Fadda, S; Pisu, M; Cincotti, A; Arras, M; La Nasa, G; Concas, A; Cao, G

2010-06-01

This study focuses on analysis of in vitro cultures of chondrocytes from ovine articular cartilage. Isolated cells were seeded in Petri dishes, then expanded to confluence and phenotypically characterized by flow cytometry. The sigmoidal temporal profile of total counts was obtained by classic haemocytometry and corresponding cell size distributions were measured electronically using a Coulter Counter. A mathematical model recently proposed (1) was adopted for quantitative interpretation of these experimental data. The model is based on a 1-D (that is, mass-structured), single-staged population balance approach capable of taking into account contact inhibition at confluence. The model's parameters were determined by fitting measured total cell counts and size distributions. Model reliability was verified by predicting cell proliferation counts and corresponding size distributions at culture times longer than those used when tuning the model's parameters. It was found that adoption of cell mass as the intrinsic characteristic of a growing chondrocyte population enables sigmoidal temporal profiles of total counts in the Petri dish, as well as cell size distributions at 'balanced growth', to be adequately predicted.

School-readiness profiles of children with language impairment: linkages to home and classroom experiences.

PubMed

Pentimonti, Jill M; Justice, Laura M; Kaderavek, Joan N

2014-01-01

This study represents an effort to advance our understanding of the nature of school readiness among children with language impairment (LI), a population of children acknowledged to be at risk of poor academic achievement. The academic, social-emotional, and behavioural competencies with which children arrive at kindergarten affect the nature of their future educational experiences, and their overall academic achievement. To examine whether there are reliable profiles that characterize children with LI just prior to kindergarten entrance, and the extent to which profile membership is associated with characteristics of children's homes and preschool experiences. Questions addressed were twofold: (1) To what extent are there reliable profiles of children with LI with respect to their school readiness? (2) To what extent is children's profile membership associated with characteristics of their homes and preschool classrooms? Participants were 136 children with LI from early childhood special education classrooms. We utilized latent class analysis (LCA) to classify individuals into profiles based on individual responses on school readiness measures. We then used multilevel hierarchical generalized linear models to examine the relations between profile membership and children's home/classroom experiences. LCA analyses revealed that a four-profile solution was the most appropriate fit for the data and that classroom experiences were predictive of these profiles, such that children in classrooms with more instructional/emotional support were more likely to be placed in profiles characterized by higher school readiness skills. These results suggest that the school readiness profiles of young children with LI are associated with the quality of children's classroom experiences, and that high-quality classroom experiences can be influential for ensuring that young children with LI arrive in kindergarten ready to learn. © 2014 Royal College of Speech and Language Therapists.

Diversity of Staphylococcus pseudintermedius in carriage sites and skin lesions of dogs with superficial bacterial folliculitis: potential implications for diagnostic testing and therapy.

PubMed

Larsen, Rikke Friis; Boysen, Lene; Jessen, Lisbeth Rem; Guardabassi, Luca; Damborg, Peter

2018-05-21

Staphylococcus pseudintermedius is genotypically diverse within the canine population and multiple strains may colonize individual dogs at any given time. If multiple strains with distinct antimicrobial resistance profiles are present in superficial bacterial folliculitis (SBF), sampling a single skin lesion for culture and antimicrobial susceptibility testing (AST) might be inadequate to select effective therapy. To investigate S. pseudintermedius diversity in carriage sites and lesions of dogs with SBF. Fourteen dogs with SBF. Staphylococcus pseudintermedius isolates obtained from perineum, gingiva and four to six skin lesions per dog were subjected to pulsed-field gel electrophoresis (PFGE) and AST to assess diversity between lesions. For two dogs, 14-16 isolates per lesion were included in the analysis to assess diversity within lesions. Analysis of one isolate per lesion revealed one to four strains displaying unique PFGE profiles, and up to three unique antimicrobial resistance (AMR) profiles for each dog. Multiple pustules from the same dog always harboured the same strain, whereas papules, crusts and collarettes did not. Up to four strains with distinct AMR profiles were isolated from the same lesion in two dogs. In 12 dogs, at least one carriage site strain also was represented in lesions. Lesions of SBF may harbour multiple S. pseudintermedius strains with distinct antimicrobial resistance profiles. Pustules are the best target for bacterial culture. It remains unclear whether isolation of different strains from other lesion types is a consequence of contamination or co-infection by multiple strains. © 2018 ESVD and ACVD.

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

Kalesse, Heike; Szyrmer, Wanda; Kneifel, Stefan

In this paper, Radar Doppler spectra measurements are exploited to study a riming event when precipitating ice from a seeder cloud sediment through a supercooled liquid water (SLW) layer. The focus is on the "golden sample" case study for this type of analysis based on observations collected during the deployment of the Atmospheric Radiation Measurement Program's (ARM) mobile facility AMF2 at Hyytiälä, Finland, during the Biogenic Aerosols – Effects on Clouds and Climate (BAECC) field campaign. The presented analysis of the height evolution of the radar Doppler spectra is a state-of-the-art retrieval with profiling cloud radars in SLW layers beyondmore » the traditional use of spectral moments. Dynamical effects are considered by following the particle population evolution along slanted tracks that are caused by horizontal advection of the cloud under wind shear conditions. In the SLW layer, the identified liquid peak is used as an air motion tracer to correct the Doppler spectra for vertical air motion and the ice peak is used to study the radar profiles of rimed particles. A 1-D steady-state bin microphysical model is constrained using the SLW and air motion profiles and cloud top radar observations. The observed radar moment profiles of the rimed snow can be simulated reasonably well by the model, but not without making several assumptions about the ice particle concentration and the relative role of deposition and aggregation. In conclusion, this suggests that in situ observations of key ice properties are needed to complement the profiling radar observations before process-oriented studies can effectively evaluate ice microphysical parameterizations.« less

Pneumocystis jirovecii multilocus genotyping profiles in patients from Portugal and Spain.

PubMed

Esteves, F; Montes-Cano, M A; de la Horra, C; Costa, M C; Calderón, E J; Antunes, F; Matos, O

2008-04-01

Pneumonia caused by the opportunistic organism Pneumocystis jirovecii is a clinically important infection affecting AIDS and other immunocompromised patients. The present study aimed to compare and characterise the frequency pattern of DNA sequences from the P. jirovecii mitochondrial large-subunit rRNA (mtLSU rRNA) gene, the dihydropteroate synthase (DHPS) gene and the internal transcribed spacer (ITS) regions of the nuclear rRNA operon in specimens from Lisbon (Portugal) and Seville (Spain). Total DNA was extracted and used for specific molecular sequence analysis of the three loci. In both populations, mtLSU rRNA gene analysis revealed an overall prevalence of genotype 1. In the Portuguese population, genotype 2 was the second most common, followed by genotype 3. Inversely, in the Spanish population, genotype 3 was the second most common, followed by genotype 2. The DHPS wild-type sequence was the genotype observed most frequently in both populations, and the DHPS genotype frequency pattern was identical to distribution patterns revealed in other European studies. ITS types showed a significant diversity in both populations because of the high sequence variability in these genomic regions. The most prevalent ITS type in the Portuguese population was Eg, followed by Cg. In contrast to other European studies, Bi was the most common ITS type in the Spanish samples, followed by Eg. A statistically significant association between mtLSU rRNA genotype 1 and ITS type Eg was revealed.

Independent components of neural activity carry information on individual populations.

PubMed

Głąbska, Helena; Potworowski, Jan; Łęski, Szymon; Wójcik, Daniel K

2014-01-01

Local field potential (LFP), the low-frequency part of the potential recorded extracellularly in the brain, reflects neural activity at the population level. The interpretation of LFP is complicated because it can mix activity from remote cells, on the order of millimeters from the electrode. To understand better the relation between the recordings and the local activity of cells we used a large-scale network thalamocortical model to compute simultaneous LFP, transmembrane currents, and spiking activity. We used this model to study the information contained in independent components obtained from the reconstructed Current Source Density (CSD), which smooths transmembrane currents, decomposed further with Independent Component Analysis (ICA). We found that the three most robust components matched well the activity of two dominating cell populations: superior pyramidal cells in layer 2/3 (rhythmic spiking) and tufted pyramids from layer 5 (intrinsically bursting). The pyramidal population from layer 2/3 could not be well described as a product of spatial profile and temporal activation, but by a sum of two such products which we recovered in two of the ICA components in our analysis, which correspond to the two first principal components of PCA decomposition of layer 2/3 population activity. At low noise one more cell population could be discerned but it is unlikely that it could be recovered in experiment given typical noise ranges.

Independent Components of Neural Activity Carry Information on Individual Populations

PubMed Central

Głąbska, Helena; Potworowski, Jan; Łęski, Szymon; Wójcik, Daniel K.

2014-01-01

Local field potential (LFP), the low-frequency part of the potential recorded extracellularly in the brain, reflects neural activity at the population level. The interpretation of LFP is complicated because it can mix activity from remote cells, on the order of millimeters from the electrode. To understand better the relation between the recordings and the local activity of cells we used a large-scale network thalamocortical model to compute simultaneous LFP, transmembrane currents, and spiking activity. We used this model to study the information contained in independent components obtained from the reconstructed Current Source Density (CSD), which smooths transmembrane currents, decomposed further with Independent Component Analysis (ICA). We found that the three most robust components matched well the activity of two dominating cell populations: superior pyramidal cells in layer 2/3 (rhythmic spiking) and tufted pyramids from layer 5 (intrinsically bursting). The pyramidal population from layer 2/3 could not be well described as a product of spatial profile and temporal activation, but by a sum of two such products which we recovered in two of the ICA components in our analysis, which correspond to the two first principal components of PCA decomposition of layer 2/3 population activity. At low noise one more cell population could be discerned but it is unlikely that it could be recovered in experiment given typical noise ranges. PMID:25153730

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

Genetic differentiation in Pyrenophora teres f. teres populations from Syria and Tunisia as assessed by AFLP markers.

PubMed

Bouajila, A; Zoghlami, N; Murad, S; Baum, M; Ghorbel, A; Nazari, K

2013-06-01

To investigate the level of genetic differentiation and diversity among Pyrenophora teres isolate populations originating from different agro-ecological areas of Syria and Tunisia and to determine the potential of AFLP profiling in genotyping Pyrenophora teres f. teres. In this study, AFLP markers have been employed to identify patterns of population structure in 20 Pyrenophora teres f. teres populations from Syria and Tunisia. Ninety-four isolates were studied by the use of a protocol that involved stringent PCR amplification of fragments derived from digestion of genomic DNA with restriction enzymes EcoRI and MesI. Based on 401 amplified polymorphic DNA markers (AFLP), variance analyses indicated that most of the variation was partitioned within rather than between populations. Genotypic diversity (GD) was high for populations from Rihane, local landraces and different agro-ecological zones (GD = 0·75-0·86). There was high genetic differentiation among pathogen populations from different host populations in Syria (Gst  = 0·31, ht = 0·190) and Tunisia (Gst  = 0·39, ht = 0·263), which may be partly explained by the low gene flow around the areas sampled. A phenetic tree revealed three groups with high bootstrap values (55, 68, 76) and reflected the grouping of isolates based on host, or agro-ecological areas. AFLP profiling is an effective method for typing the genetically diverse pathogen Pyrenophora teres f. teres. The study represents a comparative analysis of the genetic diversity in P. teres isolates from two countries spanning two continents and also shows that several distinct P. teres genotypes may be found in a given environment. The implications of these findings for Pyrenophora teres f. teres evolutionary potential and net blotch-resistance breeding in Syria and Tunisia were also discussed. © 2012 The Society for Applied Microbiology.

The 80:20 phenomenon: help or hindrance to planning caries prevention programmes?

PubMed

Tickle, Martin

2002-03-01

to compare the outcomes of population segmentation analyses according to caries experience using the distribution of dmft and the Super Profiles geodemographic classification. The study population consisted of all 15,747 children in seven districts in the North West Region, England who were examined in whole population surveys during the 1995/6 NHS epidemiological survey of 5-year-old children. Market penetration analyses were used to segment this population according to caries experience by their dmft score and by the Super Profiles geodemographic classification. Lorenz curves were plotted and Gini coefficients were calculated from the outputs. When dmft was used to segment the population approximately 80% of carious teeth were found in some 42% of the total population, producing a Lorenz Curve with a Gini coefficient of 66%. The population was then segmented using Super Profiles Target Markets. The target markets were ranked according to caries experience and the denominator population living in each of these area types. Some 81% of the total population dmft was found in the topmost ranked 73.8% of the total population. The resultant Lorenz curve produced a Gini coefficient of 16.2%. About half of the population disease was confined to a minority of the population but not to the extent of 80% of the disease in 20% of the population. Although these high risk children were more commonly found in underprivileged area types, they did not live exclusively in a small number of deprived areas. These findings shed doubt on the wisdom of a targeted approach to oral health promotion and disease prevention programmes.

Mono-allelic expression of variegating transgene locus in the mouse.

PubMed

Opsahl, Margaret L; Springbett, Anthea; Lathe, Richard; Colman, Alan; McClenaghan, Margaret; Whitelaw, C Bruce A

2003-12-01

We have generated transgenic mice which express an ovine beta-lactoglobulin transgene during lactation. In two transgenic lines, BLG/7 and BLG/45, beta-lactoglobulin protein levels vary between siblings, reflected at the cellular level by a mosaic transgene expression pattern in the mammary tissue that is reminiscent of position effect variegation. To investigate whether this variegating expression profile can be affected by the introduction of an identical variegating locus on the homologous chromosome, we compared the beta-lactoglobulin expression profiles in mice hemizygous or homozygous for the transgene locus. In BLG/45 mice, milk protein analysis revealed that transgene expression was effectively doubled in homozygous compared to hemizygous mice. In contrast, beta-lactoglobulin protein in hemizygous and homozygous BLG/7 mice displayed a similar range; although minimum expression levels were doubled in the homozygous population, the maximum level of expression was indistinguishable between the two populations. Fluorescent in situ hybridisation (FISH) for transgene mRNA indicated that for a given protein level, the extent of cellular expression is similar in both BLG/7 populations. In homozygous mice genomic DNA and nuclear RNA FISH demonstrated that only one of the two BLG/7 loci is active in expressing cells, while two transcription foci were present in BLG/45 homozygous mice. This mono-allelic transgene expression pattern is not inherited through the germline, as hemizygous mice bred from homozygous parents expressed at the expected hemizygous population level. We discuss these observations in the context of known epigenetic events such as imprinting and trans-inactivation.

The substance use risk profile scale: a scale measuring traits linked to reinforcement-specific substance use profiles.

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

Woicik, P.A.; Stewart, S.H.; Pihl, R.O.

The Substance Use Risk Profile Scale (SURPS) is based on a model of personality risk for substance abuse in which four personality dimensions (hopelessness, anxiety sensitivity, impulsivity, and sensation seeking) are hypothesized to differentially relate to specific patterns of substance use. The current series of studies is a preliminary exploration of the psychometric properties of the SURPS in two populations (undergraduate and high school students). In study 1, an analysis of the internal structure of two versions of the SURPS shows that the abbreviated version best reflects the 4-factor structure. Concurrent, discriminant, and incremental validity of the SURPS is supportedmore » by convergent/divergent relationships between the SURPS subscales and other theoretically relevant personality and drug use criterion measures. In Study 2, the factorial structure of the SURPS is confirmed and evidence is provided for its test-retest reliability and validity with respect to measuring personality vulnerability to reinforcement-specific substance use patterns. In Study 3, the SURPS was administered in a more youthful population to test its sensitivity in identifying younger problematic drinkers. The results from the current series of studies demonstrate support for the reliability and construct validity of the SURPS, and suggest that four personality dimensions may be linked to substance-related behavior through different reinforcement processes. This brief assessment tool may have important implications for clinicians and future research.« less

Clinical, epidemiological, and therapeutic profile of dermatophytosis*

PubMed Central

Pires, Carla Andréa Avelar; da Cruz, Natasha Ferreira Santos; Lobato, Amanda Monteiro; de Sousa, Priscila Oliveira; Carneiro, Francisca Regina Oliveira; Mendes, Alena Margareth Darwich

2014-01-01

BACKGROUND The cutaneous mycoses, mainly caused by dermatophyte fungi, are among the most common fungal infections worldwide. It is estimated that 10% to 15% of the population will be infected by a dermatophyte at some point in their lives, thus making this a group of diseases with great public health importance. OBJECTIVE To analyze the clinical, epidemiological, and therapeutic profile of dermatophytosis in patients enrolled at the Dermatology service of Universidade do Estado do Pará, Brazil, from July 2010 to September 2012. METHOD A total of 145 medical records of patients diagnosed with dermatophytosis were surveyed. Data were collected and subsequently recorded according to a protocol developed by the researchers. This protocol consisted of information regarding epidemiological and clinical aspects of the disease and the therapy employed. RESULTS The main clinical form of dermatophyte infection was onychomycosis, followed by tinea corporis, tinea pedis, and tinea capitis. Furthermore, the female population and the age group of 51 to 60 years were the most affected. Regarding therapy, there was a preference for treatments that combine topical and systemic drugs, and the most widely used drugs were fluconazole (systemic) and ciclopirox olamine (topical). CONCLUSION This study showed the importance of recurrent analysis of the epidemiological profile of dermatophytosis to enable correct therapeutic and preventive management of these conditions, which have significant clinical consequences, with chronic, difficult-totreat lesions that can decrease patient quality of life and cause disfigurement. PMID:24770502

Bisulfite-independent analysis of CpG island methylation enables genome-scale stratification of single cells

PubMed Central

Han, Lin; Wu, Hua-Jun; Zhu, Haiying; Kim, Kun-Yong; Marjani, Sadie L.; Riester, Markus; Euskirchen, Ghia; Zi, Xiaoyuan; Yang, Jennifer; Han, Jasper; Snyder, Michael; Park, In-Hyun; Irizarry, Rafael; Weissman, Sherman M.

2017-01-01

Abstract Conventional DNA bisulfite sequencing has been extended to single cell level, but the coverage consistency is insufficient for parallel comparison. Here we report a novel method for genome-wide CpG island (CGI) methylation sequencing for single cells (scCGI-seq), combining methylation-sensitive restriction enzyme digestion and multiple displacement amplification for selective detection of methylated CGIs. We applied this method to analyzing single cells from two types of hematopoietic cells, K562 and GM12878 and small populations of fibroblasts and induced pluripotent stem cells. The method detected 21 798 CGIs (76% of all CGIs) per cell, and the number of CGIs consistently detected from all 16 profiled single cells was 20 864 (72.7%), with 12 961 promoters covered. This coverage represents a substantial improvement over results obtained using single cell reduced representation bisulfite sequencing, with a 66-fold increase in the fraction of consistently profiled CGIs across individual cells. Single cells of the same type were more similar to each other than to other types, but also displayed epigenetic heterogeneity. The method was further validated by comparing the CpG methylation pattern, methylation profile of CGIs/promoters and repeat regions and 41 classes of known regulatory markers to the ENCODE data. Although not every minor methylation differences between cells are detectable, scCGI-seq provides a solid tool for unsupervised stratification of a heterogeneous cell population. PMID:28126923

The Substance Use Risk Profile Scale: a scale measuring traits linked to reinforcement-specific substance use profiles.

PubMed

Woicik, Patricia A; Stewart, Sherry H; Pihl, Robert O; Conrod, Patricia J

2009-12-01

The Substance Use Risk Profile Scale (SURPS) is based on a model of personality risk for substance abuse in which four personality dimensions (hopelessness, anxiety sensitivity, impulsivity, and sensation seeking) are hypothesized to differentially relate to specific patterns of substance use. The current series of studies is a preliminary exploration of the psychometric properties of the SURPS in two populations (undergraduate and high school students). In study 1, an analysis of the internal structure of two versions of the SURPS shows that the abbreviated version best reflects the 4-factor structure. Concurrent, discriminant, and incremental validity of the SURPS is supported by convergent/divergent relationships between the SURPS subscales and other theoretically relevant personality and drug use criterion measures. In Study 2, the factorial structure of the SURPS is confirmed and evidence is provided for its test-retest reliability and validity with respect to measuring personality vulnerability to reinforcement-specific substance use patterns. In Study 3, the SURPS was administered in a more youthful population to test its sensitivity in identifying younger problematic drinkers. The results from the current series of studies demonstrate support for the reliability and construct validity of the SURPS, and suggest that four personality dimensions may be linked to substance-related behavior through different reinforcement processes. This brief assessment tool may have important implications for clinicians and future research.

Finding Clothing That Fit through Cluster Analysis and Objective Interestingness Measures

NASA Astrophysics Data System (ADS)

Peña, Isis; Viktor, Herna L.; Paquet, Eric

Clothes should fit consumers well, be aesthetically pleasing and comfortable. However, repeated studies of customers’ levels of satisfaction indicate that this is often not the case. For example, more robust males often find it difficult to find pants that are the correct length and fit their waists well. What, then, are the typical body profiles of the population? Would it be possible to identify the measurements that are of importance for different sizes and genders? Furthermore, assuming that we have access to an anthropometric database would there be a way to guide the data mining process to discover only those relevant body measurements that are of the most interest for apparel designers? This paper describes our results when addressing these questions through cluster analysis and interestingness measures-based feature selection. We explore a database containing anthropometric measurements as well as 3-D body scans, of a representative sample of the Dutch population.

[Poverty profile regarding households participating in a food assistance program].

PubMed

Álvarez-Uribe, Martha C; Aguirre-Acevedo, Daniel C

2012-06-01

This study was aimed at establishing subgroups having specific socioeconomic characteristics by using latent class analysis as a method for segmenting target population members of the MANA-ICBF supplementary food program in the Antioquia department of Colombia and determine their differences regarding poverty and health conditions in efficiently addressing pertinent resources, programs and policies. The target population consisted of 200,000 children and their households involved in the MANA food assistance program; a representative sample by region was used. Latent class analysis was used, as were the expectation-maximization and Newton Raphson algorithms for identifying the appropriate number of classes. The final model classified the households into four clusters or classes, differing according to well-defined socio-demographic conditions affecting children's health. Some homes had a greater depth of poverty, therefore lowering the families' quality of life and affecting the health of the children in this age group.

Headspace screening: A novel approach for fast quality assessment of the essential oil from culinary sage.

PubMed

Cvetkovikj, Ivana; Stefkov, Gjoshe; Acevska, Jelena; Karapandzova, Marija; Dimitrovska, Aneta; Kulevanova, Svetlana

2016-07-01

Quality assessment of essential oil (EO) from culinary sage (Salvia officinalis L., Lamiaceae) is limited by the long pharmacopoeial procedure. The aim of this study was to employ headspace (HS) sampling in the quality assessment of sage EO. Different populations (30) of culinary sage were assessed using GC/FID/MS analysis of the hydrodistilled EO (pharmacopoeial method) and HS sampling directly from leaves. Compound profiles from both procedures were evaluated according to ISO 9909 and GDC standards for sage EO quality, revealing compliance for only 10 populations. Factors to convert HS values, for the target ISO and GDC components, into theoretical EO values were calculated. Statistical analysis revealed a significant relationship between HS and EO values for seven target components. Consequently, HS sampling could be used as a complementary extraction technique for rapid screening in quality assessment of sage EOs. Copyright © 2016 Elsevier Ltd. All rights reserved.

Deconstructing stem cell population heterogeneity: Single-cell analysis and modeling approaches

PubMed Central

Wu, Jincheng; Tzanakakis, Emmanuel S.

2014-01-01

Isogenic stem cell populations display cell-to-cell variations in a multitude of attributes including gene or protein expression, epigenetic state, morphology, proliferation and proclivity for differentiation. The origins of the observed heterogeneity and its roles in the maintenance of pluripotency and the lineage specification of stem cells remain unclear. Addressing pertinent questions will require the employment of single-cell analysis methods as traditional cell biochemical and biomolecular assays yield mostly population-average data. In addition to time-lapse microscopy and flow cytometry, recent advances in single-cell genomic, transcriptomic and proteomic profiling are reviewed. The application of multiple displacement amplification, next generation sequencing, mass cytometry and spectrometry to stem cell systems is expected to provide a wealth of information affording unprecedented levels of multiparametric characterization of cell ensembles under defined conditions promoting pluripotency or commitment. Establishing connections between single-cell analysis information and the observed phenotypes will also require suitable mathematical models. Stem cell self-renewal and differentiation are orchestrated by the coordinated regulation of subcellular, intercellular and niche-wide processes spanning multiple time scales. Here, we discuss different modeling approaches and challenges arising from their application to stem cell populations. Integrating single-cell analysis with computational methods will fill gaps in our knowledge about the functions of heterogeneity in stem cell physiology. This combination will also aid the rational design of efficient differentiation and reprogramming strategies as well as bioprocesses for the production of clinically valuable stem cell derivatives. PMID:24035899

State Education Finance and Governance Profile: South Carolina

ERIC Educational Resources Information Center

Conrad, Zachary

2010-01-01

This article presents the state education finance and governance profile of South Carolina. In the state of South Carolina, the population in 1990 was estimated at 3,486,310, and as of July 2008 the population was estimated at 4,479,800. In terms of education funding, the K-12 education General Fund appropriation is $2,441,044,733 for Fiscal Year…

Prevalence and cardiovascular risk profile of chronic kidney disease in Italy: results of the 2008-12 National Health Examination Survey.

PubMed

De Nicola, Luca; Donfrancesco, Chiara; Minutolo, Roberto; Lo Noce, Cinzia; Palmieri, Luigi; De Curtis, Amalia; Iacoviello, Licia; Zoccali, Carmine; Gesualdo, Loreto; Conte, Giuseppe; Vanuzzo, Diego; Giampaoli, Simona

2015-05-01

National surveys in countries outside Europe have reported a high prevalence (11-13%) of chronic kidney disease (CKD). Studies in Europe have provided a variable prevalence likely due to differences in study design, including age and extent of geographic areas, equation used to evaluate estimated glomerular filtration rate (eGFR) and CKD stages examined. The 2008-12 National Health Examination Survey in Italy randomly extracted samples from the general population aged 35-79 years, stratified by age and gender, from the resident list of each Italian region (440 persons/1.5 million of residents). We estimated the prevalence of CKD by means of urinary albumin : creatinine ratio and eGFR (CKD-EPI equation-enzymatic assay of serum creatinine). Cardiovascular (CV) risk profile was also evaluated. Three thousand eight hundred and forty-eight men and 3704 women were examined. In the whole population, mean age was 57 ± 12 and 56 ± 12 years in men and women, respectively; hypertension was prevalent in men and women, respectively (56 and 43%) and the same held true for overweight (48 and 33%), obesity (26 and 27%), diabetes (14 and 9%) and smoking (21 and 18%), whereas CV disease was less frequent (9 and 6%). Overall, the prevalence of CKD (95% confidence interval) was 7.05% (6.48-7.65). Early stages constituted 59% of the CKD population [Stage G1-2 A2-3: 4.16% (3.71-4.61) and Stage G3-5: 2.89% (2.51-3.26)]. At multivariate regression analysis, age, obesity, hypertension, diabetes, CV disease and smoking were all independent correlates of CKD. CKD has a relatively lower prevalence in Italy, in particular for advanced stages, when compared with similar national surveys outside Europe. This occurs despite older age and unfavourable CV risk profile of the whole population. © The Author 2014. Published by Oxford University Press on behalf of ERA-EDTA. All rights reserved.

Direct analysis of phycobilisomal antenna proteins and metabolites in small cyanobacterial populations by laser ablation electrospray ionization mass spectrometry.

PubMed

Parsiegla, Goetz; Shrestha, Bindesh; Carrière, Frédéric; Vertes, Akos

2012-01-03

Due to their significance in energy and environmental and natural product research, as well as their large genetic diversity, rapid in situ analysis of cyanobacteria is of increasing interest. Metabolic profiles and the composition of energy harvesting antenna protein complexes are needed to understand how environmental factors affect the functioning of these microorganisms. Here, we show that laser ablation electrospray ionization (LAESI) mass spectrometry enables the direct analysis of phycobilisomal antenna proteins and report on numerous metabolites from intact cyanobacteria. Small populations (n < 616 ± 76) of vegetative Anabaena sp. PCC7120 cyanobacterial cells are analyzed by LAESI mass spectrometry. The spectra reveal the ratio of phycocyanin (C-PC) and allophycocyanin (APC) in the antenna complex, the subunit composition of the phycobiliproteins, and the tentative identity of over 30 metabolites and lipids. Metabolites are tentatively identified by accurate mass measurements, isotope distribution patterns, and literature searches. The rapid simultaneous analysis of abundant proteins and diverse metabolites enables the evaluation of the environmental response and metabolic adaptation of cyanobacteria and other microorganisms. © 2011 American Chemical Society

Use of Pearson's Chi-Square for Testing Equality of Percentile Profiles across Multiple Populations.

PubMed

Johnson, William D; Beyl, Robbie A; Burton, Jeffrey H; Johnson, Callie M; Romer, Jacob E; Zhang, Lei

2015-08-01

In large sample studies where distributions may be skewed and not readily transformed to symmetry, it may be of greater interest to compare different distributions in terms of percentiles rather than means. For example, it may be more informative to compare two or more populations with respect to their within population distributions by testing the hypothesis that their corresponding respective 10 th , 50 th , and 90 th percentiles are equal. As a generalization of the median test, the proposed test statistic is asymptotically distributed as Chi-square with degrees of freedom dependent upon the number of percentiles tested and constraints of the null hypothesis. Results from simulation studies are used to validate the nominal 0.05 significance level under the null hypothesis, and asymptotic power properties that are suitable for testing equality of percentile profiles against selected profile discrepancies for a variety of underlying distributions. A pragmatic example is provided to illustrate the comparison of the percentile profiles for four body mass index distributions.

Active epilepsy prevalence, the treatment gap, and treatment gap risk profile in eastern China: A population-based study.

PubMed

Ding, Xiaoyan; Zheng, Yang; Guo, Yi; Shen, Chunhong; Wang, Shan; Chen, Feng; Yan, Shengqiang; Ding, Meiping

2018-01-01

We measured the prevalence of active epilepsy and investigated the treatment gap and treatment gap risk profile in eastern China. This was a cross-sectional population-based survey conducted in Zhejiang, China, from October 2013 to March 2014. A total 54,976 people were selected using multi-stage cluster sampling. A two-stage questionnaire-based process was used to identify patients with active epilepsy and to record their demographic, socioeconomic, and epilepsy-related features. Logistic regression analysis was used to analyze risk factors of the treatment gap in eastern China, as adjusted for age and sex. We interviewed 50,035 people; 118 had active epilepsy (2.4‰), among which the treatment gap was 58.5%. In multivariate analysis, failure to receive appropriate antiepileptic treatment was associated with higher seizure frequency of 12-23 times per year (adjusted odds ratio=6.874; 95% confidence interval [CI]=2.372-19.918), >24 times per year (adjusted odds ratio=19.623; 95% CI=4.999-77.024), and a lack of health insurance (adjusted odds ratio=7.284; 95% CI=1.321-40.154). Eastern China has relatively lower prevalence of active epilepsy and smaller treatment gap. Interventions aimed at reducing seizure frequency, improving the health insurance system should be investigated as potential targets to further bridge the treatment gap. Copyright © 2017 Elsevier Inc. All rights reserved.

The first USH2A mutation analysis of Japanese autosomal recessive retinitis pigmentosa patients: a totally different mutation profile with the lack of frequent mutations found in Caucasian patients.

PubMed

Zhao, Yang; Hosono, Katsuhiro; Suto, Kimiko; Ishigami, Chie; Arai, Yuuki; Hikoya, Akiko; Hirami, Yasuhiko; Ohtsubo, Masafumi; Ueno, Shinji; Terasaki, Hiroko; Sato, Miho; Nakanishi, Hiroshi; Endo, Shiori; Mizuta, Kunihiro; Mineta, Hiroyuki; Kondo, Mineo; Takahashi, Masayo; Minoshima, Shinsei; Hotta, Yoshihiro

2014-09-01

Retinitis pigmentosa (RP) is a highly heterogeneous genetic disease. The USH2A gene, which accounts for approximately 74-90% of Usher syndrome type 2 (USH2) cases, is also one of the major autosomal recessive RP (arRP) causative genes among Caucasian populations. To identify disease-causing USH2A gene mutations in Japanese RP patients, all 73 exons were screened for mutations by direct sequencing. In total, 100 unrelated Japanese RP patients with no systemic manifestations were identified, excluding families with obvious autosomal dominant inheritance. Of these 100 patients, 82 were included in this present study after 18 RP patients with very likely pathogenic EYS (eyes shut homolog) mutations were excluded. The mutation analysis of the USH2A revealed five very likely pathogenic mutations in four patients. A patient had only one very likely pathogenic mutation and the others had two of them. Caucasian frequent mutations p.C759F in arRP and p.E767fs in USH2 were not found. All the four patients exhibited typical clinical features of RP. The observed prevalence of USH2A gene mutations was approximately 4% among Japanese arRP patients, and the profile of the USH2A gene mutations differed largely between Japanese patients and previously reported Caucasian populations.

Medullospheres from DAOY, UW228 and ONS-76 cells: increased stem cell population and proteomic modifications.

PubMed

Zanini, Cristina; Ercole, Elisabetta; Mandili, Giorgia; Salaroli, Roberta; Poli, Alice; Renna, Cristiano; Papa, Valentina; Cenacchi, Giovanna; Forni, Marco

2013-01-01

Medulloblastoma (MB) is an aggressive pediatric tumor of the Central Nervous System (CNS) usually treated according to a refined risk stratification. The study of cancer stem cells (CSC) in MB is a promising approach aimed at finding new treatment strategies. The CSC compartment was studied in three characterized MB cell lines (DAOY, UW228 and ONS-76) grown in standard adhesion as well as being grown as spheres, which enables expansion of the CSC population. MB cell lines, grown in adherence and as spheres, were subjected to morphologic analysis at the light and electron microscopic level, as well as cytofluorimetric determinations. Medullospheres (MBS) were shown to express increasingly immature features, along with the stem cells markers: CD133, Nestin and β-catenin. Proteomic analysis highlighted the differences between MB cell lines, demonstrating a unique protein profile for each cell line, and minor differences when grown as spheres. In MBS, MALDI-TOF also identified some proteins, that have been linked to tumor progression and resistance, such as Nucleophosmin (NPM). In addition, immunocytochemistry detected Sox-2 as a stemness marker of MBS, as well as confirming high NPM expression. Culture conditioning based on low attachment flasks and specialized medium may provide new data on the staminal compartment of CNS tumors, although a proteomic profile of CSC is still elusive for MB.

Medullospheres from DAOY, UW228 and ONS-76 Cells: Increased Stem Cell Population and Proteomic Modifications

PubMed Central

Zanini, Cristina; Ercole, Elisabetta; Mandili, Giorgia; Salaroli, Roberta; Poli, Alice; Renna, Cristiano; Papa, Valentina; Cenacchi, Giovanna; Forni, Marco

2013-01-01

Background Medulloblastoma (MB) is an aggressive pediatric tumor of the Central Nervous System (CNS) usually treated according to a refined risk stratification. The study of cancer stem cells (CSC) in MB is a promising approach aimed at finding new treatment strategies. Methodology/Principal Findings The CSC compartment was studied in three characterized MB cell lines (DAOY, UW228 and ONS-76) grown in standard adhesion as well as being grown as spheres, which enables expansion of the CSC population. MB cell lines, grown in adherence and as spheres, were subjected to morphologic analysis at the light and electron microscopic level, as well as cytofluorimetric determinations. Medullospheres (MBS) were shown to express increasingly immature features, along with the stem cells markers: CD133, Nestin and β-catenin. Proteomic analysis highlighted the differences between MB cell lines, demonstrating a unique protein profile for each cell line, and minor differences when grown as spheres. In MBS, MALDI-TOF also identified some proteins, that have been linked to tumor progression and resistance, such as Nucleophosmin (NPM). In addition, immunocytochemistry detected Sox-2 as a stemness marker of MBS, as well as confirming high NPM expression. Conclusions/Significance Culture conditioning based on low attachment flasks and specialized medium may provide new data on the staminal compartment of CNS tumors, although a proteomic profile of CSC is still elusive for MB. PMID:23717474

Profiling Physical Activity, Diet, Screen and Sleep Habits in Portuguese Children

PubMed Central

Pereira, Sara; Katzmarzyk, Peter T.; Gomes, Thayse Natacha; Borges, Alessandra; Santos, Daniel; Souza, Michele; dos Santos, Fernanda K.; Chaves, Raquel N.; Champagne, Catherine M.; Barreira, Tiago V.; Maia, José A.R.

2015-01-01

Obesity in children is partly due to unhealthy lifestyle behaviours, e.g., sedentary activity and poor dietary choices. This trend has been seen globally. To determine the extent of these behaviours in a Portuguese population of children, 686 children 9.5 to 10.5 years of age were studied. Our aims were to: (1) describe profiles of children’s lifestyle behaviours; (2) identify behaviour pattern classes; and (3) estimate combined effects of individual/socio-demographic characteristics in predicting class membership. Physical activity and sleep time were estimated by 24-h accelerometry. Nutritional habits, screen time and socio-demographics were obtained. Latent Class Analysis was used to determine unhealthy lifestyle behaviours. Logistic regression analysis predicted class membership. About 78% of children had three or more unhealthy lifestyle behaviours, while 0.2% presented no risk. Two classes were identified: Class 1-Sedentary, poorer diet quality; and Class 2-Insufficiently active, better diet quality, 35% and 65% of the population, respectively. More mature children (Odds Ratio (OR) = 6.75; 95%CI = 4.74–10.41), and boys (OR = 3.06; 95% CI = 1.98–4.72) were more likely to be overweight/obese. However, those belonging to Class 2 were less likely to be overweight/obese (OR = 0.60; 95% CI = 0.43–0.84). Maternal education level and household income did not significantly predict weight status (p ≥ 0.05). PMID:26043034

Chapter 17: Bioimage Informatics for Systems Pharmacology

PubMed Central

Li, Fuhai; Yin, Zheng; Jin, Guangxu; Zhao, Hong; Wong, Stephen T. C.

2013-01-01

Recent advances in automated high-resolution fluorescence microscopy and robotic handling have made the systematic and cost effective study of diverse morphological changes within a large population of cells possible under a variety of perturbations, e.g., drugs, compounds, metal catalysts, RNA interference (RNAi). Cell population-based studies deviate from conventional microscopy studies on a few cells, and could provide stronger statistical power for drawing experimental observations and conclusions. However, it is challenging to manually extract and quantify phenotypic changes from the large amounts of complex image data generated. Thus, bioimage informatics approaches are needed to rapidly and objectively quantify and analyze the image data. This paper provides an overview of the bioimage informatics challenges and approaches in image-based studies for drug and target discovery. The concepts and capabilities of image-based screening are first illustrated by a few practical examples investigating different kinds of phenotypic changes caEditorsused by drugs, compounds, or RNAi. The bioimage analysis approaches, including object detection, segmentation, and tracking, are then described. Subsequently, the quantitative features, phenotype identification, and multidimensional profile analysis for profiling the effects of drugs and targets are summarized. Moreover, a number of publicly available software packages for bioimage informatics are listed for further reference. It is expected that this review will help readers, including those without bioimage informatics expertise, understand the capabilities, approaches, and tools of bioimage informatics and apply them to advance their own studies. PMID:23633943

Multivariate Analysis of the Cotton Seed Ionome Reveals a Shared Genetic Architecture

PubMed Central

Pauli, Duke; Ziegler, Greg; Ren, Min; Jenks, Matthew A.; Hunsaker, Douglas J.; Zhang, Min; Baxter, Ivan; Gore, Michael A.

2018-01-01

To mitigate the effects of heat and drought stress, a better understanding of the genetic control of physiological responses to these environmental conditions is needed. To this end, we evaluated an upland cotton (Gossypium hirsutum L.) mapping population under water-limited and well-watered conditions in a hot, arid environment. The elemental concentrations (ionome) of seed samples from the population were profiled in addition to those of soil samples taken from throughout the field site to better model environmental variation. The elements profiled in seeds exhibited moderate to high heritabilities, as well as strong phenotypic and genotypic correlations between elements that were not altered by the imposed irrigation regimes. Quantitative trait loci (QTL) mapping results from a Bayesian classification method identified multiple genomic regions where QTL for individual elements colocalized, suggesting that genetic control of the ionome is highly interrelated. To more fully explore this genetic architecture, multivariate QTL mapping was implemented among groups of biochemically related elements. This analysis revealed both additional and pleiotropic QTL responsible for coordinated control of phenotypic variation for elemental accumulation. Machine learning algorithms that utilized only ionomic data predicted the irrigation regime under which genotypes were evaluated with very high accuracy. Taken together, these results demonstrate the extent to which the seed ionome is genetically interrelated and predictive of plant physiological responses to adverse environmental conditions. PMID:29437829

Postnatal gestational age estimation using newborn screening blood spots: a proposed validation protocol

PubMed Central

Murphy, Malia S Q; Hawken, Steven; Atkinson, Katherine M; Milburn, Jennifer; Pervin, Jesmin; Gravett, Courtney; Stringer, Jeffrey S A; Rahman, Anisur; Lackritz, Eve; Chakraborty, Pranesh; Wilson, Kumanan

2017-01-01

Background Knowledge of gestational age (GA) is critical for guiding neonatal care and quantifying regional burdens of preterm birth. In settings where access to ultrasound dating is limited, postnatal estimates are frequently used despite the issues of accuracy associated with postnatal approaches. Newborn metabolic profiles are known to vary by severity of preterm birth. Recent work by our group and others has highlighted the accuracy of postnatal GA estimation algorithms derived from routinely collected newborn screening profiles. This protocol outlines the validation of a GA model originally developed in a North American cohort among international newborn cohorts. Methods Our primary objective is to use blood spot samples collected from infants born in Zambia and Bangladesh to evaluate our algorithm’s capacity to correctly classify GA within 1, 2, 3 and 4 weeks. Secondary objectives are to 1) determine the algorithm's accuracy in small-for-gestational-age and large-for-gestational-age infants, 2) determine its ability to correctly discriminate GA of newborns across dichotomous thresholds of preterm birth (≤34 weeks, <37 weeks GA) and 3) compare the relative performance of algorithms derived from newborn screening panels including all available analytes and those restricted to analyte subsets. The study population will consist of infants born to mothers already enrolled in one of two preterm birth cohorts in Lusaka, Zambia, and Matlab, Bangladesh. Dried blood spot samples will be collected and sent for analysis in Ontario, Canada, for model validation. Discussion This study will determine the validity of a GA estimation algorithm across ethnically diverse infant populations and assess population specific variations in newborn metabolic profiles. PMID:29104765

Comparison of EpCAMhighCD44+ cancer stem cells with EpCAMhighCD44- tumor cells in colon cancer by single-cell sequencing.

PubMed

Liu, Mingshan; Di, Jiabo; Liu, Yang; Su, Zhe; Jiang, Beihai; Wang, Zaozao; Su, Xiangqian

2018-03-26

Cancer stem cells (CSCs) are considered to be responsible for tumorigenesis and cancer relapse. EpCAM high CD44 + tumor cells are putative colorectal CSCs that express high levels of stem cell genes, while the EpCAM high CD44 - population mostly contains differentiated tumor cells (DTCs). This study aims to determine whether single CSC (EpCAM high CD44 + ) and DTC (EpCAM high CD44 - ) can be distinguished in terms of somatic copy number alterations (SCNAs). We applied fluorescence-activated cell sorting to isolate the CD45 - EpCAM high CD44 + and CD45 - EpCAM high CD44 - populations from two primary colon tumors, on which low-coverage single-cell whole-genome sequencing (WGS) was then performed ∼0.1x depth. We compared the SCNAs of the CSCs and DTCs at single-cell resolution. In total, 47 qualified single cells of the two populations underwent WGS. The single-cell SCNA profiles showed that there were obvious SCNAs in both the CSCs and DTCs of each patient, and each patient had a specific copy number alteration pattern. Hierarchical clustering and correlation analysis both showed that the SCNA profiles of CSCs and DTCs from the same patient had similar SCNA pattern, while there were regional differences in the CSCs and DTCs in certain patient. SCNAs of CSCs in the same patient were highly reproducible. Our data suggest that major SCNAs occurred at an early stage and were inherited steadily. The similarity of ubiquitous SCNAs between the CSCs and DTCs might have arisen from lineage differentiation. CSCs from the same patient had reproducible SCNA profiles, indicating that gain or loss in certain chromosome is required for colon cancer development.

Is an unfavourable cardiovascular risk profile a risk factor for vasomotor menopausal symptoms? Results of a population-based cohort study.

PubMed

van den Berg, M J; Herber-Gast, G C M; van der Schouw, Y T

2015-08-01

Evidence suggests an association between vasomotor menopausal symptoms (VMSs), i.e. hot flushes and night sweats, and cardiovascular disease. However, the causal pathway is unclear. We investigated whether an unfavourable cardiovascular risk profile is a risk factor for VMS later in life. Retrospective cohort study. Women aged 50-70 from the general population. The Prospect-European Prospective Investigation into Cancer and Nutrition (Prospect-EPIC) cohort is a population-based cohort of women who enrolled between 1993 and 1997. Follow-up questionnaires were sent at 5-year intervals for 15 years. Women who returned the third questionnaire, answered questions regarding lifetime VMS and did not report VMS prior to baseline were included in this study (n = 1295). At baseline, the Framingham Risk Score (FRS) was determined. We used logistic regression analysis to calculate odds ratios (ORs) for the association between baseline FRS and incident VMS. Incident VMS. At baseline (mean age ± standard deviation, 52.2 ± 3.6 years), 21.2% had a FRS > 10%. During follow-up, 40.2% of women reported the onset of VMS. Adjusted for body mass index, physical activity, education and alcohol consumption, each point increase in FRS was associated with a decreased incidence of VMS [OR, 0.94 (95% CI, 0.91-0.97)]. Additional adjustment for menopausal status attenuated the OR to null [OR, 0.98 (95% CI, 0.95-1.01)]. None of the separate FRS variables were associated with VMS after adjustment for age. In our cohort, an unfavourable cardiovascular risk profile was not associated with VMS, and therefore we found no evidence for the involvement of a vascular mechanism in the etiology of VMS. © 2014 Royal College of Obstetricians and Gynaecologists.

Comparative evaluation of microbial diversity and metabolite profiles in doenjang, a fermented soybean paste, during the two different industrial manufacturing processes.

PubMed

Lee, Sunmin; Lee, Sarah; Singh, Digar; Oh, Ji Young; Jeon, Eun Jung; Ryu, Hyung SeoK; Lee, Dong Wan; Kim, Beom Seok; Lee, Choong Hwan

2017-04-15

Two different doenjang manufacturing processes, the industrial process (IP) and the modified industrial process (mIP) with specific microbial assortments, were subjected to metabolite profiling using liquid chromatography-mass spectrometry (LC-MS) and gas chromatography time-of-flight mass spectrometry (GC-TOF-MS). The multivariate analyses indicated that both primary and secondary metabolites exhibited distinct patterns according to the fermentation processes (IP and mIP). Microbial community analysis for doenjang using denaturing gradient gel electrophoresis (DGGE), exhibited that both bacteria and fungi contributed proportionally for each step in the process viz., soybean, steaming, drying, meju fermentation, cooling, brining, and aging. Further, correlation analysis indicated that Aspergillus population was linked to sugar metabolism, Bacillus spp. with that of fatty acids, whereas Tetragenococcus and Zygosaccharomyces were found associated with amino acids. These results suggest that the components and quality of doenjang are critically influenced by the microbial assortments in each process. Copyright © 2016 Elsevier Ltd. All rights reserved.

Molecular, Pathological, Radiological, and Immune Profiling of Non-brainstem Pediatric High-Grade Glioma from the HERBY Phase II Randomized Trial.

PubMed

Mackay, Alan; Burford, Anna; Molinari, Valeria; Jones, David T W; Izquierdo, Elisa; Brouwer-Visser, Jurriaan; Giangaspero, Felice; Haberler, Christine; Pietsch, Torsten; Jacques, Thomas S; Figarella-Branger, Dominique; Rodriguez, Daniel; Morgan, Paul S; Raman, Pichai; Waanders, Angela J; Resnick, Adam C; Massimino, Maura; Garrè, Maria Luisa; Smith, Helen; Capper, David; Pfister, Stefan M; Würdinger, Thomas; Tam, Rachel; Garcia, Josep; Thakur, Meghna Das; Vassal, Gilles; Grill, Jacques; Jaspan, Tim; Varlet, Pascale; Jones, Chris

2018-05-14

The HERBY trial was a phase II open-label, randomized, multicenter trial evaluating bevacizumab (BEV) in addition to temozolomide/radiotherapy in patients with newly diagnosed non-brainstem high-grade glioma (HGG) between the ages of 3 and 18 years. We carried out comprehensive molecular analysis integrated with pathology, radiology, and immune profiling. In post-hoc subgroup analysis, hypermutator tumors (mismatch repair deficiency and somatic POLE/POLD1 mutations) and those biologically resembling pleomorphic xanthoastrocytoma ([PXA]-like, driven by BRAF_V600E or NF1 mutation) had significantly more CD8 + tumor-infiltrating lymphocytes, and longer survival with the addition of BEV. Histone H3 subgroups (hemispheric G34R/V and midline K27M) had a worse outcome and were immune cold. Future clinical trials will need to take into account the diversity represented by the term "HGG" in the pediatric population. Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved.

Simultaneous fecal microbial and metabolite profiling enables accurate classification of pediatric irritable bowel syndrome.

PubMed

Shankar, Vijay; Reo, Nicholas V; Paliy, Oleg

2015-12-09

We previously showed that stool samples of pre-adolescent and adolescent US children diagnosed with diarrhea-predominant IBS (IBS-D) had different compositions of microbiota and metabolites compared to healthy age-matched controls. Here we explored whether observed fecal microbiota and metabolite differences between these two adolescent populations can be used to discriminate between IBS and health. We constructed individual microbiota- and metabolite-based sample classification models based on the partial least squares multivariate analysis and then applied a Bayesian approach to integrate individual models into a single classifier. The resulting combined classification achieved 84 % accuracy of correct sample group assignment and 86 % prediction for IBS-D in cross-validation tests. The performance of the cumulative classification model was further validated by the de novo analysis of stool samples from a small independent IBS-D cohort. High-throughput microbial and metabolite profiling of subject stool samples can be used to facilitate IBS diagnosis.

Microarray analysis of laser capture microdissected-anulus cells from the human intervertebral disc.

PubMed

Gruber, Helen E; Mougeot, Jean-Luc; Hoelscher, Gretchen; Ingram, Jane A; Hanley, Edward N

2007-05-15

Five Thompson Grade I/II discs (Group 1), 7 Grade III discs (Group 2), and 3 Grade IV discs (Group IV) were studied here in a project approved by the authors' Human Subjects Institutional Review Board. Our objective was to use laser capture microdissection (LCM) to harvest cells from the human anulus and to derive gene expression profiles using microarray analysis. Appropriate gene expression is essential in the intervertebral disc for maintenance of extracellular matrix (ECM), ECM remodeling, and maintenance of a viable disc cell population. During disc degeneration, cell numbers drop, making gene expression studies challenging. LCM was used to harvest cells from paraffin-embedded sections of human anulus tissue. Gene profiling used Affymetrix GeneChip Human X3P arrays. ANOVA and SAM permutation analysis were applied to dCHIP normalized, filtered, and log-transformed gene expression data ( approximately 33,500 probes), and data analyzed to identify genes that were significantly differentially expressed between the 3 groups. We identified 47 genes that were significantly differentially expressed between the 3 groups (P < 0.001 and lowest q values). Compared with the healthiest discs (Grade I/II), 13 genes were up-regulated and 19 down-regulated in both the Grade III and the Grade IV discs. Genes with biologic significance regulated during degeneration involved cell senescence, low cell division rates, hypoxia-related genes, heat-shock protein 70 interacting protein, neuropilin 2, and interleukin-23p19 (interleukin-12 family). Results expand our understanding of disc aging and degeneration and show that LCM is a valuable technique that can be used to collect mRNA amounts adequate for microarray analysis from the sparse cell population of the human anulus.

Ethical, legal and social implications of forensic molecular phenotyping in South Africa.

PubMed

Slabbert, Nandi; Heathfield, Laura Jane

2018-06-01

Conventional forensic DNA analysis involves a matching principle, which compares DNA profiles from evidential samples to those from reference samples of known origin. In casework, however, the accessibility to a reference sample is not guaranteed which limits the use of DNA as an investigative tool. This has led to the development of phenotype prediction, which uses SNP analysis to estimate the physical appearance of the sample donor. Physical traits, such as eye, hair and skin colour, have been associated with certain alleles within specific genes involved in the melanogenesis pathways. These genetic markers are also associated with ancestry and their trait prediction ability has mainly been assessed in European and North American populations. This has prompted research investigating the discriminatory power of these markers in other populations, especially those exhibiting admixture. South Africa is well known for its diversity, and the viability of these particular SNPs still needs to be assessed within this population. South African law currently restricts the use of DNA for molecular phenotyping, and there are also numerous ethical and social considerations, all of which are discussed. © 2018 John Wiley & Sons Ltd.

Prevalence of Nitrosomonas cluster 7 populations in the ammonia-oxidizing community of a submerged membrane bioreactor treating urban wastewater under different operation conditions.

PubMed

Cerrone, F; Poyatos, J M; Molina-Muñoz, M; Cortés-Lorenzo, C; González-López, J; Rodelas, B

2013-07-01

A pilot-scale ultrafiltration membrane bioreactor (MBR) was used for the aerobic treatment of urban wastewater in four experimental stages influenced by seasonal temperature and different sets of operation conditions. The structure of the ammonia-oxidizing bacteria (AOB) community was profiled by temperature gradient gel electrophoresis (TGGE), based on the amplification and separation of partial ammonia-monoxygenase subunit A (amoA) genes. Canonical correspondence analysis revealed that temperature, hydraulic retention time and percentage of ammonia removal had a significant effect on the fingerprints of AOB communities. Phylogenetic analysis conducted on amoA/AmoA sequences of reamplified TGGE bands showed, however, that closely related ammonia-oxidizing populations inhabited the sludge of the MBR in all experimental stages. Nitrosomonas cluster 7 populations (N. europaea-N. eutropha cluster) prevailed under all conditions tested, even when the MBR was operated under complete biomass retention or at low temperatures, suggesting that the high ammonia concentrations in the system were determinant to select r-strategist AOB.

Microsatellite variation and genetic structure of brook trout (Salvelinus fontinalis) populations in Labrador and neighboring Atlantic Canada: evidence for ongoing gene flow and dual routes of post-Wisconsinan colonization

PubMed Central

Pilgrim, Brettney L; Perry, Robert C; Keefe, Donald G; Perry, Elizabeth A; Dawn Marshall, H

2012-01-01

In conservation genetics and management, it is important to understand the contribution of historical and contemporary processes to geographic patterns of genetic structure in order to characterize and preserve diversity. As part of a 10-year monitoring program by the Government of Newfoundland and Labrador, Canada, we measured the population genetic structure of the world's most northern native populations of brook trout (Salvelinus fontinalis) in Labrador to gather baseline data to facilitate monitoring of future impacts of the recently opened Trans-Labrador Highway. Six-locus microsatellite profiles were obtained from 1130 fish representing 32 populations from six local regions. Genetic diversity in brook trout populations in Labrador (average HE= 0.620) is within the spectrum of variability found in other brook trout across their northeastern range, with limited ongoing gene flow occurring between populations (average pairwise FST= 0.139). Evidence for some contribution of historical processes shaping genetic structure was inferred from an isolation-by-distance analysis, while dual routes of post-Wisconsinan recolonization were indicated by STRUCTURE analysis: K= 2 was the most likely number of genetic groups, revealing a separation between northern and west-central Labrador from all remaining populations. Our results represent the first data from the nuclear genome of brook trout in Labrador and emphasize the usefulness of microsatellite data for revealing the extent to which genetic structure is shaped by both historical and contemporary processes. PMID:22837834

Tropospheric Ozonesonde Profiles at Long-term U.S. Monitoring Sites: 1. A Climatology Based on Self-Organizing Maps

NASA Technical Reports Server (NTRS)

Stauffer, Ryan M.; Thompson, Anne M.; Young, George S.

2016-01-01

Sonde-based climatologies of tropospheric ozone (O3) are vital for developing satellite retrieval algorithms and evaluating chemical transport model output. Typical O3 climatologies average measurements by latitude or region, and season. A recent analysis using self-organizing maps (SOM) to cluster ozonesondes from two tropical sites found that clusters of O3 mixing ratio profiles are an excellent way to capture O3variability and link meteorological influences to O3 profiles. Clusters correspond to distinct meteorological conditions, e.g., convection, subsidence, cloud cover, and transported pollution. Here the SOM technique is extended to four long-term U.S. sites (Boulder, CO; Huntsville, AL; Trinidad Head, CA; and Wallops Island, VA) with4530 total profiles. Sensitivity tests on k-means algorithm and SOM justify use of 3 3 SOM (nine clusters). Ateach site, SOM clusters together O3 profiles with similar tropopause height, 500 hPa height temperature, and amount of tropospheric and total column O3. Cluster means are compared to monthly O3 climatologies.For all four sites, near-tropopause O3 is double (over +100 parts per billion by volume; ppbv) the monthly climatological O3 mixing ratio in three clusters that contain 1316 of profiles, mostly in winter and spring.Large midtropospheric deviations from monthly means (6 ppbv, +710 ppbv O3 at 6 km) are found in two of the most populated clusters (combined 3639 of profiles). These two clusters contain distinctly polluted(summer) and clean O3 (fall-winter, high tropopause) profiles, respectively. As for tropical profiles previously analyzed with SOM, O3 averages are often poor representations of U.S. O3 profile statistics.

Tropospheric ozonesonde profiles at long-term U.S. monitoring sites: 1. A climatology based on self-organizing maps

PubMed Central

Stauffer, Ryan M.; Thompson, Anne M.; Young, George S.

2018-01-01

Sonde-based climatologies of tropospheric ozone (O3) are vital for developing satellite retrieval algorithms and evaluating chemical transport model output. Typical O3 climatologies average measurements by latitude or region, and season. Recent analysis using self-organizing maps (SOM) to cluster ozonesondes from two tropical sites found clusters of O3 mixing ratio profiles are an excellent way to capture O3 variability and link meteorological influences to O3 profiles. Clusters correspond to distinct meteorological conditions, e.g. convection, subsidence, cloud cover, and transported pollution. Here, the SOM technique is extended to four long-term U.S. sites (Boulder, CO; Huntsville, AL; Trinidad Head, CA; Wallops Island, VA) with 4530 total profiles. Sensitivity tests on k-means algorithm and SOM justify use of 3×3 SOM (nine clusters). At each site, SOM clusters together O3 profiles with similar tropopause height, 500 hPa height/temperature, and amount of tropospheric and total column O3. Cluster means are compared to monthly O3 climatologies. For all four sites, near-tropopause O3 is double (over +100 parts per billion by volume; ppbv) the monthly climatological O3 mixing ratio in three clusters that contain 13 – 16% of profiles, mostly in winter and spring. Large mid-tropospheric deviations from monthly means (−6 ppbv, +7 – 10 ppbv O3 at 6 km) are found in two of the most populated clusters (combined 36 – 39% of profiles). These two clusters contain distinctly polluted (summer) and clean O3 (fall-winter, high tropopause) profiles, respectively. As for tropical profiles previously analyzed with SOM, O3 averages are often poor representations of U.S. O3 profile statistics. PMID:29619288

Tropospheric ozonesonde profiles at long-term U.S. monitoring sites: 1. A climatology based on self-organizing maps.

PubMed

Stauffer, Ryan M; Thompson, Anne M; Young, George S

2016-02-16

Sonde-based climatologies of tropospheric ozone (O 3 ) are vital for developing satellite retrieval algorithms and evaluating chemical transport model output. Typical O 3 climatologies average measurements by latitude or region, and season. Recent analysis using self-organizing maps (SOM) to cluster ozonesondes from two tropical sites found clusters of O 3 mixing ratio profiles are an excellent way to capture O 3 variability and link meteorological influences to O 3 profiles. Clusters correspond to distinct meteorological conditions, e.g. convection, subsidence, cloud cover, and transported pollution. Here, the SOM technique is extended to four long-term U.S. sites (Boulder, CO; Huntsville, AL; Trinidad Head, CA; Wallops Island, VA) with 4530 total profiles. Sensitivity tests on k-means algorithm and SOM justify use of 3×3 SOM (nine clusters). At each site, SOM clusters together O 3 profiles with similar tropopause height, 500 hPa height/temperature, and amount of tropospheric and total column O 3 . Cluster means are compared to monthly O 3 climatologies. For all four sites, near-tropopause O 3 is double (over +100 parts per billion by volume; ppbv) the monthly climatological O 3 mixing ratio in three clusters that contain 13 - 16% of profiles, mostly in winter and spring. Large mid-tropospheric deviations from monthly means (-6 ppbv, +7 - 10 ppbv O 3 at 6 km) are found in two of the most populated clusters (combined 36 - 39% of profiles). These two clusters contain distinctly polluted (summer) and clean O 3 (fall-winter, high tropopause) profiles, respectively. As for tropical profiles previously analyzed with SOM, O 3 averages are often poor representations of U.S. O 3 profile statistics.

Performance in College Chemistry: a Statistical Comparison Using Gender and Jungian Personality Type

NASA Astrophysics Data System (ADS)

Greene, Susan V.; Wheeler, Henry R.; Riley, Wayne D.

This study sorted college introductory chemistry students by gender and Jungian personality type. It recognized differences from the general population distribution and statistically compared the students' grades with their Jungian personality types. Data from 577 female students indicated that ESFP (extroverted, sensory, feeling, perceiving) and ENFP (extroverted, intuitive, feeling, perceiving) profiles performed poorly at statistically significant levels when compared with the distribution of females enrolled in introductory chemistry. The comparable analysis using data from 422 male students indicated that the poorly performing male profiles were ISTP (introverted, sensory, thinking, perceiving) and ESTP (extroverted, sensory, thinking, perceiving). ESTJ (extroverted, sensory, thinking, judging) female students withdrew from the course at a statistically significant level. For both genders, INTJ (introverted, intuitive, thinking, judging) students were the best performers. By examining the documented characteristics of Jungian profiles that correspond with poorly performing students in chemistry, one may more effectively assist the learning process and the retention of these individuals in the fields of natural science, engineering, and technology.

Nuclear, chloroplast, and mitochondrial data of a US cannabis DNA database.

PubMed

Houston, Rachel; Birck, Matthew; LaRue, Bobby; Hughes-Stamm, Sheree; Gangitano, David

2018-05-01

As Cannabis sativa (marijuana) is a controlled substance in many parts of the world, the ability to track biogeographical origin of cannabis could provide law enforcement with investigative leads regarding its trade and distribution. Population substructure and inbreeding may cause cannabis plants to become more genetically related. This genetic relatedness can be helpful for intelligence purposes. Analysis of autosomal, chloroplast, and mitochondrial DNA allows for not only prediction of biogeographical origin of a plant but also discrimination between individual plants. A previously validated, 13-autosomal STR multiplex was used to genotype 510 samples. Samples were analyzed from four different sites: 21 seizures at the US-Mexico border, Northeastern Brazil, hemp seeds purchased in the US, and the Araucania area of Chile. In addition, a previously reported multi-loci system was modified and optimized to genotype five chloroplast and two mitochondrial markers. For this purpose, two methods were designed: a homopolymeric STR pentaplex and a SNP triplex with one chloroplast (Cscp001) marker shared by both methods for quality control. For successful mitochondrial and chloroplast typing, a novel real-time PCR quantitation method was developed and validated to accurately estimate the quantity of the chloroplast DNA (cpDNA) using a synthetic DNA standard. Moreover, a sequenced allelic ladder was also designed for accurate genotyping of the homopolymeric STR pentaplex. For autosomal typing, 356 unique profiles were generated from the 425 samples that yielded full STR profiles and 25 identical genotypes within seizures were observed. Phylogenetic analysis and case-to-case pairwise comparisons of 21 seizures at the US-Mexico border, using the Fixation Index (F ST ) as genetic distance, revealed the genetic association of nine seizures that formed a reference population. For mitochondrial and chloroplast typing, subsampling was performed, and 134 samples were genotyped. Complete haplotypes (STRs and SNPs) were observed for 127 samples. As expected, extensive haplotype sharing was observed; five distinguishable haplotypes were detected. In the reference population, the same haplotype was observed 39 times and two unique haplotypes were also detected. Haplotype sharing was observed between the US border seizures, Brazil, and Chile, while the hemp samples generated a distinct haplotype. Phylogenetic analysis of the four populations was performed, and results revealed that both autosomal and lineage markers could discern population substructure.

DNA profiling, telomere analysis and antioxidant properties as tools for monitoring ex situ seed longevity

PubMed Central

Donà, M.; Balestrazzi, A.; Mondoni, A.; Rossi, G.; Ventura, L.; Buttafava, A.; Macovei, A.; Sabatini, M. E.; Valassi, A.; Carbonera, D.

2013-01-01

Background and Aims The germination test currently represents the most used method to assess seed viability in germplasm banks, despite the difficulties caused by the occurrence of seed dormancy. Furthermore, seed longevity can vary considerably across species and populations from different environments, and studies related to the eco-physiological processes underlying such variations are still limited in their depth. The aim of the present work was the identification of reliable molecular markers that might help in monitoring seed deterioration. Methods Dry seeds were subjected to artificial ageing and collected at different time points for molecular/biochemical analyses. DNA damage was measured using the RAPD (random amplified polymorphic DNA) approach while the seed antioxidant profile was obtained using both the DPPH (1,1-diphenyl, 2-picrylhydrazyl) assay and the Folin–Ciocalteu reagent method. Electron paramagnetic resonance (EPR) provided profiles of free radicals. Quantitative real-time polymerase chain reaction (QRT-PCR) was used to assess the expression profiles of the antioxidant genes MT2 (type 2 metallothionein) and SOD (superoxide dismutase). A modified QRT-PCR protocol was used to determine telomere length. Key Results The RAPD profiles highlighted different capacities of the two Silene species to overcome DNA damage induced by artificial ageing. The antioxidant profiles of dry and rehydrated seeds revealed that the high-altitude taxon Silene acaulis was characterized by a lower antioxidant specific activity. Significant upregulation of the MT2 and SOD genes was observed only in the rehydrated seeds of the low-altitude species. Rehydration resulted in telomere lengthening in both Silene species. Conclusions Different seed viability markers have been selected for plant species showing inherent variation of seed longevity. RAPD analysis, quantification of redox activity of non-enzymatic antioxidant compounds and gene expression profiling provide deeper insights to study seed viability during storage. Telomere lengthening is a promising tool to discriminate between short- and long-lived species. PMID:23532044

Profiles of influenza A/H1N1 vaccine response using hemagglutination-inhibition titers.

PubMed

Jacobson, Robert M; Grill, Diane E; Oberg, Ann L; Tosh, Pritish K; Ovsyannikova, Inna G; Poland, Gregory A

2015-01-01

To identify distinct antibody profiles among adults 50-to-74 years old using influenza A/H1N1 HI titers up to 75 days after vaccination. Healthy subjects 50 to 74 years old received the 2010-2011 trivalent inactivated influenza vaccine. We measured venous samples from Days 0, 28, and 75 for HI and VNA and B-cell ELISPOTs. Of 106 subjects, HI titers demonstrated a ceiling effect for 11 or 10% for those with a pre-vaccination HI titer of 1:640 where no subject post-vaccination had an increase in titer. Of the remaining 95 subjects, only 37 or 35% overall had at least a 4-fold increase by Day 28. Of these 37, 3 waned at least 4-fold, and 13 others 2-fold. Thus 15% of the subjects showed waning antibody titers by Day 75. More than half failed to respond at all. The profiles populated by these subjects as defined by HI did not vary with age or gender. The VNA results mimicked the HI profiles, but the profiles for B-cell ELISPOT did not. HI titers at Days 0, 28, and 75 populate 4 biologically plausible profiles. Limitations include lack of consensus for operationally defining waning as well as for the apparent ceiling. Furthermore, though well accepted as a marker for vaccine response, assigning thresholds with HI has limitations. However, VNA closely matches HI in populating these profiles. Thus, we hold that these profiles, having face- and content-validity, may provide a basis for understanding variation in genomic and transcriptomic response to influenza vaccination in this age group.

Mapping in an apple (Malus x domestica) F1 segregating population based on physical clustering of differentially expressed genes.

PubMed

Jensen, Philip J; Fazio, Gennaro; Altman, Naomi; Praul, Craig; McNellis, Timothy W

2014-04-04

Apple tree breeding is slow and difficult due to long generation times, self-incompatibility, and complex genetics. The identification of molecular markers linked to traits of interest is a way to expedite the breeding process. In the present study, we aimed to identify genes whose steady-state transcript abundance was associated with inheritance of specific traits segregating in an apple (Malus × domestica) rootstock F1 breeding population, including resistance to powdery mildew (Podosphaera leucotricha) disease and woolly apple aphid (Eriosoma lanigerum). Transcription profiling was performed for 48 individual F1 apple trees from a cross of two highly heterozygous parents, using RNA isolated from healthy, actively-growing shoot tips and a custom apple DNA oligonucleotide microarray representing 26,000 unique transcripts. Genome-wide expression profiles were not clear indicators of powdery mildew or woolly apple aphid resistance phenotype. However, standard differential gene expression analysis between phenotypic groups of trees revealed relatively small sets of genes with trait-associated expression levels. For example, thirty genes were identified that were differentially expressed between trees resistant and susceptible to powdery mildew. Interestingly, the genes encoding twenty-four of these transcripts were physically clustered on chromosome 12. Similarly, seven genes were identified that were differentially expressed between trees resistant and susceptible to woolly apple aphid, and the genes encoding five of these transcripts were also clustered, this time on chromosome 17. In each case, the gene clusters were in the vicinity of previously identified major quantitative trait loci for the corresponding trait. Similar results were obtained for a series of molecular traits. Several of the differentially expressed genes were used to develop DNA polymorphism markers linked to powdery mildew disease and woolly apple aphid resistance. Gene expression profiling and trait-associated transcript analysis using an apple F1 population readily identified genes physically linked to powdery mildew disease resistance and woolly apple aphid resistance loci. This result was especially useful in apple, where extreme levels of heterozygosity make the development of reliable DNA markers quite difficult. The results suggest that this approach could prove effective in crops with complicated genetics, or for which few genomic information resources are available.

Different molecular types of Pseudomonas fragi have the same overall behaviour as meat spoilers.

PubMed

Ercolini, Danilo; Casaburi, Annalisa; Nasi, Antonella; Ferrocino, Ilario; Di Monaco, Rossella; Ferranti, Pasquale; Mauriello, Gianluigi; Villani, Francesco

2010-08-15

The functional diversity of a population of sixty-five different strains of P. fragi isolated from fresh and spoiled meat was studied in order to evaluate the population heterogeneity related to meat spoilage potential. The strains were characterized for the proteolytic activity at 4 degrees C on beef sarcoplasmic proteins and only 9 strains were found to be proteolytic. An iron-dependent growth behaviour was shown when each strain was grown in citrate medium containing either myoglobin, haemoglobin or iron chloride as iron sources. Increase of maximum population and mu(max) in presence of different iron sources was registered. The release of volatile organic compounds (VOC) by each strain in beef during aerobic storage at 4 degrees C was evaluated by GC-MS. A considerable variability of occurrence of each molecule in the GC-MS profiles obtained by the different strains was observed ranging from 3% to 79% although the strains showed a high degree of similarity. In particular, ethylhexanoate, ethyloctanoate, ethylnonenoate, ethyldecanoate, 1-octen-3-ol, 3-octanone, 4-methylthiophenol, and 2-pentylfurane were produced by more than 50% of the strains. Representative strains were used to spoil meat in the same conditions used for the VOC analysis and the samples were evaluated by a sensory panel. The results of the sensory analysis indicated that the different strains could significantly affect the odour of meat and strains characterized by production of esters gave fruity odours to the spoiled meat. However, the similarity of strains based on the sensory profiles does not necessarily match the similarity shown in VOC profiles. P. fragi has a significant role in the microbial ecology of meat and the influence of meat-related sources of iron on the growth behaviour of many different strains suggests that meat can be an ecological niche for P. fragi. Regardless of the proteolytic and lipolytic capacities shown in vitro, different molecular types of P. fragi can release odour active volatile molecules and play a similar overall role as spoilage agents of meat. Copyright 2010 Elsevier B.V. All rights reserved.

Physical performance analysis: A new approach to assessing free-living physical activity in musculoskeletal pain and mobility-limited populations

PubMed Central

Smuck, Matthew; Tomkins-Lane, Christy; Ith, Ma Agnes; Jarosz, Renata; Kao, Ming-Chih Jeffrey

2017-01-01

Background Accurate measurement of physical performance in individuals with musculoskeletal pain is essential. Accelerometry is a powerful tool for this purpose, yet the current methods designed to evaluate energy expenditure are not optimized for this population. The goal of this study is to empirically derive a method of accelerometry analysis specifically for musculoskeletal pain populations. Methods We extracted data from 6,796 participants in the 2003–4 National Health and Nutrition Examination Survey (NHANES) including: 7-day accelerometry, health and pain questionnaires, and anthropomorphics. Custom macros were used for data processing, complex survey regression analyses, model selection, and statistical adjustment. After controlling for a multitude of variables that influence physical activity, we investigated whether distinct accelerometry profiles accompany pain in different locations of the body; and we identified the intensity intervals that best characterized these profiles. Results Unique accelerometry profiles were observed for pain in different body regions, logically clustering together based on proximity. Based on this, the following novel intervals (counts/minute) were identified and defined: Performance Sedentary (PSE) = 1–100, Performance Light 1 (PL1) = 101–350, Performance Light 2 (PL2) = 351–800, Performance Light 3 (PL3) = 801–2500, and Performance Moderate/Vigorous (PMV) = 2501–30000. The refinement of accelerometry signals into these new intervals, including 3 distinct ranges that fit inside the established light activity range, best captures alterations in real-life physical performance as a result of regional pain. Discussion and conclusions These new accelerometry intervals provide a model for objective measurement of real-life physical performance in people with pain and musculoskeletal disorders, with many potential uses. They may be used to better evaluate the relationship between pain and daily physical function, monitor musculoskeletal disease progression, gauge disease severity, inform exercise prescription, and quantify the functional impact of treatments. Based on these findings, we recommend that future studies of pain and musculoskeletal disorders analyze accelerometry output based on these new “physical performance” intervals. PMID:28235039

Age profiles in elephant and mammoth bone assemblages

NASA Astrophysics Data System (ADS)

Haynes, Gary

1985-11-01

Age profiles of modern African elephant ( Loxodonta africana) populations are significantly affected by drought conditions that cause local die-offs. Subadult animals die in proportions that may be nearly twice what is recorded in live populations. Such biasing of death sample age profiles might also have occurred during late Pleistocene die-offs of Mammuthus. This comparative study of modern and fossil proboscidean age structures supports a tentative interpretation that late Pleistocene extinction of Mammuthus (at least in the southwestern United States) resulted from severe drought conditions, at which Clovis hunters were witnesses, but not necessarily frequent participants.

Transcriptome profiling of Diachasmimorpha longicaudata towards useful molecular tools for population management.

PubMed

Mannino, M Constanza; Rivarola, Máximo; Scannapieco, Alejandra C; González, Sergio; Farber, Marisa; Cladera, Jorge L; Lanzavecchia, Silvia B

2016-10-12

Diachasmimorpha longicaudata (Hymenoptera: Braconidae) is a solitary parasitoid of Tephritidae (Diptera) fruit flies of economic importance currently being mass-reared in bio-factories and successfully used worldwide. A peculiar biological aspect of Hymenoptera is its haplo-diploid life cycle, where females (diploid) develop from fertilized eggs and males (haploid) from unfertilized eggs. Diploid males were described in many species and recently evidenced in D. longicaudata by mean of inbreeding studies. Sex determination in this parasitoid is based on the Complementary Sex Determination (CSD) system, with alleles from at least one locus involved in early steps of this pathway. Since limited information is available about genetics of this parasitoid species, a deeper analysis on D. longicaudata's genomics is required to provide molecular tools for achieving a more cost effective production under artificial rearing conditions. We report here the first transcriptome analysis of male-larvae, adult females and adult males of D. longicaudata using 454-pyrosequencing. A total of 469766 reads were analyzed and 8483 high-quality isotigs were assembled. After functional annotation, a total of 51686 unigenes were produced, from which, 7021 isotigs and 20227 singletons had at least one BLAST hit against the NCBI non-redundant protein database. A preliminary comparison of adult female and male evidenced that 98 transcripts showed differential expression profiles, with at least a 10-fold difference. Among the functionally annotated transcripts we detected four sequences potentially involved in sex determination and three homologues to two known genes involved in the sex determination cascade. Finally, a total of 4674SimpleSequence Repeats (SSRs) were in silico identified and characterized. The information obtained here will significantly contribute to the development of D. longicaudata functional genomics, genetics and population-based genome studies. Thousands of new microsatellite markers were identified as toolkits for population genetics analysis. The transcriptome characterized here is the starting point to elucidate the molecular bases of the sex determination mechanism in this species.

Taxonomic Structure and Monitoring of the Dominant Population of Lactic Acid Bacteria during Wheat Flour Sourdough Type I Propagation Using Lactobacillus sanfranciscensis Starters▿

PubMed Central

Siragusa, Sonya; Di Cagno, Raffaella; Ercolini, Danilo; Minervini, Fabio; Gobbetti, Marco; De Angelis, Maria

2009-01-01

The structure and stability of the dominant lactic acid bacterium population were assessed during wheat flour sourdough type I propagation by using singly nine strains of Lactobacillus sanfranciscensis. Under back-slopping propagation with wheat flour type 0 F114, cell numbers of presumptive lactic acid bacteria varied slightly between and within starters. As determined by randomly amplified polymorphic DNA-PCR and restriction endonuclease analysis-pulsed-field gel electrophoresis analyses, only three (LS8, LS14, and LS44) starters dominated throughout 10 days of propagation. The others progressively decreased to less than 3 log CFU g−1. Partial sequence analysis of the 16S rRNA and recA genes and PCR-denaturating gradient gel electrophoresis analysis using the rpoB gene allowed identification of Weissella confusa, Lactobacillus sanfranciscensis, Lactobacillus plantarum, Lactobacillus rossiae, Lactobacillus brevis, Lactococcus lactis subsp. lactis, Pediococcus pentosaceus, and Lactobacillus spp. as the dominant species of the raw wheat flour. At the end of propagation, one autochthonous strain of L. sanfranciscensis was found in all the sourdoughs. Except for L. brevis, strains of the above species were variously found in the mature sourdoughs. Persistent starters were found in association with other biotypes of L. sanfranciscensis and with W. confusa or L. plantarum. Sourdoughs were characterized for acidification, quotient of fermentation, free amino acids, and community-level catabolic profiles by USING Biolog 96-well Eco microplates. In particular, catabolic profiles of sourdoughs containing persistent starters behaved similarly and were clearly differentiated from the others. The three persistent starters were further used for the production of sourdoughs and propagated by using another wheat flour whose lactic acid bacterium population in part differed from the previous one. Also, in this case all three starter strains persisted during propagation. PMID:19088320

Modelling multi-pulse population dynamics from ultrafast spectroscopy.

PubMed

van Wilderen, Luuk J G W; Lincoln, Craig N; van Thor, Jasper J

2011-03-21

Current advanced laser, optics and electronics technology allows sensitive recording of molecular dynamics, from single resonance to multi-colour and multi-pulse experiments. Extracting the occurring (bio-) physical relevant pathways via global analysis of experimental data requires a systematic investigation of connectivity schemes. Here we present a Matlab-based toolbox for this purpose. The toolbox has a graphical user interface which facilitates the application of different reaction models to the data to generate the coupled differential equations. Any time-dependent dataset can be analysed to extract time-independent correlations of the observables by using gradient or direct search methods. Specific capabilities (i.e. chirp and instrument response function) for the analysis of ultrafast pump-probe spectroscopic data are included. The inclusion of an extra pulse that interacts with a transient phase can help to disentangle complex interdependent pathways. The modelling of pathways is therefore extended by new theory (which is included in the toolbox) that describes the finite bleach (orientation) effect of single and multiple intense polarised femtosecond pulses on an ensemble of randomly oriented particles in the presence of population decay. For instance, the generally assumed flat-top multimode beam profile is adapted to a more realistic Gaussian shape, exposing the need for several corrections for accurate anisotropy measurements. In addition, the (selective) excitation (photoselection) and anisotropy of populations that interact with single or multiple intense polarised laser pulses is demonstrated as function of power density and beam profile. Using example values of real world experiments it is calculated to what extent this effectively orients the ensemble of particles. Finally, the implementation includes the interaction with multiple pulses in addition to depth averaging in optically dense samples. In summary, we show that mathematical modelling is essential to model and resolve the details of physical behaviour of populations in ultrafast spectroscopy such as pump-probe, pump-dump-probe and pump-repump-probe experiments.

Modelling Multi-Pulse Population Dynamics from Ultrafast Spectroscopy

PubMed Central

van Wilderen, Luuk J. G. W.; Lincoln, Craig N.; van Thor, Jasper J.

2011-01-01

Current advanced laser, optics and electronics technology allows sensitive recording of molecular dynamics, from single resonance to multi-colour and multi-pulse experiments. Extracting the occurring (bio-) physical relevant pathways via global analysis of experimental data requires a systematic investigation of connectivity schemes. Here we present a Matlab-based toolbox for this purpose. The toolbox has a graphical user interface which facilitates the application of different reaction models to the data to generate the coupled differential equations. Any time-dependent dataset can be analysed to extract time-independent correlations of the observables by using gradient or direct search methods. Specific capabilities (i.e. chirp and instrument response function) for the analysis of ultrafast pump-probe spectroscopic data are included. The inclusion of an extra pulse that interacts with a transient phase can help to disentangle complex interdependent pathways. The modelling of pathways is therefore extended by new theory (which is included in the toolbox) that describes the finite bleach (orientation) effect of single and multiple intense polarised femtosecond pulses on an ensemble of randomly oriented particles in the presence of population decay. For instance, the generally assumed flat-top multimode beam profile is adapted to a more realistic Gaussian shape, exposing the need for several corrections for accurate anisotropy measurements. In addition, the (selective) excitation (photoselection) and anisotropy of populations that interact with single or multiple intense polarised laser pulses is demonstrated as function of power density and beam profile. Using example values of real world experiments it is calculated to what extent this effectively orients the ensemble of particles. Finally, the implementation includes the interaction with multiple pulses in addition to depth averaging in optically dense samples. In summary, we show that mathematical modelling is essential to model and resolve the details of physical behaviour of populations in ultrafast spectroscopy such as pump-probe, pump-dump-probe and pump-repump-probe experiments. PMID:21445294

Metagenomic analysis of the bacterial communities and their functional profiles in water and sediments of the Apies River, South Africa, as a function of land use.

PubMed

Abia, Akebe Luther King; Alisoltani, Arghavan; Keshri, Jitendra; Ubomba-Jaswa, Eunice

2018-03-01

Water quality is an important public health issue given that the presence of pathogenic organisms in such waters can adversely affect human and animal health. Despite the numerous studies conducted to assess the quality of environmental waters in many countries, limited efforts have been put on investigating the microbial quality of the sediments in developing countries and how this relates to different land uses. The present study evaluated the bacterial diversity in water and sediments in a highly used South African river to find out how the different land uses influenced the bacterial diversity, and to verify the human diseases functional classes of the bacterial populations. Samples were collected on river stretches influenced by an informal, a peri-urban and a rural settlement. Genomic DNA was extracted from water and sediment samples and sequenced on an Illumina® MiSeq platform targeting the 16S rRNA gene variable region V3-V4 from the genomic DNA. Metagenomic data analysis revealed that there was a great diversity in the microbial populations associated with the different land uses, with the informal settlement having the most considerable influence on the bacterial diversity in the water and sediments of the Apies River. The Proteobacteria (69.8%), Cyanobacteria (4.3%), Bacteroidetes (2.7%), and Actinobacteria (2.7%) were the most abundant phyla; the Alphaproteobacteria, Betaproteobacteria and Anaerolineae were the most recorded classes. Also, the sediments had a greater diversity and abundance in bacterial population than the water column. The functional profiles of the bacterial populations revealed an association with many human diseases including cancer pathways. Further studies that would isolate these potentially pathogenic organisms in the aquatic environment are therefore needed as this would help in protecting the lives of communities using such rivers, especially against emerging bacterial pathogens. Copyright © 2017 Elsevier B.V. All rights reserved.

Antitumor activity and safety of the PARP inhibitor rucaparib in patients with high-grade ovarian carcinoma and a germline or somatic BRCA1 or BRCA2 mutation: Integrated analysis of data from Study 10 and ARIEL2.

PubMed

Oza, Amit M; Tinker, Anna V; Oaknin, Ana; Shapira-Frommer, Ronnie; McNeish, Iain A; Swisher, Elizabeth M; Ray-Coquard, Isabelle; Bell-McGuinn, Katherine; Coleman, Robert L; O'Malley, David M; Leary, Alexandra; Chen, Lee-May; Provencher, Diane; Ma, Ling; Brenton, James D; Konecny, Gottfried E; Castro, Cesar M; Giordano, Heidi; Maloney, Lara; Goble, Sandra; Lin, Kevin K; Sun, James; Raponi, Mitch; Rolfe, Lindsey; Kristeleit, Rebecca S

2017-11-01

An integrated analysis was undertaken to characterize the antitumor activity and safety profile of the oral poly(ADP-ribose) polymerase inhibitor rucaparib in patients with relapsed high-grade ovarian carcinoma (HGOC). Eligible patients from Study 10 (NCT01482715) and ARIEL2 (NCT01891344) who received a starting dose of oral rucaparib 600mg twice daily (BID) with or without food were included in these analyses. The integrated efficacy population included patients with HGOC and a deleterious germline or somatic BRCA1 or BRCA2 (BRCA1/2) mutation who received at least two prior chemotherapies and were sensitive, resistant, or refractory to platinum-based chemotherapy. The primary endpoint was investigator-assessed confirmed objective response rate (ORR). Secondary endpoints included duration of response (DOR) and progression-free survival (PFS). The integrated safety population included patients with HGOC who received at least one dose of rucaparib 600mg BID, irrespective of BRCA1/2 mutation status and prior treatments. In the efficacy population (n=106), ORR was 53.8% (95% confidence interval [CI], 43.8-63.5); 8.5% and 45.3% of patients achieved complete and partial responses, respectively. Median DOR was 9.2months (95% CI, 6.6-11.6). In the safety population (n=377), the most frequent treatment-emergent adverse events (AEs) were nausea, asthenia/fatigue, vomiting, and anemia/hemoglobin decreased. The most common grade ≥3 treatment-emergent AE was anemia/hemoglobin decreased. Treatment-emergent AEs led to treatment interruption, dose reduction, and treatment discontinuation in 58.6%, 45.9%, and 9.8% of patients, respectively. No treatment-related deaths occurred. Rucaparib has antitumor activity in advanced BRCA1/2-mutated HGOC and a manageable safety profile. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Variability in chemical composition and abundance of the rare tertiary relict Pinus heldreichii in Serbia.

PubMed

Bojović, Srdjan; Nikolić, Biljana; Ristić, Mihailo; Orlović, Saša; Veselinović, Milorad; Rakonjac, Ljubinko; Dražić, Dragana

2011-09-01

The particular significance of the whitebark pine (Pinus heldreichii Christ.) stems from the fact that it is a tertiary relict and Balkanic subendemite covering a very narrow and intermittent area in Serbia. A representative pool of 48 adult trees originating from three populations, one recently discovered natural (Population I) and two planted populations (Populations II and III) was investigated in order to evaluate the intra- and interpopulation variability of the essential oil of the complete fund of P. heldreichii in Serbia. In the pine-needle-terpene profile, 104 compounds were detected, 84 of which could be identified. Among the essential-oil constituents, monoterpenes and sesquiterpenes dominated, comprising ca. 90% of the essential oil. The terpenic profile of Population I was characterized by a predominance of monoterpenes (e.g., limonene (1), α-pinene, and Δ(3) -carene (4)), while sesquiterpenes (e.g., germacrene D (2) and β-caryophyllene (3)) obviously preponderated in the profile of Populations II and III. This study also demonstrated that the abundance of whitebark pines in Serbia had significantly changed over the last few decades. The number of individuals in the natural population had increased, while the number of individuals in the planted populations had decreased. Today, the whitebark pine fund in Serbia comprises less than 250 trees. 2011 Verlag Helvetica Chimica Acta AG, Zürich.

Immune System Dysregulation, Viral Reactivation and Stress During Short-Duration Spaceflight

NASA Technical Reports Server (NTRS)

Pierson, Duane; Sams, Clarence; Crucian, Brian; Mehta, Satish; Stowe, Raymond; Uchakin, Peter; Quiriarte, Heather

2010-01-01

The objective of this NASA Short-Duration Bioastronautics Investigation (SDBI) was to assess spaceflight-associated immune dysregulation. Many previous studies have investigated this phenomenon post-flight, and found altered distribution and function of the peripheral leukocyte populations. Alterations in cytokine production profiles have also been reported. Unfortunately, post-flight data may be altered by the stress associated with high-G re-entry and readaptation to unit gravity following deconditioning. Therefore, the current study collected blood and saliva samples from crewmembers immediately before landing, and returned those samples to Earth for terrestrial analysis. Assays include peripheral comprehensive immunophenotype, T cell function, cytokine profiles, viral-specific immunity, latent viral reactivation (EBV, CMV, VZV), and stress hormone measurements. A total of 18 short duration crewmembers completed the study and the final data will be presented.

Exhaust Plume Effects on Sonic Boom for a Delta Wing and a Swept Wing-Body Model

NASA Technical Reports Server (NTRS)

Castner, Raymond; Lake, Troy

2012-01-01

Supersonic travel is not allowed over populated areas due to the disturbance caused by the sonic boom. Research has been performed on sonic boom reduction and has included the contribution of the exhaust nozzle plume. Plume effect on sonic boom has progressed from the study of isolated nozzles to a study with four exhaust plumes integrated with a wing-body vehicle. This report provides a baseline analysis of the generic wing-body vehicle to demonstrate the effect of the nozzle exhaust on the near-field pressure profile. Reductions occurred in the peak-to-peak magnitude of the pressure profile for a swept wing-body vehicle. The exhaust plumes also had a favorable effect as the nozzles were moved outward along the wing-span.

Geocoding and social marketing in Alabama's cancer prevention programs.

PubMed

Miner, Julianna W; White, Arica; Lubenow, Anne E; Palmer, Sally

2005-11-01

The Alabama Department of Public Health (ADPH) is collaborating with the National Cancer Institute to develop detailed profiles of underserved Alabama communities most at risk for cancer. These profiles will be combined with geocoded data to create a pilot project, Cancer Prevention for Alabama's Underserved Populations: A Focused Approach. The project's objectives are to provide the ADPH's cancer prevention programs with a more accurate and cost-effective means of planning, implementing, and evaluating its prevention activities in an outcomes-oriented and population-appropriate manner. The project links geocoded data from the Alabama Statewide Cancer Registry with profiles generated by the National Cancer Institute's cancer profiling system, Consumer Health Profiles. These profiles have been successfully applied to market-focused cancer prevention messages across the United States. The ADPH and the National Cancer Institute will evaluate the efficacy of using geocoded data and lifestyle segmentation information in strategy development and program implementation. Alabama is the first state in the nation not only to link geocoded cancer registry data with lifestyle segmentation data but also to use the National Cancer Institute's profiles and methodology in combination with actual state data.

Cluster analysis of particulate matter (PM10) and black carbon (BC) concentrations

NASA Astrophysics Data System (ADS)

Žibert, Janez; Pražnikar, Jure

2012-09-01

The monitoring of air-pollution constituents like particulate matter (PM10) and black carbon (BC) can provide information about air quality and the dynamics of emissions. Air quality depends on natural and anthropogenic sources of emissions as well as the weather conditions. For a one-year period the diurnal concentrations of PM10 and BC in the Port of Koper were analysed by clustering days into similar groups according to the similarity of the BC and PM10 hourly derived day-profiles without any prior assumptions about working and non-working days, weather conditions or hot and cold seasons. The analysis was performed by using k-means clustering with the squared Euclidean distance as the similarity measure. The analysis showed that 10 clusters in the BC case produced 3 clusters with just one member day and 7 clusters that encompasses more than one day with similar BC profiles. Similar results were found in the PM10 case, where one cluster has a single-member day, while 7 clusters contain several member days. The clustering analysis revealed that the clusters with less pronounced bimodal patterns and low hourly and average daily concentrations for both types of measurements include the most days in the one-year analysis. A typical day profile of the BC measurements includes a bimodal pattern with morning and evening peaks, while the PM10 measurements reveal a less pronounced bimodality. There are also clusters with single-peak day-profiles. The BC data in such cases exhibit morning peaks, while the PM10 data consist of noon or afternoon single peaks. Single pronounced peaks can be explained by appropriate cluster wind speed profiles. The analysis also revealed some special day-profiles. The BC cluster with a high midnight peak at 30/04/2010 and the PM10 cluster with the highest observed concentration of PM10 at 01/05/2010 (208.0 μg m-3) coincide with 1 May, which is a national holiday in Slovenia and has very strong tradition of bonfire parties. The clustering of the diurnal concentration showed that various different day-profiles are presented in a cold period, while this is not the case for the hot season. Additional analysis of ship traffic and rain fall data showed that there is no statistically significant difference between the ship gross (bruto) registered tonnage (BRT) values in the case of BC and PM10 clusters, but that there is statistically significant differences between the rain fall in the BC and PM10 clusters. The wind-rose for clusters which included most days in the sampling period indicating that emitted PM10 and BC from Port of Koper were manly transported in the west direction over the sea and in the east direction, where there is in no populated area. Presented analysis showed that both BC and PM10 concentrations were driven by rain intensity and wind speed.

Multi-locus variable-number tandem repeat analysis of Bordetella pertussis isolates circulating in Poland in the period 1959-2013.

PubMed

Mosiej, Ewa; Krysztopa-Grzybowska, Katarzyna; Polak, Maciej; Prygiel, Marta; Lutyńska, Anna

2017-06-01

Despite the long history of pertussis vaccination and high vaccination coverage in Poland and many other developed countries, pertussis incidence rates have increased substantially, making whooping cough one of the most prevalent vaccine-preventable diseases. Among the factors potentially involved in pertussis resurgence, the adaptation of the Bordetella pertussis population to country-specific vaccine-induced immunity through selection of non-vaccine-type strains still needs detailed studies. Multi-locus variable-number tandem repeat analysis (MLVA), also linked to MLST and PFGE profiling, was applied to trace the genetic changes in the B. pertussis population circulating in Poland in the period 1959-2013 versus country-specific vaccine strains. Generally, among 174 B. pertussis isolates, 31 MLVA types were detected, of which 11 were not described previously. The predominant MLVA types of recent isolates in Poland were different from those of the typical isolates circulating in other European countries. The MT27 type, currently predominant in Europe, was rarely seen and detected in only five isolates among all studied. The features of the vaccine strains used for production of the pertussis component of a national whole-cell diphtheria-tetanus-pertussis (DTP) vaccine, as studied by MLVA and MLST tools, were found to not match those observed in the currently circulating B. pertussis isolates in Poland. Differences traced by MLVA in relation to the MLST and PFGE profiling confirmed that the B. pertussis strain types currently observed elsewhere in Europe, even if appearing in Poland, were not able to successfully disseminate within a human population in Poland that has been vaccinated with a whole-cell pertussis vaccine not used in other countries.

From Lesions to Viral Clones: Biological and Molecular Diversity amongst Autochthonous Brazilian Vaccinia Virus

PubMed Central

Oliveira, Graziele; Assis, Felipe; Almeida, Gabriel; Albarnaz, Jonas; Lima, Maurício; Andrade, Ana Cláudia; Calixto, Rafael; Oliveira, Cairo; Neto, José Diomedes; Trindade, Giliane; Ferreira, Paulo César; Kroon, Erna Geessien; Abrahão, Jônatas

2015-01-01

Vaccinia virus (VACV) has had an important role for humanity because of its use during the smallpox eradication campaign. VACV is the etiologic agent of the bovine vaccinia (BV), an emerging zoonosis that has been associated with economic, social, veterinary and public health problems, mainly in Brazil and India. Despite the current and historical VACV importance, there is little information about its circulation, prevalence, origins and maintenance in the environment, natural reservoirs and diversity. Brazilian VACV (VACV-BR) are grouped into at least two groups based on genetic and biological diversity: group 1 (G1) and group 2 (G2). In this study, we went to the field and investigated VACV clonal diversity directly from exanthemous lesions, during BV outbreaks. Our results demonstrate that the G1 VACV-BR were more frequently isolated. Furthermore, we were able to co-detect the two variants (G1 and G2) in the same sample. Molecular and biological analysis corroborated previous reports and confirmed the co-circulation of two VACV-BR lineages. The detected G2 clones presented exclusive genetic and biological markers, distinct to reference isolates, including VACV-Western Reserve. Two clones presented a mosaic profile, with both G1 and G2 features based on the molecular analysis of A56R, A26L and C23L genes. Indeed, some SNPs and INDELs in A56R nucleotide sequences were observed among clones of the same virus population, maybe as a result of an increased mutation rate in a mixed population. These results provide information about the diversity profile in VACV populations, highlighting its importance to VACV evolution and maintenance in the environment. PMID:25785515

Speed, age, sex, and body mass index provide a rigorous basis for comparing the kinematic and kinetic profiles of the lower extremity during walking.

PubMed

Chehab, E F; Andriacchi, T P; Favre, J

2017-06-14

The increased use of gait analysis has raised the need for a better understanding of how walking speed and demographic variations influence asymptomatic gait. Previous analyses mainly reported relationships between subsets of gait features and demographic measures, rendering it difficult to assess whether gait features are affected by walking speed or other demographic measures. The purpose of this study was to conduct a comprehensive analysis of the kinematic and kinetic profiles during ambulation that tests for the effect of walking speed in parallel to the effects of age, sex, and body mass index. This was accomplished by recruiting a population of 121 asymptomatic subjects and analyzing characteristic 3-dimensional kinematic and kinetic features at the ankle, knee, hip, and pelvis during walking trials at slow, normal, and fast speeds. Mixed effects linear regression models were used to identify how each of 78 discrete gait features is affected by variations in walking speed, age, sex, and body mass index. As expected, nearly every feature was associated with variations in walking speed. Several features were also affected by variations in demographic measures, including age affecting sagittal-plane knee kinematics, body mass index affecting sagittal-plane pelvis and hip kinematics, body mass index affecting frontal-plane knee kinematics and kinetics, and sex affecting frontal-plane kinematics at the pelvis, hip, and knee. These results could aid in the design of future studies, as well as clarify how walking speed, age, sex, and body mass index may act as potential confounders in studies with small populations or in populations with insufficient demographic variations for thorough statistical analyses. Copyright © 2017 Elsevier Ltd. All rights reserved.

Strong profiling is not mathematically optimal for discovering rare malfeasors

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

Press, William H

2008-01-01

In a large population of individuals labeled j = 1,2,...,N, governments attempt to find the rare malfeasor j = j, (terrorist, for example) by making use of priors p{sub j} that estimate the probability of individual j being a malfeasor. Societal resources for secondary random screening such as airport search or police investigation are concentrated against individuals with the largest priors. They may call this 'strong profiling' if the concentration is at least proportional to p{sub j} for the largest values. Strong profiling often results in higher probability, but otherwise innocent, individuals being repeatedly subjected to screening. They show heremore » that, entirely apart from considerations of social policy, strong profiling is not mathematically optimal at finding malfeasors. Even if prior probabilities were accurate, their optimal use would be only as roughly the geometric mean between a strong profiling and a completely uniform sampling of the population.« less

Influence analysis in quantitative trait loci detection.

PubMed

Dou, Xiaoling; Kuriki, Satoshi; Maeno, Akiteru; Takada, Toyoyuki; Shiroishi, Toshihiko

2014-07-01

This paper presents systematic methods for the detection of influential individuals that affect the log odds (LOD) score curve. We derive general formulas of influence functions for profile likelihoods and introduce them into two standard quantitative trait locus detection methods-the interval mapping method and single marker analysis. Besides influence analysis on specific LOD scores, we also develop influence analysis methods on the shape of the LOD score curves. A simulation-based method is proposed to assess the significance of the influence of the individuals. These methods are shown useful in the influence analysis of a real dataset of an experimental population from an F2 mouse cross. By receiver operating characteristic analysis, we confirm that the proposed methods show better performance than existing diagnostics. © 2014 The Author. Biometrical Journal published by WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

OUTER-DISK POPULATIONS IN NGC 7793: EVIDENCE FOR STELLAR RADIAL MIGRATION

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

Radburn-Smith, David J.; Dalcanton, Julianne J.; Roskar, Rok

2012-07-10

We analyzed the radial surface brightness profile of the spiral galaxy NGC 7793 using HST/ACS images from the GHOSTS survey and a new HST/WFC3 image across the disk break. We used the photometry of resolved stars to select distinct populations covering a wide range of stellar ages. We found breaks in the radial profiles of all stellar populations at 280'' ({approx}5.1 kpc). Beyond this disk break, the profiles become steeper for younger populations. This same trend is seen in numerical simulations where the outer disk is formed almost entirely by radial migration. We also found that the older stars ofmore » NGC 7793 extend significantly farther than the underlying H I disk. They are thus unlikely to have formed entirely at their current radii, unless the gas disk was substantially larger in the past. These observations thus provide evidence for substantial stellar radial migration in late-type disks.« less

Lipid profile, cardiovascular disease and mortality in a Mediterranean high-risk population: The ESCARVAL-RISK study

PubMed Central

Orozco-Beltran, Domingo; Gil-Guillen, Vicente F.; Redon, Josep; Martin-Moreno, Jose M.; Pallares-Carratala, Vicente; Navarro-Perez, Jorge; Valls-Roca, Francisco; Sanchis-Domenech, Carlos; Fernandez-Gimenez, Antonio; Perez-Navarro, Ana; Bertomeu-Martinez, Vicente; Bertomeu-Gonzalez, Vicente; Cordero, Alberto; Pascual de la Torre, Manuel; Trillo, Jose L.; Carratala-Munuera, Concepcion; Pita-Fernandez, Salvador; Uso, Ruth; Durazo-Arvizu, Ramon; Cooper, Richard; Sanz, Gines; Castellano, Jose M.; Ascaso, Juan F.; Carmena, Rafael; Tellez-Plaza, Maria

2017-01-01

Introduction The potential impact of targeting different components of an adverse lipid profile in populations with multiple cardiovascular risk factors is not completely clear. This study aims to assess the association between different components of the standard lipid profile with all-cause mortality and hospitalization due to cardiovascular events in a high-risk population. Methods This prospective registry included high risk adults over 30 years old free of cardiovascular disease (2008–2012). Diagnosis of hypertension, dyslipidemia or diabetes mellitus was inclusion criterion. Lipid biomarkers were evaluated. Primary endpoints were all-cause mortality and hospital admission due to coronary heart disease or stroke. We estimated adjusted rate ratios (aRR), absolute risk differences and population attributable risk associated with adverse lipid profiles. Results 51,462 subjects were included with a mean age of 62.6 years (47.6% men). During an average follow-up of 3.2 years, 919 deaths, 1666 hospitalizations for coronary heart disease and 1510 hospitalizations for stroke were recorded. The parameters that showed an increased rate for total mortality, coronary heart disease and stroke hospitalization were, respectively, low HDL-Cholesterol: aRR 1.25, 1.29 and 1.23; high Total/HDL-Cholesterol: aRR 1.22, 1.38 and 1.25; and high Triglycerides/HDL-Cholesterol: aRR 1.21, 1.30, 1.09. The parameters that showed highest population attributable risk (%) were, respectively, low HDL-Cholesterol: 7.70, 11.42, 8.40; high Total/HDL-Cholesterol: 6.55, 12.47, 8.73; and high Triglycerides/HDL-Cholesterol: 8.94, 15.09, 6.92. Conclusions In a population with cardiovascular risk factors, HDL-cholesterol, Total/HDL-cholesterol and triglycerides/HDL-cholesterol ratios were associated with a higher population attributable risk for cardiovascular disease compared to other common biomarkers. PMID:29045483

Lipid profile, cardiovascular disease and mortality in a Mediterranean high-risk population: The ESCARVAL-RISK study.

PubMed

Orozco-Beltran, Domingo; Gil-Guillen, Vicente F; Redon, Josep; Martin-Moreno, Jose M; Pallares-Carratala, Vicente; Navarro-Perez, Jorge; Valls-Roca, Francisco; Sanchis-Domenech, Carlos; Fernandez-Gimenez, Antonio; Perez-Navarro, Ana; Bertomeu-Martinez, Vicente; Bertomeu-Gonzalez, Vicente; Cordero, Alberto; Pascual de la Torre, Manuel; Trillo, Jose L; Carratala-Munuera, Concepcion; Pita-Fernandez, Salvador; Uso, Ruth; Durazo-Arvizu, Ramon; Cooper, Richard; Sanz, Gines; Castellano, Jose M; Ascaso, Juan F; Carmena, Rafael; Tellez-Plaza, Maria

2017-01-01

The potential impact of targeting different components of an adverse lipid profile in populations with multiple cardiovascular risk factors is not completely clear. This study aims to assess the association between different components of the standard lipid profile with all-cause mortality and hospitalization due to cardiovascular events in a high-risk population. This prospective registry included high risk adults over 30 years old free of cardiovascular disease (2008-2012). Diagnosis of hypertension, dyslipidemia or diabetes mellitus was inclusion criterion. Lipid biomarkers were evaluated. Primary endpoints were all-cause mortality and hospital admission due to coronary heart disease or stroke. We estimated adjusted rate ratios (aRR), absolute risk differences and population attributable risk associated with adverse lipid profiles. 51,462 subjects were included with a mean age of 62.6 years (47.6% men). During an average follow-up of 3.2 years, 919 deaths, 1666 hospitalizations for coronary heart disease and 1510 hospitalizations for stroke were recorded. The parameters that showed an increased rate for total mortality, coronary heart disease and stroke hospitalization were, respectively, low HDL-Cholesterol: aRR 1.25, 1.29 and 1.23; high Total/HDL-Cholesterol: aRR 1.22, 1.38 and 1.25; and high Triglycerides/HDL-Cholesterol: aRR 1.21, 1.30, 1.09. The parameters that showed highest population attributable risk (%) were, respectively, low HDL-Cholesterol: 7.70, 11.42, 8.40; high Total/HDL-Cholesterol: 6.55, 12.47, 8.73; and high Triglycerides/HDL-Cholesterol: 8.94, 15.09, 6.92. In a population with cardiovascular risk factors, HDL-cholesterol, Total/HDL-cholesterol and triglycerides/HDL-cholesterol ratios were associated with a higher population attributable risk for cardiovascular disease compared to other common biomarkers.

Minimizing the dependency ratio in a population with below-replacement fertility through immigration

PubMed Central

Simon, C.; Belyakov, A.O.; Feichtinger, G.

2012-01-01

Many industrialized countries face fertility rates below replacement level, combined with declining mortality especially in older ages. Consequently, the populations of these countries have started to age. One important indicator of age structures is the dependency ratio which is the ratio of the nonworking age population to the working age population. In this work we find the age-specific immigration profile that minimizes the dependency ratio in a stationary population with below-replacement fertility. It is assumed that the number of immigrants per age is limited. We consider two alternative policies. In the first one, we fix the total number of people who annually immigrate to a country. In the second one, we prescribe the size of the receiving country’s population. For both cases we provide numerical results for the optimal immigration profile, for the resulting age structure of the population, as well as for the dependency ratio. PMID:22781918

The Integrated Epidemiologic Profile: Using Multiple Data Sources in Developing Profiles to Inform HIV Prevention and Care Planning

ERIC Educational Resources Information Center

Whitmore, Suzanne K.; Zaidi, Irum F.; Dean, Hazel D.

2005-01-01

HIV/AIDS epidemiologic profiles describe the HIV/AIDS epidemic among state and local populations. The Centers for Disease Control and Prevention and the Health Resources Services Administration collaborated to develop one set of guidelines for developing epidemiologic profiles that would serve as the basis for both prevention and care planning.…

A Descriptive Study on the Neonatal Morbidity Profile of Autism Spectrum Disorders, Including a Comparison with Other Neurodevelopmental Disorders

ERIC Educational Resources Information Center

Atladóttir, H. Ó.; Schendel, D. E.; Parner, E. T.; Henriksen, T. B.

2015-01-01

The aim of this study was to describe the profile of specific neonatal morbidities in children later diagnosed with autism spectrum disorder (ASD), and to compare this profile with the profile of children with hyperkinetic disorder, cerebral palsy, epilepsy or intellectual disability. This is a Danish population based cohort study, including all…

Core microbial functional activities in ocean environments revealed by global metagenomic profiling analyses.

PubMed

Ferreira, Ari J S; Siam, Rania; Setubal, João C; Moustafa, Ahmed; Sayed, Ahmed; Chambergo, Felipe S; Dawe, Adam S; Ghazy, Mohamed A; Sharaf, Hazem; Ouf, Amged; Alam, Intikhab; Abdel-Haleem, Alyaa M; Lehvaslaiho, Heikki; Ramadan, Eman; Antunes, André; Stingl, Ulrich; Archer, John A C; Jankovic, Boris R; Sogin, Mitchell; Bajic, Vladimir B; El-Dorry, Hamza

2014-01-01

Metagenomics-based functional profiling analysis is an effective means of gaining deeper insight into the composition of marine microbial populations and developing a better understanding of the interplay between the functional genome content of microbial communities and abiotic factors. Here we present a comprehensive analysis of 24 datasets covering surface and depth-related environments at 11 sites around the world's oceans. The complete datasets comprises approximately 12 million sequences, totaling 5,358 Mb. Based on profiling patterns of Clusters of Orthologous Groups (COGs) of proteins, a core set of reference photic and aphotic depth-related COGs, and a collection of COGs that are associated with extreme oxygen limitation were defined. Their inferred functions were utilized as indicators to characterize the distribution of light- and oxygen-related biological activities in marine environments. The results reveal that, while light level in the water column is a major determinant of phenotypic adaptation in marine microorganisms, oxygen concentration in the aphotic zone has a significant impact only in extremely hypoxic waters. Phylogenetic profiling of the reference photic/aphotic gene sets revealed a greater variety of source organisms in the aphotic zone, although the majority of individual photic and aphotic depth-related COGs are assigned to the same taxa across the different sites. This increase in phylogenetic and functional diversity of the core aphotic related COGs most probably reflects selection for the utilization of a broad range of alternate energy sources in the absence of light.

Core Microbial Functional Activities in Ocean Environments Revealed by Global Metagenomic Profiling Analyses

PubMed Central

Ferreira, Ari J. S.; Siam, Rania; Setubal, João C.; Moustafa, Ahmed; Sayed, Ahmed; Chambergo, Felipe S.; Dawe, Adam S.; Ghazy, Mohamed A.; Sharaf, Hazem; Ouf, Amged; Alam, Intikhab; Abdel-Haleem, Alyaa M.; Lehvaslaiho, Heikki; Ramadan, Eman; Antunes, André; Stingl, Ulrich; Archer, John A. C.; Jankovic, Boris R.; Sogin, Mitchell; Bajic, Vladimir B.; El-Dorry, Hamza

2014-01-01

Metagenomics-based functional profiling analysis is an effective means of gaining deeper insight into the composition of marine microbial populations and developing a better understanding of the interplay between the functional genome content of microbial communities and abiotic factors. Here we present a comprehensive analysis of 24 datasets covering surface and depth-related environments at 11 sites around the world's oceans. The complete datasets comprises approximately 12 million sequences, totaling 5,358 Mb. Based on profiling patterns of Clusters of Orthologous Groups (COGs) of proteins, a core set of reference photic and aphotic depth-related COGs, and a collection of COGs that are associated with extreme oxygen limitation were defined. Their inferred functions were utilized as indicators to characterize the distribution of light- and oxygen-related biological activities in marine environments. The results reveal that, while light level in the water column is a major determinant of phenotypic adaptation in marine microorganisms, oxygen concentration in the aphotic zone has a significant impact only in extremely hypoxic waters. Phylogenetic profiling of the reference photic/aphotic gene sets revealed a greater variety of source organisms in the aphotic zone, although the majority of individual photic and aphotic depth-related COGs are assigned to the same taxa across the different sites. This increase in phylogenetic and functional diversity of the core aphotic related COGs most probably reflects selection for the utilization of a broad range of alternate energy sources in the absence of light. PMID:24921648

Biochemical Association of Metabolic Profile and Microbiome in Chronic Pressure Ulcer Wounds

PubMed Central

Ammons, Mary Cloud B.; Morrissey, Kathryn; Tripet, Brian P.; Van Leuven, James T.; Han, Anne; Lazarus, Gerald S.; Zenilman, Jonathan M.; Stewart, Philip S.; James, Garth A.; Copié, Valérie

2015-01-01

Chronic, non-healing wounds contribute significantly to the suffering of patients with co-morbidities in the clinical population with mild to severely compromised immune systems. Normal wound healing proceeds through a well-described process. However, in chronic wounds this process seems to become dysregulated at the transition between resolution of inflammation and re-epithelialization. Bioburden in the form of colonizing bacteria is a major contributor to the delayed headlining in chronic wounds such as pressure ulcers. However how the microbiome influences the wound metabolic landscape is unknown. Here, we have used a Systems Biology approach to determine the biochemical associations between the taxonomic and metabolomic profiles of wounds colonized by bacteria. Pressure ulcer biopsies were harvested from primary chronic wounds and bisected into top and bottom sections prior to analysis of microbiome by pyrosequencing and analysis of metabolome using 1H nuclear magnetic resonance (NMR) spectroscopy. Bacterial taxonomy revealed that wounds were colonized predominantly by three main phyla, but differed significantly at the genus level. While taxonomic profiles demonstrated significant variability between wounds, metabolic profiles shared significant similarity based on the depth of the wound biopsy. Biochemical association between taxonomy and metabolic landscape indicated significant wound-to-wound similarity in metabolite enrichment sets and metabolic pathway impacts, especially with regard to amino acid metabolism. To our knowledge, this is the first demonstration of a statistically robust correlation between bacterial colonization and metabolic landscape within the chronic wound environment. PMID:25978400

Linked Patient-Reported Outcomes Data From Patients With Multiple Sclerosis Recruited on an Open Internet Platform to Health Care Claims Databases Identifies a Representative Population for Real-Life Data Analysis in Multiple Sclerosis.

PubMed

Risson, Valery; Ghodge, Bhaskar; Bonzani, Ian C; Korn, Jonathan R; Medin, Jennie; Saraykar, Tanmay; Sengupta, Souvik; Saini, Deepanshu; Olson, Melvin

2016-09-22

An enormous amount of information relevant to public health is being generated directly by online communities. To explore the feasibility of creating a dataset that links patient-reported outcomes data, from a Web-based survey of US patients with multiple sclerosis (MS) recruited on open Internet platforms, to health care utilization information from health care claims databases. The dataset was generated by linkage analysis to a broader MS population in the United States using both pharmacy and medical claims data sources. US Facebook users with an interest in MS were alerted to a patient-reported survey by targeted advertisements. Eligibility criteria were diagnosis of MS by a specialist (primary progressive, relapsing-remitting, or secondary progressive), ≥12-month history of disease, age 18-65 years, and commercial health insurance. Participants completed a questionnaire including data on demographic and disease characteristics, current and earlier therapies, relapses, disability, health-related quality of life, and employment status and productivity. A unique anonymous profile was generated for each survey respondent. Each anonymous profile was linked to a number of medical and pharmacy claims datasets in the United States. Linkage rates were assessed and survey respondents' representativeness was evaluated based on differences in the distribution of characteristics between the linked survey population and the general MS population in the claims databases. The advertisement was placed on 1,063,973 Facebook users' pages generating 68,674 clicks, 3719 survey attempts, and 651 successfully completed surveys, of which 440 could be linked to any of the claims databases for 2014 or 2015 (67.6% linkage rate). Overall, no significant differences were found between patients who were linked and not linked for educational status, ethnicity, current or prior disease-modifying therapy (DMT) treatment, or presence of a relapse in the last 12 months. The frequencies of the most common MS symptoms did not differ significantly between linked patients and the general MS population in the databases. Linked patients were slightly younger and less likely to be men than those who were not linkable. Linking patient-reported outcomes data, from a Web-based survey of US patients with MS recruited on open Internet platforms, to health care utilization information from claims databases may enable rapid generation of a large population of representative patients with MS suitable for outcomes analysis.

Genetic Diversity and Phylogenetic Analysis of South-East Asian Duck Populations Based on the mtDNA D-loop Sequences

PubMed Central

Sultana, H.; Seo, D. W.; Bhuiyan, M. S. A.; Choi, N. R.; Hoque, M. R.; Heo, K. N.; Lee, J. H.

2016-01-01

The maternally inherited mitochondrial DNA (mtDNA) D–loop region is widely used for exploring genetic relationships and for investigating the origin of various animal species. Currently, domestic ducks play an important role in animal protein supply. In this study, partial mtDNA D–loop sequences were obtained from 145 samples belonging to six South-East Asian duck populations and commercial duck population. All these populations were closely related to the mallard duck (Anas platyrhynchos), as indicated by their mean overall genetic distance. Sixteen nucleotide substitutions were identified in sequence analyses allowing the distinction of 28 haplotypes. Around 42.76% of the duck sequences were classified as Hap_02, which completely matched with Anas platyrhynchos duck species. The neighbor-joining phylogenetic tree also revealed that South-East Asian duck populations were closely related to Anas platyrhynchos. Network profiles were also traced using the 28 haplotypes. Overall, results showed that those duck populations D-loop haplotypes were shared between several duck breeds from Korea and Bangladesh sub continental regions. Therefore, these results confirmed that South-East Asian domestic duck populations have been domesticated from Anas platyrhynchos duck as the maternal origins. PMID:27004808

A Mayan founder mutation is a common cause of deafness in Guatemala.

PubMed

Carranza, C; Menendez, I; Herrera, M; Castellanos, P; Amado, C; Maldonado, F; Rosales, L; Escobar, N; Guerra, M; Alvarez, D; Foster, J; Guo, S; Blanton, S H; Bademci, G; Tekin, M

2015-09-08

Over 5% of the world's population has varying degrees of hearing loss. Mutations in GJB2 are the most common cause of autosomal recessive non-syndromic hearing loss (ARNHL) in many populations. The frequency and type of mutations are influenced by ethnicity. Guatemala is a multi-ethnic country with four major populations: Maya, Ladino, Xinca, and Garifuna. To determine the mutation profile of GJB2 in a ARNHL population from Guatemala, we sequenced both exons of GJB2 in 133 unrelated families. A total of six pathogenic variants were detected. The most frequent pathogenic variant is c.131G>A (p.Trp44*) detected in 21 of 266 alleles. We show that c.131G>A is associated with a conserved haplotype in Guatemala suggesting a single founder. The majority of Mayan population lives in the west region of the country from where all c.131G>A carriers originated. Further analysis of genome-wide variation of individuals carrying the c.131G>A mutation compared with those of Native American, European, and African populations shows a close match with the Mayan population. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Cell type specific gene expression analysis of prostate needle biopsies resolves tumor tissue heterogeneity

PubMed Central

Krönig, Malte; Walter, Max; Drendel, Vanessa; Werner, Martin; Jilg, Cordula A.; Richter, Andreas S.; Backofen, Rolf; McGarry, David; Follo, Marie; Schultze-Seemann, Wolfgang; Schüle, Roland

2015-01-01

A lack of cell surface markers for the specific identification, isolation and subsequent analysis of living prostate tumor cells hampers progress in the field. Specific characterization of tumor cells and their microenvironment in a multi-parameter molecular assay could significantly improve prognostic accuracy for the heterogeneous prostate tumor tissue. Novel functionalized gold-nano particles allow fluorescence-based detection of absolute mRNA expression levels in living cells by fluorescent activated flow cytometry (FACS). We use of this technique to separate prostate tumor and benign cells in human prostate needle biopsies based on the expression levels of the tumor marker alpha-methylacyl-CoA racemase (AMACR). We combined RNA and protein detection of living cells by FACS to gate for epithelial cell adhesion molecule (EPCAM) positive tumor and benign cells, EPCAM/CD45 double negative mesenchymal cells and CD45 positive infiltrating lymphocytes. EPCAM positive epithelial cells were further sub-gated into AMACR high and low expressing cells. Two hundred cells from each population and several biopsies from the same patient were analyzed using a multiplexed gene expression profile to generate a cell type resolved profile of the specimen. This technique provides the basis for the clinical evaluation of cell type resolved gene expression profiles as pre-therapeutic prognostic markers for prostate cancer. PMID:25514598

Studying Military Community Health, Well-being, and Discourse through the Social Media Lens

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

Pavalanathan, Umashanthi; Datla, Vivek V.; Volkova, Svitlana

Social media can provide a resource for characterizing communities and targeted populations through activities and content shared online. For instance, studying the armed forces‚Äô use of social media may provide insights into their health and wellbeing. In this paper, we address three broad research questions: (1) How do military populations use social media? (2) What topics do military users discuss in social media? (3) Do military users talk about health and well-being differently than civilians? Military Twitter users were identified through keywords in the profile description of users who posted geotagged tweets at military installations. These military tweets were comparedmore » with the tweets from remaining population. Our analysis indicate that military users talk more about military related responsibilities and events, whereas non-military users talk more about school, work, and leisure activities. A significant difference in online content generated by both populations was identified, involving sentiment, health, language, and social media features.« less

Gender Differences in Depressive Symptom Profile: Results from Nationwide General Population Surveys in Korea.

PubMed

Kim, Ji-Hyun; Cho, Maeng Je; Hong, Jin Pyo; Bae, Jae Nam; Cho, Seong-Jin; Hahm, Bong-Jin; Lee, Dong-Woo; Park, Jong-Ik; Lee, Jun-Young; Jeon, Hong Jin; Chang, Sung Man

2015-11-01

This study investigated gender differences in symptom profiles of major depressive disorder (MDD) in the Korean general population. Data were pooled from the series of nationwide Korean Epidemiologic Catchment Area surveys conducted in 2001, 2006 and 2011, respectively. Of the 18,807 participants, 507 (397 women and 110 men) were diagnosed with MDD within the prior 12 months. In agreement with previous studies, women with MDD appeared to be more vulnerable to experiencing atypical depressive episodes defined as depression with two or more symptoms of fatigue, increased appetite and hypersomnia (P < 0.001). In terms of individual symptoms, female gender was significantly related with higher prevalence of fatigue (P = 0.008), hypersomnia (P = 0.001), noticeable psychomotor retardation (P = 0.029) and suicidal attempts (P = 0.016) with adjustment for birth cohort effect, partner status, and employment status. In the same analysis, men with MDD appeared more vulnerable to decreased libido than women (P = 0.009). This is the first report to demonstrate gender differences in symptomatology of MDD in the general Korean population, and the results are comparable to previous investigations from western societies. Assumingly, the intercultural similarity in female preponderance to atypical depression might reflect the common biological construct underlying the gender difference in mechanism of MDD. In clinical settings, gender differences of MDD should be carefully considered, because these features could be related with treatment response and drug side effects.

Comparison of bacteroides-prevotella 16S rRNA genetic markers for fecal samples from different animal species.

PubMed

Fogarty, Lisa R; Voytek, Mary A

2005-10-01

To effectively manage surface and ground waters it is necessary to improve our ability to detect and identify sources of fecal contamination. We evaluated the use of the anaerobic bacterial group Bacteroides-Prevotella as a potential fecal indicator. Terminal restriction length polymorphism (T-RFLP) of the 16S rRNA genes from this group was used to determine differences in populations and to identify any unique populations in chickens, cows, deer, dogs, geese, horses, humans, pigs, and seagulls. The group appears to be a good potential fecal indicator in all groups tested except for avians. Cluster analysis of Bacteroides-Prevotella community T-RFLP profiles indicates that Bacteroides-Prevotella populations from samples of the same host species are much more similar to each other than to samples from different source species. We were unable to identify unique peaks that were exclusive to any source species; however, for most host species, at least one T-RFLP peak was identified to be more commonly found in that species, and a combination of peaks could be used to identify the source. T-RFLP profiles obtained from water spiked with known-source feces contained the expected diagnostic peaks from the source. These results indicate that the approach of identifying Bacteroides-Prevotella molecular markers associated with host species might be useful in identifying sources of fecal contamination in the environment.

Comparison of Bacteroides-Prevotella 16S rRNA Genetic Markers for Fecal Samples from Different Animal Species

PubMed Central

Fogarty, Lisa R.; Voytek, Mary A.

2005-01-01

To effectively manage surface and ground waters it is necessary to improve our ability to detect and identify sources of fecal contamination. We evaluated the use of the anaerobic bacterial group Bacteroides-Prevotella as a potential fecal indicator. Terminal restriction length polymorphism (T-RFLP) of the 16S rRNA genes from this group was used to determine differences in populations and to identify any unique populations in chickens, cows, deer, dogs, geese, horses, humans, pigs, and seagulls. The group appears to be a good potential fecal indicator in all groups tested except for avians. Cluster analysis of Bacteroides-Prevotella community T-RFLP profiles indicates that Bacteroides-Prevotella populations from samples of the same host species are much more similar to each other than to samples from different source species. We were unable to identify unique peaks that were exclusive to any source species; however, for most host species, at least one T-RFLP peak was identified to be more commonly found in that species, and a combination of peaks could be used to identify the source. T-RFLP profiles obtained from water spiked with known-source feces contained the expected diagnostic peaks from the source. These results indicate that the approach of identifying Bacteroides-Prevotella molecular markers associated with host species might be useful in identifying sources of fecal contamination in the environment. PMID:16204514

Population variation in neuroendocrine activity is associated with behavioral inhibition and hemispheric brain structure in young rhesus monkeys

PubMed Central

Short, Sarah J.; Lubach, Gabriele R.; Shirtcliff, Elizabeth A.; Styner, Martin A.; Gilmore, John H.; Coe, Christopher L.

2014-01-01

Summary Population variation in hypothalamic-pituitary-adrenal (HPA) activity and reactivity was assessed in a healthy sample of 48 juvenile rhesus monkeys. Cluster analysis of the HPA profiles revealed four distinct neuroendocrine phenotypes based on six indices of HPA functioning. Behavioral reactivity was also evaluated in response to novel stimuli, and revealed marked differences between animals in the highest- and lowest-cortisol clusters. Specifically, animals in the high-cortisol cluster showed larger stress-induced cortisol responses and blunted feedback sensitivity to dexamethasone. They were also emotionally reactive, displayed more aggressive behaviors, and were less likely to approach novel objects. In contrast, monkeys in the low-cortisol cluster were more likely to approach and explore novel objects. Representative animals with high or low cortisol profiles were scanned with Magnetic Resonance Imaging to evaluate structural differences in global and regional gray matter (GM) and white matter (WM) volumes. Monkeys with higher cortisol reactivity evinced less hemispheric brain asymmetry, due to decreased GM in the right hemisphere. Stress reactivity was inversely related to global GM and positively related to total cerebrospinal fluid volume. This inverse relationship was also observed in several stress-sensitive regions, including prefrontal and frontal cortices. Our study demonstrates that population variation in pituitary-adrenal activity is related to behavioral disposition and cerebral structure in this nonhuman primate species. PMID:24954302

The Bacterial Communities of Full-Scale Biologically Active, Granular Activated Carbon Filters Are Stable and Diverse and Potentially Contain Novel Ammonia-Oxidizing Microorganisms

PubMed Central

Hope Wilkinson, Katheryn; Strait, Jacqueline M.; Hozalski, Raymond M.; Sadowksy, Michael J.; Hamilton, Matthew J.

2015-01-01

The bacterial community composition of the full-scale biologically active, granular activated carbon (BAC) filters operated at the St. Paul Regional Water Services (SPRWS) was investigated using Illumina MiSeq analysis of PCR-amplified 16S rRNA gene fragments. These bacterial communities were consistently diverse (Shannon index, >4.4; richness estimates, >1,500 unique operational taxonomic units [OTUs]) throughout the duration of the 12-month study period. In addition, only modest shifts in the quantities of individual bacterial populations were observed; of the 15 most prominent OTUs, the most highly variable population (a Variovorax sp.) modulated less than 13-fold over time and less than 8-fold from filter to filter. The most prominent population in the profiles was a Nitrospira sp., representing 13 to 21% of the community. Interestingly, very few of the known ammonia-oxidizing bacteria (AOB; <0.07%) and no ammonia-oxidizing Archaea were detected in the profiles. Quantitative PCR of amoA genes, however, suggested that AOB were prominent in the bacterial communities (amoA/16S rRNA gene ratio, 1 to 10%). We conclude, therefore, that the BAC filters at the SPRWS potentially contained significant numbers of unidentified and novel ammonia-oxidizing microorganisms that possess amoA genes similar to those of previously described AOB. PMID:26209671

[Health profile of a population as a predictor of health resources utilization: results of the implementation of an epidemiologic model for needs analysis].

PubMed

Nascetti, Simona; Falasca, Pasquale; Mengolini, Barbara; Francesco, Arrigo; Cicero, Giuseppe; Linarello, Simona; Gaddi, Antonio

2003-01-01

The integration of the scientific researches in the assistance process is one of the most important challenges that is currently set to the health operators. In this paper a model for the health needs-assessment will be applied to verify if and how the prevalence of some classical risk factors for cardiovascular disease foretells mortality and hospitalisation episodes at 3 years, and if it could express the health need of that population. The "sanitary history" of 1704 subjects, enrolled in 1996 during the Brisighella Study, has been followed. We know the health profile of these subjects at 1996 and data about their hospitalizations, mortality, and general assistance from 1996 to 1999. In this population the risk of cardiovascular disease is inferior to that esteemed by the hospitalisation rate, attributable mostly to a little group of subjects with well-defined characteristics of exposure. The resources spent on a hospitalization do not adequately describe either the sanitary need nor the relief load and the "cost" associated to the disease. The methodology used allows to explore in detail the relative weight of the different subjects involved in the sanitary assistance in order to better reach the objective of producing the maximum quantity of benefits for the patient at the smallest possible quantity of risk.

The study on facial soft tissue thickness using Han population in Xinjiang.

PubMed

Wang, Jierui; Zhao, Xi; Mi, Congbo; Raza, Iqbal

2016-09-01

Facial profile is an important aspect in physical anthropology, forensic science, and cosmetic research. Thus, facial soft tissue measurement technology plays a significant role in facial restoration. A considerable amount of work has investigated facial soft tissue thickness, which significantly varies according to gender, age, and race. However, only few studies have considered the nutritional status of the investigated individuals. Moreover, no sufficient research among Chinese ethnic groups, particularly Xinjiang population in China, is currently available. Hence, the current study investigated the adaptability of facial soft tissue to the underlying hard tissue among young adults of Han population in Xinjiang, China; the analysis was performed on the basis of gender, skeletal class, and body mass index (BMI). Measurements were obtained from the lateral cephalometric radiographs of 256 adults aged 18-26 years old. Differences in soft tissue thickness were observed between genders and among skeletal classes. With regard to gender, significant differences in soft tissue thickness were found at rhinion, glabella, subnasale, stomion, labrale superius, pogonion, and gnathion among different BMI groups. Thus, nutritional status should be considered when reconstructing an individual's facial profile. Results showed that the thinnest and thickest craniofacial soft tissues existed in rhinion and lip regions, respectively. Overall, this research provides valuable data for forensic facial reconstruction and identification of young adults in Xinjiang, China. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Comparison of Bacteroides-Prevotella 16S rRNA genetic markers for fecal samples from different animal species

USGS Publications Warehouse

Fogarty, L.R.; Voytek, M.A.

2005-01-01

To effectively manage surface and ground waters it is necessary to improve our ability to detect and identify sources of fecal contamination. We evaluated the use of the anaerobic bacterial group Bacteroides-Prevotella as a potential fecal indicator. Terminal restriction length polymorphism (T-RFLP) of the 16S rRNA genes from this group was used to determine differences in populations and to identify any unique populations in chickens, cows, deer, dogs, geese, horses, humans, pigs, and seagulls. The group appears to be a good potential fecal indicator in all groups tested except for avians. Cluster analysis of Bacteroides-Prevotella community T-RFLP profiles indicates that Bacteroides-Prevotella populations from samples of the same host species are much more similar to each other than to samples from different source species. We were unable to identify unique peaks that were exclusive to any source species; however, for most host species, at least one T-RFLP peak was identified to be more commonly found in that species, and a combination of peaks could be used to identify the source. T-RFLP profiles obtained from water spiked with known-source feces contained the expected diagnostic peaks from the source. These results indicate that the approach of identifying Bacteroides-Prevotella molecular markers associated with host species might be useful in identifying sources of fecal contamination in the environment.

Factors discriminating among profiles of resilience and psychopathology in children exposed to intimate partner violence (IPV).

PubMed

Graham-Bermann, Sandra A; Gruber, Gabrielle; Howell, Kathryn H; Girz, Laura

2009-09-01

To evaluate the social and emotional adjustment of 219 children in families with varying levels of intimate partner violence (IPV) using a model of risk and protection. To explore factors that differentiate children with poor adjustment from those with resilience. Mothers who experienced IPV in the past year and their children ages 6-12 were interviewed. Standardized measures assessed family violence, parenting, family functioning, maternal mental health, and children's adjustment and beliefs. Using cluster analysis, all cases with valid data on the Child Behavior Checklist, Child Depression Inventory, General Self-Worth and Social Self-Competence measures were described by four profiles of children's adjustment: Severe Adjustment Problems (24%); children who were Struggling (45%); those with Depression Only (11%); and Resilient (20%) with high competence and low adjustment problems. Multinomial logistic regression analyses showed children in the Severe Problems cluster witnessed more family violence and had mothers higher in depression and trauma symptoms than other children. Resilient and Struggling children had mothers with better parenting, more family strengths and no past violent partner. Parents of children with Severe Problems were lacking these attributes. The Depressed profile children witnessed less violence but had greater fears and worries about mother's safety. Factors related to the child, to the mother and to the family distinguish different profiles of adjustment for children exposed to IPV who are living in the community. Resilient children have less violence exposure, fewer fears and worries, and mothers with better mental health and parenting skills, suggesting avenues for intervention with this population. Findings suggest that child adjustment is largely influenced by parent functioning. Thus, services should be targeted at both the child and the parent. Clinical interventions shaped to the unique needs of the child might also be tested with this population.

An approach to analyzing a single subject's scores obtained in a standardized test with application to the Aachen Aphasia Test (AAT).

PubMed

Willmes, K

1985-08-01

Methods for the analysis of a single subject's test profile(s) proposed by Huber (1973) are applied to the Aachen Aphasia Test (AAT). The procedures are based on the classical test theory model (Lord & Novick, 1968) and are suited for any (achievement) test with standard norms from a large standardization sample and satisfactory reliability estimates. Two test profiles of a Wernicke's aphasic, obtained before and after a 3-month period of speech therapy, are analyzed using inferential comparisons between (groups of) subtest scores on one test application and between two test administrations for single (groups of) subtests. For each of these comparisons, the two aspects of (i) significant (reliable) differences in performance beyond measurement error and (ii) the diagnostic validity of that difference in the reference population of aphasic patients are assessed. Significant differences between standardized subtest scores and a remarkably better preserved reading and writing ability could be found for both test administrations using the multiple test procedure of Holm (1979). Comparison of both profiles revealed an overall increase in performance for each subtest as well as changes in level of performance relations between pairs of subtests.

Creativity and mental health: A profile of writers and musicians

PubMed Central

Pavitra, K. S.; Chandrashekar, C. R.; Choudhury, Partha

2007-01-01

Creativity and its link with mental health have always been much speculated about. However there have been a handful of methodologically sound studies to clearly establish the relationship between creativity and mental health. The objective of the study therefore was to examine the psychiatric morbidity stress profile, coping skills and personality profile in creative versus non-creative populations. Forty writers, 40 musicians and 40 controls chosen after randomization, who met the inclusion and exclusion criteria constituted the sample of the study. All the subjects were administered GHQ-28; SCAN for all GHQ positives (and 10% of GHQ-ves), Perceived stress scale and coping check list and NEO-FFI. Statistical analysis was done using SPSS 11.0 version. Pearson's correlation, Chi-square and ANOVA one-way tests were used. The present study corroborated the findings of earlier studies in 70's and 80's that there was no difference between creative and non-creative groups in terms of mental illness and stress profile. The writers differed significantly from the other two groups on religious and faith domain of coping skills. The two creative groups had similar personality characteristics and scored significantly high on all dimensions compared to the non-creative group. PMID:20640063

The neglected 95%: why American psychology needs to become less American.

PubMed

Arnett, Jeffrey J

2008-10-01

This article proposes that psychological research published in APA journals focuses too narrowly on Americans, who comprise less than 5% of the world's population. The result is an understanding of psychology that is incomplete and does not adequately represent humanity. First, an analysis of articles published in six premier APA journals is presented, showing that the contributors, samples, and editorial leadership of the journals are predominantly American. Then, a demographic profile of the human population is presented to show that the majority of the world's population lives in conditions vastly different from the conditions of Americans, underlining doubts of how well American psychological research can be said to represent humanity. The reasons for the narrowness of American psychological research are examined, with a focus on a philosophy of science that emphasizes fundamental processes and ignores or strips away cultural context. Finally, several suggestions for broadening the scope of American psychology are offered.

A Trans-Theoretical Approach to Physical Activity Profile in General Population of Mashhad

PubMed Central

Shaye, Zahra Abbasi; Bazzaz, Mojtaba Mousavi; Vakili, Veda

2015-01-01

Regular physical-activity is necessity for a healthy lifestyle. Despite public health efforts, a minority of population are involved in healthy levels of physical-activity. This study provides evidence about exercise patterns and predictors of Mashhad-Iran population according to TTM change stages. In this cross-sectional study, we surveyed a total number of 564 participants from Mashhad in 2014 by using stages of change questionnaire. Analysis showed 23.4% of participants were in pre-contemplation stage, 18 in contemplation, 24.6% in preparation, 8.10% in action, 14.4% in maintenance and 11.5% were in termination phase. Age, gender, BMI, alcohol consumption, sleep duration, having compeer and encouragement were identified as predictors of pre-contemplation stage. Genders, having company and using bicycle for transportation were predictors of termination phase. Tailor interventions based on the predictors to enhance the physical activity among specific subgroups would be of interest. PMID:26153203

Droplet barcoding for single cell transcriptomics applied to embryonic stem cells

PubMed Central

Klein, Allon M; Mazutis, Linas; Akartuna, Ilke; Tallapragada, Naren; Veres, Adrian; Li, Victor; Peshkin, Leonid; Weitz, David A; Kirschner, Marc W

2015-01-01

Summary It has long been the dream of biologists to map gene expression at the single cell level. With such data one might track heterogeneous cell sub-populations, and infer regulatory relationships between genes and pathways. Recently, RNA sequencing has achieved single cell resolution. What is limiting is an effective way to routinely isolate and process large numbers of individual cells for quantitative in-depth sequencing. We have developed a high-throughput droplet-microfluidic approach for barcoding the RNA from thousands of individual cells for subsequent analysis by next-generation sequencing. The method shows a surprisingly low noise profile and is readily adaptable to other sequencing-based assays. We analyzed mouse embryonic stem cells, revealing in detail the population structure and the heterogeneous onset of differentiation after LIF withdrawal. The reproducibility of these high-throughput single cell data allowed us to deconstruct cell populations and infer gene expression relationships. PMID:26000487

X-ray Pulsars Across the Parameter Space of Luminosity, Accretion Mode, and Spin

NASA Astrophysics Data System (ADS)

Laycock, Silas

We propose to expand the scope of our successful project providing a multi-satellite library of X-ray Pulsar observations to the community. The library provides high-level products, activity monitoring, pulse-profiles, phased event files, spectra, and a unique pulse-profile modeling interface. The library's scientific footprint will expand in 4 key directions: (1) Update, by processing all new XMM-Newton and Chandra observations (2015-2017) of X-ray Binary Pulsars in the Magellanic Clouds. (2) Expand, by including all archival Suzaku, Swift and NuStar observations, and including Galactic pulsars. (3) Improve, by offering innovative data products that provide deeper insight. (4) Advance, by implementing a new generation of physically motivated emission and pulse-profile models. The library currently includes some 2000 individual RXTE-PCA, 200 Chandra ACIS-I, and 120 XMM-PN observations of the SMC spanning 15 years, creating an unrivaled record of pulsar temporal behavior. In Phase-2, additional observations of SMC pulsars will be added: 221 Chandra (ACIS-S and ACIS-I), 22 XMM-PN, 142 XMM-MOS, 92 Suzaku, 25 NuSTAR, and >10,000 Swift; leveraging our pipeline and analysis techniques already developed. With the addition of 7 Galactic pulsars each having many hundred multisatellite observations, these datasets cover the entire range of variability timescales and accretion regimes. We will model the pulse-profiles using state of the art techniques to parameterize their morphology and obtain the distribution of offsets between magnetic and spin axes, and create samples of profiles under specific accretion modes (whether pencil-beam or fan-beam dominated). These products are needed for the next generation of advances in neutron star theory and modeling. The long-duration of the dataset and “whole-galaxy" nature of the SMC sample make possible a new statistical approach to uncover the duty-cycle distribution and hence population demographics of transient High Mass X-ray Binary (HMXB) populations. Our unique library is already fueling progress on fundamental NS parameters and accretion physics.

Asian Pacific Americans in Cambridge. Community Profiles in Massachusetts.

ERIC Educational Resources Information Center

Massachusetts Univ., Boston. Inst. for Asian American Studies.

The Community Profiles Project uses data from the 1990 U.S. Census to describe some of the population characteristics of Asian Pacific Americans in selected Massachusetts cities and towns. The profiles include basic statistics relating to income, employment, education, and housing. This information can assist policy makers and practitioners in…

MMPI Modal Profiles in a Juvenile Delinquent Population.

ERIC Educational Resources Information Center

Pickett, Lawrence K., Jr.

1981-01-01

The MMPI results obtained from 245 adolescent males referred to the evaluation unit of a Juvenile Court were submitted to a multivariate classification system. By correlating individual subject profiles with the modal profiles, six membership groups were formed. No relationship was found between group membership and age or race. (Author)

Allele Frequencies for 15 Short Tandem Repeat Loci in Representative Sample of Croatian Population

PubMed Central

Projić, Petar; Škaro, Vedrana; Šamija, Ivana; Pojskić, Naris; Durmić-Pašić, Adaleta; Kovačević, Lejla; Bakal, Narcisa; Primorac, Dragan; Marjanović, Damir

2007-01-01

Aim To study the distribution of allele frequencies of 15 short tandem repeat (STR) loci in a representative sample of the Croatian population. Methods A total of 195 unrelated Caucasian individuals born in Croatia, from 14 counties and the City of Zagreb, were sampled for the analysis. All the tested individuals were voluntary donors. Buccal swab was used as the DNA source. AmpFlSTR® Identifiler® was applied to simultaneously amplify 15 STR loci. Total reaction volume was 12.5 μL. The polymerase chain reaction (PCR) amplification was carried out in PE Gene Amp PCR System Thermal Cycler. Electrophoresis of the amplification products was preformed on an ABI PRISM 3130 Genetic Analyzer. After PCR amplification and separation by electrophoresis, raw data were compiled, analyzed, and numerical allele designations of the profiles were obtained. Deviation from Hardy-Weinberg equilibrium, observed and expected heterozygosity, power of discrimination, and power of exclusion were calculated. Bonferroni’s correction was used before each comparative analysis. Results We compared Croatian data with those obtained from geographically neighboring European populations. The significant difference (at P<0.01) in allele frequencies was recorded only between the Croatian and Slovenian populations for vWA locus. There was no significant deviation from Hardy-Weinberg equilibrium for all the observed loci. Conclusion Obtained population data concurred with the expected “STR data frame” for this part of Europe. PMID:17696301

Low-energy particle population. [in Jupiter magnetosphere

NASA Technical Reports Server (NTRS)

Krimigis, S. M.; Roelof, E. C.

1983-01-01

A review is conducted of the measurements of the intensities, energy spectra, angular variations, and composition characteristics of the low-energy ion population in and around the Jovian magnetosphere, taking into account data obtained by both Voyager spacecraft. A description is provided of some novel analysis techniques which have been employed to generate density, pressure, composition, and plasma flow profiles in the magnetosphere. The obtained results are compared with data reported in connection with other investigations related to the spacecraft. Attention is given to the Low-Energy Charged Particle investigation, the Voyager 1 and 2 trajectories within 1000 Jupiter radii, and a hot plasma model of the Jovian magnetosphere. The measurement of hot multispecies convected plasmas using energetic particle detectors is also discussed.

A content analysis of displayed alcohol references on a social networking web site.

PubMed

Moreno, Megan A; Briner, Leslie R; Williams, Amanda; Brockman, Libby; Walker, Leslie; Christakis, Dimitri A

2010-08-01

Exposure to alcohol use in media is associated with adolescent alcohol use. Adolescents frequently display alcohol references on Internet media, such as social networking web sites. The purpose of this study was to conduct a theoretically based content analysis of older adolescents' displayed alcohol references on a social networking web site. We evaluated 400 randomly selected public MySpace profiles of self-reported 17- to 20-year-olds from zip codes, representing urban, suburban, and rural communities in one Washington county. Content was evaluated for alcohol references, suggesting: (1) explicit versus figurative alcohol use, (2) alcohol-related motivations, associations, and consequences, including references that met CRAFFT problem drinking criteria. We compared profiles from four target zip codes for prevalence and frequency of alcohol display. Of 400 profiles, 225 (56.3%) contained 341 references to alcohol. Profile owners who displayed alcohol references were mostly male (54.2%) and white (70.7%). The most frequent reference category was explicit use (49.3%); the most commonly displayed alcohol use motivation was peer pressure (4.7%). Few references met CRAFFT problem drinking criteria (3.2%). There were no differences in prevalence or frequency of alcohol display among the four sociodemographic communities. Despite alcohol use being illegal and potentially stigmatizing in this population, explicit alcohol use is frequently referenced on adolescents' MySpace profiles across several sociodemographic communities. Motivations, associations, and consequences regarding alcohol use referenced on MySpace appear consistent with previous studies of adolescent alcohol use. These references may be a potent source of influence on adolescents, particularly given that they are created and displayed by peers. (c) 2010 Society for Adolescent Health and Medicine. Published by Elsevier Inc. All rights reserved.

Fingerprints of a riming event on cloud radar Doppler spectra: observations and modeling

DOE PAGES

Kalesse, Heike; Szyrmer, Wanda; Kneifel, Stefan; ...

2016-03-09

In this paper, Radar Doppler spectra measurements are exploited to study a riming event when precipitating ice from a seeder cloud sediment through a supercooled liquid water (SLW) layer. The focus is on the "golden sample" case study for this type of analysis based on observations collected during the deployment of the Atmospheric Radiation Measurement Program's (ARM) mobile facility AMF2 at Hyytiälä, Finland, during the Biogenic Aerosols – Effects on Clouds and Climate (BAECC) field campaign. The presented analysis of the height evolution of the radar Doppler spectra is a state-of-the-art retrieval with profiling cloud radars in SLW layers beyondmore » the traditional use of spectral moments. Dynamical effects are considered by following the particle population evolution along slanted tracks that are caused by horizontal advection of the cloud under wind shear conditions. In the SLW layer, the identified liquid peak is used as an air motion tracer to correct the Doppler spectra for vertical air motion and the ice peak is used to study the radar profiles of rimed particles. A 1-D steady-state bin microphysical model is constrained using the SLW and air motion profiles and cloud top radar observations. The observed radar moment profiles of the rimed snow can be simulated reasonably well by the model, but not without making several assumptions about the ice particle concentration and the relative role of deposition and aggregation. In conclusion, this suggests that in situ observations of key ice properties are needed to complement the profiling radar observations before process-oriented studies can effectively evaluate ice microphysical parameterizations.« less

Rapid skin profiling with non-contact full-field optical coherence tomography: study of patients with diabetes mellitus type I

NASA Astrophysics Data System (ADS)

Zakharov, P.; Talary, M. S.; Kolm, I.; Caduff, A.

2009-07-01

The application of the full-field optical coherence tomography (OCT) microscope to the characterisation of skin morphology is described. An automated procedure for analysis and interpretation of the OCT data has been developed which provides measures of the laterally averaged depth profiles of the skin reflectance. The skin at the dorsal side of the upper arm of 22 patients with Type 1 Diabetes Mellitus has been characterised in a non-contact way. The OCT signal profile was compared with the optical histological data obtained with a commercial confocal microscope (CM). The highest correlation to the epidermal thickness (ET) obtained using CM was found for the distance from the entrance OCT peak to the first minimum of the reflection profile (R2=0.657, p<0.0001). The distance to the second OCT reflection peak was found to be less correlated to ET (R2=0.403, p=0.0009). A further analysis was undertaken to explore the relation between the subjects' demographical data and the OCT reflection profile. The distance to the second OCT peak demonstrated a correlation with a marginal statistical significance for the body-mass index (positive correlation with p=0.01) and age (negative correlation with p=0.062). At the same time the amplitude of the OCT signal, when compensated for signal attenuation with depth, is negatively correlated with age (p<0.0002). We suggest that this may be an effect of photo degradation of the dermal collagen. In the patient population studied, no relation could be determined between the measured skin morphology and the duration of diabetes or concentration of glycated haemoglobin in the blood.

K-means cluster analysis of rehabilitation service users in the Home Health Care System of Ontario: examining the heterogeneity of a complex geriatric population.

PubMed

Armstrong, Joshua J; Zhu, Mu; Hirdes, John P; Stolee, Paul

2012-12-01

To examine the heterogeneity of home care clients who use rehabilitation services by using the K-means algorithm to identify previously unknown patterns of clinical characteristics. Observational study of secondary data. Home care system. Assessment information was collected on 150,253 home care clients using the provincially mandated Resident Assessment Instrument-Home Care (RAI-HC) data system. Not applicable. Assessment information from every long-stay (>60 d) home care client that entered the home care system between 2005 and 2008 and used rehabilitation services within 3 months of their initial assessment was analyzed. The K-means clustering algorithm was applied using 37 variables from the RAI-HC assessment. The K-means cluster analysis resulted in the identification of 7 relatively homogeneous subgroups that differed on characteristics such as age, sex, cognition, and functional impairment. Client profiles were created to illustrate the diversity of this geriatric population. The K-means algorithm provided a useful way to segment a heterogeneous rehabilitation client population into more homogeneous subgroups. This analysis provides an enhanced understanding of client characteristics and needs, and could enable more appropriate targeting of rehabilitation services for home care clients. Copyright © 2012 American Congress of Rehabilitation Medicine. Published by Elsevier Inc. All rights reserved.

The Effect of T'ai Chi Exercise on Lipid Profiles: A Systematic Review and Meta-Analysis of Randomized Clinical Trials.

PubMed

Alenazi, Aqeel M; Alshehri, Mohammed M; Hoover, Jeffrey C; Yabroudi, Mohammad A; Kachanathu, Shaji John; Liu, Wen

2018-03-01

Cardiovascular disease is a common health problem resulting from many factors, including dyslipidemia. T'ai chi is one of the interventions assigned to improve lipid profiles and other physical outcomes. However, conflicting results might be attributed to different study designs and interventional approaches. A systematic review and meta-analysis are needed to evaluate existing evidence. The aim of this systematic review and meta-analysis is to evaluate existing randomized clinical trials (RCTs) regarding the overall effect of t'ai chi exercise on lipid profiles. Electronic databases (MEDLINE and Cumulative Index to Nursing and Allied Health Literature) were searched. The authors included only English peer reviewed published RCTs that used a t'ai chi intervention and high-density lipoprotein cholesterol (HDL-C) as the primary outcome along with low-density lipoprotein cholesterol (LDL-C) and/or total cholesterol (TC) as secondary outcomes. The authors identified 37 potentially eligible studies. Only eight RCTs were eligible for their qualitative review, and seven studies were eligible for meta-analysis. The included studies were rated as having a low risk of bias. Despite the overall low risk of bias, all studies failed to blind participants to group assignment and were generally unclear about whether they were selectively reporting data. A fixed effect model (I 2  = 38.16%) demonstrated a small positive effect of t'ai chi on HDL-C (Cohen d = 0.12; standard error [SE] = 0.067; p = 0.037). A random effect model demonstrated a medium effect and small effect for LDL-C (Cohen d = 0.47; SE = 0.347; p = 0.089) and TC (Cohen d = 0.34; SE = 0.225; p = 0.066), respectively. T'ai chi may potentially be beneficial on lipid profiles across different age groups and populations. Although there were conflicting results regarding the effect of t'ai chi on lipid profiles, the majority of studies had at least a small positive effect indicating a potential positive effect of t'ai chi on HDL-C, LDL-C, and/or TC. Therefore, further research is needed to confirm the small positive effect of t'ai chi on lipid profiles found in this review.

Pacifiplex: an ancestry-informative SNP panel centred on Australia and the Pacific region.

PubMed

Santos, Carla; Phillips, Christopher; Fondevila, Manuel; Daniel, Runa; van Oorschot, Roland A H; Burchard, Esteban G; Schanfield, Moses S; Souto, Luis; Uacyisrael, Jolame; Via, Marc; Carracedo, Ángel; Lareu, Maria V

2016-01-01

The analysis of human population variation is an area of considerable interest in the forensic, medical genetics and anthropological fields. Several forensic single nucleotide polymorphism (SNP) assays provide ancestry-informative genotypes in sensitive tests designed to work with limited DNA samples, including a 34-SNP multiplex differentiating African, European and East Asian ancestries. Although assays capable of differentiating Oceanian ancestry at a global scale have become available, this study describes markers compiled specifically for differentiation of Oceanian populations. A sensitive multiplex assay, termed Pacifiplex, was developed and optimized in a small-scale test applicable to forensic analyses. The Pacifiplex assay comprises 29 ancestry-informative marker SNPs (AIM-SNPs) selected to complement the 34-plex test, that in a combined set distinguish Africans, Europeans, East Asians and Oceanians. Nine Pacific region study populations were genotyped with both SNP assays, then compared to four reference population groups from the HGDP-CEPH human diversity panel. STRUCTURE analyses estimated population cluster membership proportions that aligned with the patterns of variation suggested for each study population's currently inferred demographic histories. Aboriginal Taiwanese and Philippine samples indicated high East Asian ancestry components, Papua New Guinean and Aboriginal Australians samples were predominantly Oceanian, while other populations displayed cluster patterns explained by the distribution of divergence amongst Melanesians, Polynesians and Micronesians. Genotype data from Pacifiplex and 34-plex tests is particularly well suited to analysis of Australian Aboriginal populations and when combined with Y and mitochondrial DNA variation will provide a powerful set of markers for ancestry inference applied to modern Australian demographic profiles. On a broader geographic scale, Pacifiplex adds highly informative data for inferring the ancestry of individuals from Oceanian populations. The sensitivity of Pacifiplex enabled successful genotyping of population samples from 50-year-old serum samples obtained from several Oceanian regions that would otherwise be unlikely to produce useful population data. This indicates tests primarily developed for forensic ancestry analysis also provide an important contribution to studies of populations where useful samples are in limited supply. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Cell population structure prior to bifurcation predicts efficiency of directed differentiation in human induced pluripotent cells

PubMed Central

Bargaje, Rhishikesh; Trachana, Kalliopi; Shelton, Martin N.; McGinnis, Christopher S.; Zhou, Joseph X.; Chadick, Cora; Cook, Savannah; Cavanaugh, Christopher; Huang, Sui; Hood, Leroy

2017-01-01

Steering the differentiation of induced pluripotent stem cells (iPSCs) toward specific cell types is crucial for patient-specific disease modeling and drug testing. This effort requires the capacity to predict and control when and how multipotent progenitor cells commit to the desired cell fate. Cell fate commitment represents a critical state transition or “tipping point” at which complex systems undergo a sudden qualitative shift. To characterize such transitions during iPSC to cardiomyocyte differentiation, we analyzed the gene expression patterns of 96 developmental genes at single-cell resolution. We identified a bifurcation event early in the trajectory when a primitive streak-like cell population segregated into the mesodermal and endodermal lineages. Before this branching point, we could detect the signature of an imminent critical transition: increase in cell heterogeneity and coordination of gene expression. Correlation analysis of gene expression profiles at the tipping point indicates transcription factors that drive the state transition toward each alternative cell fate and their relationships with specific phenotypic readouts. The latter helps us to facilitate small molecule screening for differentiation efficiency. To this end, we set up an analysis of cell population structure at the tipping point after systematic variation of the protocol to bias the differentiation toward mesodermal or endodermal cell lineage. We were able to predict the proportion of cardiomyocytes many days before cells manifest the differentiated phenotype. The analysis of cell populations undergoing a critical state transition thus affords a tool to forecast cell fate outcomes and can be used to optimize differentiation protocols to obtain desired cell populations. PMID:28167799

Cell population structure prior to bifurcation predicts efficiency of directed differentiation in human induced pluripotent cells.

PubMed

Bargaje, Rhishikesh; Trachana, Kalliopi; Shelton, Martin N; McGinnis, Christopher S; Zhou, Joseph X; Chadick, Cora; Cook, Savannah; Cavanaugh, Christopher; Huang, Sui; Hood, Leroy

2017-02-28

Steering the differentiation of induced pluripotent stem cells (iPSCs) toward specific cell types is crucial for patient-specific disease modeling and drug testing. This effort requires the capacity to predict and control when and how multipotent progenitor cells commit to the desired cell fate. Cell fate commitment represents a critical state transition or "tipping point" at which complex systems undergo a sudden qualitative shift. To characterize such transitions during iPSC to cardiomyocyte differentiation, we analyzed the gene expression patterns of 96 developmental genes at single-cell resolution. We identified a bifurcation event early in the trajectory when a primitive streak-like cell population segregated into the mesodermal and endodermal lineages. Before this branching point, we could detect the signature of an imminent critical transition: increase in cell heterogeneity and coordination of gene expression. Correlation analysis of gene expression profiles at the tipping point indicates transcription factors that drive the state transition toward each alternative cell fate and their relationships with specific phenotypic readouts. The latter helps us to facilitate small molecule screening for differentiation efficiency. To this end, we set up an analysis of cell population structure at the tipping point after systematic variation of the protocol to bias the differentiation toward mesodermal or endodermal cell lineage. We were able to predict the proportion of cardiomyocytes many days before cells manifest the differentiated phenotype. The analysis of cell populations undergoing a critical state transition thus affords a tool to forecast cell fate outcomes and can be used to optimize differentiation protocols to obtain desired cell populations.

Population Profile of the United States: 1976. Current Population Reports, Population Characteristics, Series P-20, No. 307.

ERIC Educational Resources Information Center

Bureau of the Census (DOC), Suitland, MD. Population Div.

This booklet summarizes population characteristics of the United States for 1976. A preliminary section of highlights reviews trends in five areas: population growth, social characteristics, population distribution, employment and income, and ethnic groups. The birth rate has declined, and the rate of childlessness has risen. This probably is due…

Country Profiles. Japan.

ERIC Educational Resources Information Center

Muramatsu, Minoru

This occasional paper on Japan is one of a series setting forth the nature, scope, and accomplishments of population activities in specified countries. Here, an overview is given of population characteristics and growth patterns, the relationship of population growth to socioeconomic development, and the history of population concerns and…

Sexual selection and population divergence I: The influence of socially flexible cuticular hydrocarbon expression in male field crickets (Teleogryllus oceanicus).

PubMed

Pascoal, Sonia; Mendrok, Magdalena; Mitchell, Christopher; Wilson, Alastair J; Hunt, John; Bailey, Nathan W

2016-01-01

Debates about how coevolution of sexual traits and preferences might promote evolutionary diversification have permeated speciation research for over a century. Recent work demonstrates that the expression of such traits can be sensitive to variation in the social environment. Here, we examined social flexibility in a sexually selected male trait-cuticular hydrocarbon (CHC) profiles-in the field cricket Teleogryllus oceanicus and tested whether population genetic divergence predicts the extent or direction of social flexibility in allopatric populations. We manipulated male crickets' social environments during rearing and then characterized CHC profiles. CHC signatures varied considerably across populations and also in response to the social environment, but our prediction that increased social flexibility would be selected in more recently founded populations exposed to fluctuating demographic environments was unsupported. Furthermore, models examining the influence of drift and selection failed to support a role of sexual selection in driving population divergence in CHC profiles. Variation in social environments might alter the dynamics of sexual selection, but our results align with theoretical predictions that the role social flexibility plays in modulating evolutionary divergence depends critically on whether responses to variation in the social environment are homogeneous across populations, or whether gene by social environment interactions occur. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

Sex determination from the talus in a contemporary Greek population using discriminant function analysis.

PubMed

Peckmann, Tanya R; Orr, Kayla; Meek, Susan; Manolis, Sotiris K

2015-07-01

The determination of sex is an important part of building the biological profile for unknown human remains. Many of the bones traditionally used for the determination of sex are often found fragmented or incomplete in forensic and archaeological cases. The goal of the present research was to derive discriminant function equations from the talus, a preservationally favoured bone, for sexing skeletons from a contemporary Greek population. Nine parameters were measured on 182 individuals (96 males and 86 females) from the University of Athens Human Skeletal Reference Collection. The individuals ranged in age from 20 to 99 years old. The statistical analyses showed that all measured parameters were sexually dimorphic. Discriminant function score equations were generated for use in sex determination. The average accuracy of sex classification ranged from 65.2% to 93.4% for the univariate analysis, 90%-96.5% for the direct method and 86.7% for the stepwise method. Comparisons to other populations were made. Overall, the cross-validated accuracies ranged from 65.5% to 83.2% and males were most often correctly identified. The talus was shown to be useful for sex determination in the modern Greek population. Copyright © 2015 Elsevier Ltd and Faculty of Forensic and Legal Medicine. All rights reserved.

On the origins, rapid expansion and genetic diversity of Native Americans from hunting-gatherers to agriculturalists.

PubMed

Regueiro, Maria; Alvarez, Joseph; Rowold, Diane; Herrera, Rene J

2013-03-01

Given the importance of Y-chromosome haplogroup Q to better understand the source populations of contemporary Native Americans, we studied 8 biallelic and 17 microsatellite polymorphisms on the background of 128 Q Y-chromosomes from geographically targeted populations. The populations examined in this study include three from the Tuva Republic in Central Asia (Bai-Tai, Kungurtug, and Toora-Hem, n = 146), two from the northeastern tip of Siberia (New Chaplino and Chukchi, n = 32), and two from Mesoamerica (Mayans from Yucatan, Mexico n = 72, and Mayans from the Guatemalan Highlands, n = 43). We also see evidence of a dramatic Mesoamerican post-migration population growth in the ubiquitous and diverse Y-STR profiles of the Mayan and other Mesoamerican populations. In the case of the Mayans, this demographic growth was most likely fueled by the agricultural- and trade-based subsistence adopted during the Pre-Classic, Classic and Post-Classic periods of their empire. The limited diversity levels observed in the Altaian and Tuvinian regions of Central Asia, the lowest of all populations examined, may be the consequence of bottleneck events fostered by the spatial isolation and low effective population size characteristic of a nomadic lifestyle. Furthermore, our data illustrate how a sociocultural characteristic such as mode of subsistence may be of impact on the genetic structure of populations. We analyzed our genetic data using Multidimensional Scaling Analysis of populations, Principal Component Analysis of individuals, Median-joining networks of M242, M346, L54, and M3 individuals, age estimations based on microsatellite variation utilizing genealogical and evolutionary mutation rates/generation times and estimation of Y- STR average gene diversity indices. Copyright © 2013 Wiley Periodicals, Inc.

Comparative Microsatellite Typing of New World Leishmania infantum Reveals Low Heterogeneity among Populations and Its Recent Old World Origin

PubMed Central

Kuhls, Katrin; Alam, Mohammad Zahangir; Cupolillo, Elisa; Ferreira, Gabriel Eduardo M.; Mauricio, Isabel L.; Oddone, Rolando; Feliciangeli, M. Dora; Wirth, Thierry; Miles, Michael A.; Schönian, Gabriele

2011-01-01

Leishmania infantum (syn. L. chagasi) is the causative agent of visceral leishmaniasis (VL) in the New World (NW) with endemic regions extending from southern USA to northern Argentina. The two hypotheses about the origin of VL in the NW suggest (1) recent importation of L. infantum from the Old World (OW), or (2) an indigenous origin and a distinct taxonomic rank for the NW parasite. Multilocus microsatellite typing was applied in a survey of 98 L. infantum isolates from different NW foci. The microsatellite profiles obtained were compared to those of 308 L. infantum and 20 L. donovani strains from OW countries previously assigned to well-defined populations. Two main populations were identified for both NW and OW L. infantum. Most of the NW strains belonged to population 1, which corresponded to the OW MON-1 population. However, the NW population was much more homogeneous. A second, more heterogeneous, population comprised most Caribbean strains and corresponded to the OW non-MON-1 population. All Brazilian L. infantum strains belonged to population 1, although they represented 61% of the sample and originated from 9 states. Population analysis including the OW L. infantum populations indicated that the NW strains were more similar to MON-1 and non-MON-1 sub-populations of L. infantum from southwest Europe, than to any other OW sub-population. Moreover, similarity between NW and Southwest European L. infantum was higher than between OW L. infantum from distinct parts of the Mediterranean region, Middle East and Central Asia. No correlation was found between NW L. infantum genotypes and clinical picture or host background. This study represents the first continent-wide analysis of NW L. infantum population structure. It confirmed that the agent of VL in the NW is L. infantum and that the parasite has been recently imported multiple times to the NW from southwest Europe. PMID:21666787

Safety and Efficacy of D-Tagatose in Glycemic Control in Subjects with Type 2 Diabetes.

PubMed

Ensor, Mark; Banfield, Amy B; Smith, Rebecca R; Williams, Jarrod; Lodder, Robert A

The primary objectives of this study were to evaluate the treatment effect of D-tagatose on glycemic control, determined by a statistically significant decrease in hemoglobin A1c (HbA1c), and safety profile of D-tagatose compared to placebo. The secondary objectives were to evaluate the treatment effects on fasting blood glucose, insulin, lipid profiles, changes in BMI, and the proportion of subjects achieving HbA1c targets of <7%. Type 2 diabetic patients not taking any blood glucose lowering medications were administered either 15 g of D-tagatose dissolved in 125-250 ml of water three times a day or placebo with meals. Reduction in HbA1c was statistically significant compared to placebo at all post-baseline time points in the ITT population. Additionally, secondary endpoints were achieved in the ITT population with regard to LDL, total cholesterol, fasting blood glucose, and proportion of subjects achieving HbA1c targets of <7%. D-tagatose was unable to lower triglycerides or raise HDL compared to placebo. A subgroup LOCF analysis on the ITT US population showed a greater and statistically significant LS mean reduction in HbA1c in the D-tagatose group at all post-baseline visits. Based on these results it is concluded that in the ITT population D-tagatose is an effective single agent at treating many of the therapy targets of type 2 diabetes including lowering fasting blood glucose and HbA1c, and lowering of LDL and total cholesterol.

Safety and Efficacy of D-Tagatose in Glycemic Control in Subjects with Type 2 Diabetes

PubMed Central

Ensor, Mark; Banfield, Amy B.; Smith, Rebecca R.; Williams, Jarrod; Lodder, Robert A.

2015-01-01

The primary objectives of this study were to evaluate the treatment effect of D-tagatose on glycemic control, determined by a statistically significant decrease in hemoglobin A1c (HbA1c), and safety profile of D-tagatose compared to placebo. The secondary objectives were to evaluate the treatment effects on fasting blood glucose, insulin, lipid profiles, changes in BMI, and the proportion of subjects achieving HbA1c targets of <7%. Type 2 diabetic patients not taking any blood glucose lowering medications were administered either 15 g of D-tagatose dissolved in 125–250 ml of water three times a day or placebo with meals. Reduction in HbA1c was statistically significant compared to placebo at all post-baseline time points in the ITT population. Additionally, secondary endpoints were achieved in the ITT population with regard to LDL, total cholesterol, fasting blood glucose, and proportion of subjects achieving HbA1c targets of <7%. D-tagatose was unable to lower triglycerides or raise HDL compared to placebo. A subgroup LOCF analysis on the ITT US population showed a greater and statistically significant LS mean reduction in HbA1c in the D-tagatose group at all post-baseline visits. Based on these results it is concluded that in the ITT population D-tagatose is an effective single agent at treating many of the therapy targets of type 2 diabetes including lowering fasting blood glucose and HbA1c, and lowering of LDL and total cholesterol. PMID:27054147

Safety of Tamsulosin: A Systematic Review of Randomized Trials with a Focus on Women and Children.

PubMed

Kaplan, Steven A; Chughtai, Bilal I

2018-05-08

Although tamsulosin is indicated for the treatment of the signs and symptoms of benign prostatic hyperplasia (BPH), it has also been assessed in clinical studies for other conditions/symptoms and in other populations such as women and children. In this systematic review of randomized studies, the overall safety of tamsulosin was assessed, focusing on these understudied populations. Literature searches were conducted using Embase, Medline, and PubMed (inception-December 2015). A study was included if patients were randomized to receive treatment with any dose of tamsulosin capsules, tablets, or an oral controlled absorption system and numerical safety results were reported. Overall, 160 articles involving 46,072 participants met the inclusion criteria. Of these, four studies included women only and three included children. The mean [standard deviation (SD)] age ranged from 7.3 (4.2) to 76.8 (7.1) years. The studies (n; %) evaluated healthy subjects (18; 11%) or patients with lower urinary tract symptoms/BPH (90; 56%), ureteral stones/renal colic (42; 26%), prostatitis (4; 3%), or other conditions (6; 4%). Patients discontinued tamsulosin primarily because of adverse events (AEs) or insufficient response. AEs in women and children were abdominal pain, asthenia, constipation, dizziness, dry mouth, drowsiness, dyspepsia, headache, incontinence, nasal congestion, nausea, orthostatic hypotension, and somnolence. Due to heterogeneity across studies, statistical analysis could not be conducted. No unexpected AEs were observed in an all-comers population treated with tamsulosin for various conditions/symptoms. The overall safety profile in women and children seemed to be generally consistent with the profile in men, the indicated population.

Development of a novel forensic STR multiplex for ancestry analysis and extended identity testing.

PubMed

Phillips, Chris; Fernandez-Formoso, Luis; Gelabert-Besada, Miguel; Garcia-Magariños, Manuel; Santos, Carla; Fondevila, Manuel; Carracedo, Angel; Lareu, Maria Victoria

2013-04-01

There is growing interest in developing additional DNA typing techniques to provide better investigative leads in forensic analysis. These include inference of genetic ancestry and prediction of common physical characteristics of DNA donors. To date, forensic ancestry analysis has centered on population-divergent SNPs but these binary loci cannot reliably detect DNA mixtures, common in forensic samples. Furthermore, STR genotypes, forming the principal DNA profiling system, are not routinely combined with forensic SNPs to strengthen frequency data available for ancestry inference. We report development of a 12-STR multiplex composed of ancestry informative marker STRs (AIM-STRs) selected from 434 tetranucleotide repeat loci. We adapted our online Bayesian classifier for AIM-SNPs: Snipper, to handle multiallele STR data using frequency-based training sets. We assessed the ability of the 12-plex AIM-STRs to differentiate CEPH Human Genome Diversity Panel populations, plus their informativeness combined with established forensic STRs and AIM-SNPs. We found combining STRs and SNPs improves the success rate of ancestry assignments while providing a reliable mixture detection system lacking from SNP analysis alone. As the 12 STRs generally show a broad range of alleles in all populations, they provide highly informative supplementary STRs for extended relationship testing and identification of missing persons with incomplete reference pedigrees. Lastly, mixed marker approaches (combining STRs with binary loci) for simple ancestry inference tests beyond forensic analysis bring advantages and we discuss the genotyping options available. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Bisulfite-independent analysis of CpG island methylation enables genome-scale stratification of single cells.

PubMed

Han, Lin; Wu, Hua-Jun; Zhu, Haiying; Kim, Kun-Yong; Marjani, Sadie L; Riester, Markus; Euskirchen, Ghia; Zi, Xiaoyuan; Yang, Jennifer; Han, Jasper; Snyder, Michael; Park, In-Hyun; Irizarry, Rafael; Weissman, Sherman M; Michor, Franziska; Fan, Rong; Pan, Xinghua

2017-06-02

Conventional DNA bisulfite sequencing has been extended to single cell level, but the coverage consistency is insufficient for parallel comparison. Here we report a novel method for genome-wide CpG island (CGI) methylation sequencing for single cells (scCGI-seq), combining methylation-sensitive restriction enzyme digestion and multiple displacement amplification for selective detection of methylated CGIs. We applied this method to analyzing single cells from two types of hematopoietic cells, K562 and GM12878 and small populations of fibroblasts and induced pluripotent stem cells. The method detected 21 798 CGIs (76% of all CGIs) per cell, and the number of CGIs consistently detected from all 16 profiled single cells was 20 864 (72.7%), with 12 961 promoters covered. This coverage represents a substantial improvement over results obtained using single cell reduced representation bisulfite sequencing, with a 66-fold increase in the fraction of consistently profiled CGIs across individual cells. Single cells of the same type were more similar to each other than to other types, but also displayed epigenetic heterogeneity. The method was further validated by comparing the CpG methylation pattern, methylation profile of CGIs/promoters and repeat regions and 41 classes of known regulatory markers to the ENCODE data. Although not every minor methylation differences between cells are detectable, scCGI-seq provides a solid tool for unsupervised stratification of a heterogeneous cell population. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

High-coverage methylation data of a gene model before and after DNA damage and homologous repair.

PubMed

Pezone, Antonio; Russo, Giusi; Tramontano, Alfonso; Florio, Ermanno; Scala, Giovanni; Landi, Rosaria; Zuchegna, Candida; Romano, Antonella; Chiariotti, Lorenzo; Muller, Mark T; Gottesman, Max E; Porcellini, Antonio; Avvedimento, Enrico V

2017-04-11

Genome-wide methylation analysis is limited by its low coverage and the inability to detect single variants below 10%. Quantitative analysis provides accurate information on the extent of methylation of single CpG dinucleotide, but it does not measure the actual polymorphism of the methylation profiles of single molecules. To understand the polymorphism of DNA methylation and to decode the methylation signatures before and after DNA damage and repair, we have deep sequenced in bisulfite-treated DNA a reporter gene undergoing site-specific DNA damage and homologous repair. In this paper, we provide information on the data generation, the rationale for the experiments and the type of assays used, such as cytofluorimetry and immunoblot data derived during a previous work published in Scientific Reports, describing the methylation and expression changes of a model gene (GFP) before and after formation of a double-strand break and repair by homologous-recombination or non-homologous-end-joining. These data provide: 1) a reference for the analysis of methylation polymorphism at selected loci in complex cell populations; 2) a platform and the tools to compare transcription and methylation profiles.

High-coverage methylation data of a gene model before and after DNA damage and homologous repair

PubMed Central

Pezone, Antonio; Russo, Giusi; Tramontano, Alfonso; Florio, Ermanno; Scala, Giovanni; Landi, Rosaria; Zuchegna, Candida; Romano, Antonella; Chiariotti, Lorenzo; Muller, Mark T.; Gottesman, Max E.; Porcellini, Antonio; Avvedimento, Enrico V.

2017-01-01

Genome-wide methylation analysis is limited by its low coverage and the inability to detect single variants below 10%. Quantitative analysis provides accurate information on the extent of methylation of single CpG dinucleotide, but it does not measure the actual polymorphism of the methylation profiles of single molecules. To understand the polymorphism of DNA methylation and to decode the methylation signatures before and after DNA damage and repair, we have deep sequenced in bisulfite-treated DNA a reporter gene undergoing site-specific DNA damage and homologous repair. In this paper, we provide information on the data generation, the rationale for the experiments and the type of assays used, such as cytofluorimetry and immunoblot data derived during a previous work published in Scientific Reports, describing the methylation and expression changes of a model gene (GFP) before and after formation of a double-strand break and repair by homologous-recombination or non-homologous-end-joining. These data provide: 1) a reference for the analysis of methylation polymorphism at selected loci in complex cell populations; 2) a platform and the tools to compare transcription and methylation profiles. PMID:28398335