Transcriptional activation of human adult alpha-globin genes by hypersensitive site-40 enhancer: function of nuclear factor-binding motifs occupied in erythroid cells.

The developmental stage- and erythroid lineage-specific activation of the human embryonic zeta- and fetal/adult alpha-globin genes is controlled by an upstream regulatory element [hypersensitive site (HS)-40] with locus control region properties, a process mediated by multiple nuclear factor-DNA complexes. In vitro DNase I protection experiments of the two G+C-rich, adult alpha-globin promoters have revealed a number of binding sites for nuclear factors that are common to HeLa and K-562 extracts. However, genomic footprinting analysis has demonstrated that only a subset of these sites, clustered between -130 and +1, is occupied in an erythroid tissue-specific manner. The function of these in vivo-occupied motifs of the alpha-globin promoters, as well as those previously mapped in the HS-40 region, is assayed by site-directed mutagenesis and transient expression in embryonic/fetal erythroid K-562 cells. These studies, together with our expression data on the human embryonic zeta-globin promoter, provide a comprehensive view of the functional roles of individual nuclear factor-DNA complexes in the final stages of transcriptional activation of the human alpha-like globin promoters by the HS-40 element.

(Table S1) Relative abundances of coccolithophore taxa in surface sediment samples from the Equatorial and Southeastern Pacific

This study aims to contribute to a more detailed knowledge of the biogeography of coccolithophores in the Equatorial and Southeastern Pacific Ocean. Census data of fossil coccoliths are presented in a suite of core-top sediment samples from 15°N to 50.6°S and from 71°W to 93°W. Following standard preparation of smear slides, a total of 19 taxa are recognized in light microscopy and their relative abundances are determined for 134 surface sediment samples. Considering the multivariate character of oceanic conditions and their effects on phytoplankton, a Factor Analysis was performed and three factors were retained. Factor 1, dominated by Florisphaera profunda and Gephyrocapsa oceanica, includes samples located under warm water masses and indicates the occurrence of calcite dissolution in the water column in the area offshore Chile. Factor 2 is related to cold, low-salinity surface-water masses from the Chilean upwelling, and is dominated by Emiliania huxleyi, Gephyrocapsa sp. < 3 µm, Coccolithus pelagicus and Gephyrocapsa muellerae. Factor 3 is linked to more saline, coastal upwelling areas where Calcidiscus leptoporus and Helicosphaera carteri are the dominant species.

Pliocene-Pleistocene distribution of benthic foraminifers from ODP Hole 110-672A (Table 2)

Site 672 is located on the Atlantic abyssal plain to the east of the Lesser Antilles forearc region. It serves as a stratigraphic reference section for sediments entering the Barbados accretionary prism. A relatively complete Pliocene through lower Pleistocene section was recovered from Site 672 that contains a moderately well-preserved population of benthic foraminifers. Q-mode factor analysis of the benthic population data identified three Pliocene-Pleistocene assemblages that inhabited this site. The Factor 1 fauna, characterized by Nuttallides umboniferus, is commonly associated with the presence of Antarctic Bottom Water (AABW). The Factor 2 assemblage is characterized by Globocassidulina subglobosa, Epistominella exigua, and a combined category of unilocular species. The Factor 3 assemblage is characterized by Epistominella exigua, and Planulina wuellerstorfi. The Factor 2 and 3 faunas are associated with bottom water significantly warmer than that preferred by the Factor 1 assemblage. The distribution of these assemblages has been used to distinguish three climatic intervals in the abyssal environment during the Pliocene-Pleistocene. An early Pliocene warm interval occurred from the Ceratolithus rugosus Subzone to the middle of the Discoaster tamalis Subzone. The upper Pliocene is characterized by oscillations between the Factor 1 and Factor 2 assemblages, which suggests climatic deterioration and increased pulses of AABW flow. The persistence of an essentially modern (Factor 1) fauna throughout the early Pleistocene suggests full glacial development at both poles and a substantial volume of AABW production.

Examining Gender Differences in Writing Skill with Latent Factor Modeling

Thesis (Master's)--University of Washington, 2016-06

Statnote 27: Principal components analysis (PCA)

In Statnotes 24 and 25, multiple linear regression, a statistical method that examines the relationship between a single dependent variable (Y) and two or more independent variables (X), was described. The principle objective of such an analysis was to determine which of the X variables had a significant influence on Y and to construct an equation that predicts Y from the X variables. ‘Principal components analysis’ (PCA) and ‘factor analysis’ (FA) are also methods of examining the relationships between different variables but they differ from multiple regression in that no distinction is made between the dependent and independent variables, all variables being essentially treated the same. Originally, PCA and FA were regarded as distinct methods but in recent times they have been combined into a single analysis, PCA often being the first stage of a FA. The basic objective of a PCA/FA is to examine the relationships between the variables or the ‘structure’ of the variables and to determine whether these relationships can be explained by a smaller number of ‘factors’. This statnote describes the use of PCA/FA in the analysis of the differences between the DNA profiles of different MRSA strains introduced in Statnote 26.

What's in a broken promissory obligation? Developing and testing a multiple component form measure of psychological contract breach

While the literature has suggested the possibility of breach being composed of multiple facets, no previous study has investigated this possibility empirically. This study examined the factor structure of typical component forms in order to develop a multiple component form measure of breach. Two studies were conducted. In study 1 (N = 420) multi-item measures based on causal indicators representing promissory obligations were developed for the five potential component forms (delay, magnitude, type/form, inequity and reciprocal imbalance). Exploratory factor analysis showed that the five components loaded onto one higher order factor, namely psychological contract breach suggesting that breach is composed of different aspects rather than types of breach. Confirmatory factor analysis provided further evidence for the proposed model. In addition, the model achieved high construct reliability and showed good construct, convergent, discriminant and predictive validity. Study 2 data (N = 189), used to validate study 1 results, compared the multiple-component measure with an established multiple item measure of breach (rather than a single item as in study 1) and also tested for discriminant validity with an established multiple item measure of violation. Findings replicated those in study 1. The findings have important implications for considering alternative, more comprehensive and elaborate ways of assessing breach.

(Table 1) Relative abundance of planktonic foraminifers in ODP Hole 164-997A sediments

Hole 997A was drilled during Leg 164 of the Ocean Drilling Program at a depth of 2770 m on the topographic crest of the Blake Ridge in the western Atlantic Ocean. We report here an analysis of the faunal assemblages of planktonic foraminifers in a total of 91 samples (0.39-91.89 mbsf interval) spanning the last 2.15 m.y., latest Pliocene to Holocene. The abundant species, Globigerinoides ruber, Globigerinoides sacculifer, Neogloboquadrina dutertrei, Globorotalia inflata, and Globigerinita glutinata together exceed over ~70% of the total fauna. Each species exhibits fluctuations with amplitudes of 10%-20% or more. Despite their generally low abundance, the distinct presence/absence behavior of the Globorotalia menardii group is almost synchronous with glacial-interglacial climate cycles during the upper part of Brunhes Chron. The quantitative study and factor analysis of planktonic foraminiferal assemblages shows that the planktonic foraminiferal fauna in Hole 997A consists of four groups: warm water, subtropical gyre (mixed-layer species), gyre margin (thermocline/upwelling species), and subpolar assemblages. The subtropical gyre assemblage dominates throughout the studied section, whereas the abundance of gyre margin taxa strongly control the overall variability in faunal abundance at Site 997. In sediments older than the Olduvai Subchron, the planktonic foraminiferal faunas are characterized by fluctuations in both the subtropical gyre and gyre margin assemblages, similar to those in the Brunhes Chron. The upwelling/gyre margin fauna increased in abundance just before the Jaramillo Subchron and was dominant between 0.7 and 1.07 Ma. The transition from this gyre margin-dominated assemblage to an increase in abundance of the subtropical gyre and gyre margin species occurred around 0.7 Ma, near the Brunhes/Matuyama boundary. The presence of low-oxygen-tolerant benthic foraminifers, pyrite tubes, and abundant diatoms below the Brunhes/Matuyama boundary suggests decreased oxygenation of intermediate waters and more upwelling over the Blake-Bahama Outer Ridge, perhaps because of weaker Upper North Atlantic Deep Water ventilation. The changes in the relative composition of foraminifer assemblages took place at least twice, around 700 and 1000 ka, close to the ~930-ka switch from obliquity-forced climate variation to the 100-k.y. eccentricity cycle. The climate shift at 700 ka suggests a transition from relatively warmer conditions in the early Pleistocene to warm-cool oscillations in the Brunhes Chron.

Gaussian Process Kernels for Cross-Spectrum Analysis in Electrophysiological Time Series

Multi-output Gaussian processes provide a convenient framework for multi-task problems. An illustrative and motivating example of a multi-task problem is multi-region electrophysiological time-series data, where experimentalists are interested in both power and phase coherence between channels. Recently, the spectral mixture (SM) kernel was proposed to model the spectral density of a single task in a Gaussian process framework. This work develops a novel covariance kernel for multiple outputs, called the cross-spectral mixture (CSM) kernel. This new, flexible kernel represents both the power and phase relationship between multiple observation channels. The expressive capabilities of the CSM kernel are demonstrated through implementation of 1) a Bayesian hidden Markov model, where the emission distribution is a multi-output Gaussian process with a CSM covariance kernel, and 2) a Gaussian process factor analysis model, where factor scores represent the utilization of cross-spectral neural circuits. Results are presented for measured multi-region electrophysiological data.

(Table DR1) Biofacies, percentages of important benthic foraminifera and isotope data at ODP Site 758

The Indian monsoon system, as recorded by ocean-floor biota (benthic foraminifera) at Ocean Drilling Program Site 758 in the eastern equatorial Indian Ocean, has varied dramatically over the past 5.5 m.y., long after the onset of the monsoons at 10-8 Ma. Benthic foraminifera that thrive with high productivity year-round were common before the formation of Northern Hemisphere continental ice sheets ca. 3.1-2.5 Ma, indicating that the summer (southwest) monsoon had high intensity and long seasonal duration. Ca. 2.8 Ma benthic faunas became dominated by taxa that flourish with a seasonally strongly fluctuating food supply, indicating that the northeast (winter) monsoon, during which primary productivity is relatively low, increased in duration and strength to form a system similar to that of today. The change occurred coeval with the initiation of the Northern Hemisphere glaciation, documenting a close link between the development of the Indian monsoon and Northern Hemisphere glaciation.

(Table 1) Salinity, dissolved organic carbon and absorption characteristics of surface river waters around Hudson Bay

Composition and concentration of colored dissolved organic matter (CDOM) have been determined in Hudson Bay and Hudson Strait by excitation emission matrix spectroscopy (EEM) and parallel factor analysis (PARAFAC). Based on 63 surface samples, PARAFAC identified three fluorescent components, which were attributed to two humic- and one protein-like components. One humic-like component was identified as representing terrestrial organic matter and showed a conservative behaviour in Hudson Bay estuaries. The second humic-like component, traditionally identified as peak M, originated both from land and produced in the marine environment. Component 3 had spectra resembling protein-like material and thought to be plankton-derived. The distribution and composition of CDOM were largely controlled by water mass mixing with protein-like component being the least affected. Distinctive fluorescence patterns were also found between Hudson Bay and Hudson Strait, suggesting different sources of CDOM. The optically active fraction of DOC (both absorbing and fluorescing) was very high in the Hudson Bay (up to 89%) suggesting that fluorescence and absorbance can be used as proxies of the DOC concentration.

Isotope record of Nd-Sr-Pb in deep sea sediments from the Pacific (Table 2)

Pelagic clay of the east-central Pacific province is shown to be a mixture of three primary detrital components, reflecting continental source areas in Asia, North America, and Central and South America. Relative contributions from each source area are a function of geography, and this distribution appears to have remained constant over the past five million years, despite changing flux rates. A Q-mode factor analysis of downcore records for Pb, Sr, and Nd isotopes identified three factors that account for 98% of the total variance. These factors represent the radiogenic isotopic signatures of 1) late Cenozoic Asian dust, which dominates in the central North Pacific; 2) North American continental hemipelagic/eolian sources, restricted mainly to the easternmost North Pacific at ~30 °N latitude; and 3) Central and South American sources, restricted to areas east of ~100 °W longitude. South of the Intertropical Convergence Zone (~6 °N), the Asian dust signature diminishes abruptly. We conclude that late Cenozoic Asian dust sources can be isotopically differentiated downcore from both North American and South and Central American sources in the eastcentral Pacific. This approach has a utility for identifying changes in long-term Cenozoic atmospheric circulation patterns.

Setting the agenda for dental education in Scotland: a priority setting exercise including multiple stakehiolders

Introduction The Scottish Oral Health Research Collaboration identified dental education research (DER) as a key strand of their strategy,(1) leading to the formation of the Dental Education Research Group. The starting point for this group was to understand various stakeholders’ perceptions of research priorities, yet no existing studies were found. The aim of the current study was to identify DER priorities for Scotland in the next 3-5 years. Methods The study utilised a similar methodology to that of Dennis et al,(2) in medical education. Data were collected sequentially using two online questionnaires with multiple dental stakeholders represented at undergraduate and postgraduate levels across urban and rural Scotland. 85 participants completed questionnaire 1 (qualitative) and 649 participants completed questionnaire 2 (quantitative). Qualitative and quantitative data analysis approaches were used. Results Of the 24 priorities identified, the top priorities were: role of assessments in identifying competence; undergraduate curriculum prepares for practice; and promoting teamwork within the dental team. Following factor analysis, the priorities loaded on four factors: teamwork and professionalism, measuring and enhancing performance, personal and professional development challenges, and curriculum integration and innovation. The top barriers were lack of time, funding, staff motivation, valuing of DER, and resources/ infrastructure. Discussion There were many similarities between the identified priorities for dental and medical education research2, but also some notable differences, which will be discussed. Overwhelmingly, the identified priorities in dentistry related to fitness for practice and robust assessment practices. Take home message Priority setting exercises with multiple stakeholders are an important first step in developing a national research strategy. References 1. Bagg J, Macpherson L, Mossey P, Rennie J, Saunders B, Taylor M (2010) Strategy for Oral Health Research in Scotland. Edinburgh: The Scottish Government. 2. Dennis A A, Cleland J A, Johnston P, Ker JS, Lough, M Rees CE (2014) Exploring stakeholders’ views of medical education research priorities: a national study. Medical Education, 48(11): 1078-1091.

Padrões dietéticos e câncer oral e de faringe: um estudo caso-controle no Rio de Janeiro, Brasil

Investigou-se a associação entre padrões de dieta e câncer oral, como parte de um estudo multicêntrico latino-americano caso-controle de base hospitalar e incluiu 210 casos incidentes e 251 controles. Dados de consumo alimentar foram coletados por Questionário de Freqüência de Consumo Alimentar (QFCA). Análise fatorial identificou padrões alimentares, que foram categorizados em tercis. Calculou-se odds ratio (OR) com intervalo de 95 por cento de confiança (IC95 por cento ) por regressão logística múltipla não condicional. Os padrões "prudente", caracterizado em maioria por frutas e vegetais, e o padrão tradicional, por arroz e feijão, apresentaram associação inversa com o câncer oral para o mais elevado tercil, respectivamente: OR = 0,44; IC95 por cento : 0,25-0,75, valor de p de tendência (ptend) = 0,03; OR = 0,53; IC95 por cento : 0,30-0,93, ptend = 0,06. O padrão "lanches" não foi associado ao câncer oral. Além da proteção ao câncer oral conferida por dieta rica em vegetais e frutas, nossos dados sugerem que a dieta "tradicional" brasileira contendo em sua maioria arroz e feijão pode oferecer proteção ao câncer oral