The interrelationship between the goals and the objectives of a school system and Hispanic parents\u27 expectations within a small, urban industrial city in western Massachusetts.

This dissertation evolved from a need to investigate whether the goals and objectives of the school system are the same as the expectations of the client Hispanic parents, especially in a school system where over 60 percent of the student population is Hispanic. The purpose of this study is to examine the interrelationship between the goals and objectives of the school system and Hispanic parents\u27 expectations within a small, urban industrial city in Western Massachusetts. In order to implement this study, a questionnaire was devised and administered to randomly selected Hispanic parents. The questionnaire explored the attitude of Hispanic parents through responses to the following: (1) The following statements are my expectations for my son and/or daughter (18 items listed). (2) Yes, I know about or have heard of the following ideas and programs described in the goals and objectives of the school system where I live (21 items listed). (3) Yes, the following ideas and programs described in the goals and objectives of the school system satisfy my expectations as a parent for my son\u27s and/or daughter\u27s education (21 items listed). A Likert rating scale was used to measure parental expectations and the goals and objectives of the school system. The researcher utilized both qualitative and quantitative methodologies. The following research questions guided this study: (1) What are the goals and objectives of the school system? (2) What are the characteristics of the parents whose children attend these schools? (3) What do the parents do to enforce achieving these goals? (4) What is the interrelationship between parent expectations and the school system with regard to the achievement of these goals? The researcher\u27s major findings are that: (1) Hispanic parents should have the opportunity to participate in the decision-making process in developing the goals and objectives of the school system. Parental expectations can be addressed and taken into account as a result. (2) When families and communities have strong connections with schools, everyone benefits--children, families, teachers, schools, communities, and our democratic society. (3) Reliance on the delegation model in public education has created a fundamental gap between families and schools. There are other conclusions presented in this study concerning parental expectations and the goals and objectives of the school system

Understanding Diversity: Top Executives\u27 Perceptions of Racial and Ethnic Diversity in Public Relations

In public relations, minority public relations practitioners are feeling left behind by the profession (Ford & Appelbaum, 2005). Where do top executives stand on employment diversity within their organizations? An online survey of 20 top executives of small-sized public relations agencies explored how top executives’ perceptions of and normative beliefs about diversity practices were related to their future engagement in diversity practices at work. Based on the theory of reasoned action, this explanatory study found that executives’ perceptions of peer endorsement of diversity were associated with greater intention of organizational engagement in diversity practices. Neither perceived benefits of nor perceived concerns about diversity were related to future engagement. Recommendations for contacting this hard-to-reach audience, as well as suggestions for promoting diversity practices among top executives, were discussed

Search for axion-like particles using a variable baseline photon regeneration technique

We report the first results of the GammeV experiment, a search for milli-eV mass particles with axion-like couplings to two photons. The search is performed using a "light shining through a wall" technique where incident photons oscillate into new weakly interacting particles that are able to pass through the wall and subsequently regenerate back into detectable photons. The oscillation baseline of the apparatus is variable, thus allowing probes of different values of particle mass. We find no excess of events above background and are able to constrain the two-photon couplings of possible new scalar (pseudoscalar) particles to be less than 3.1x10^{-7} GeV^{-1} (3.5x10^{-7} GeV^{-1}) in the limit of massless particles.Comment: 5 pages, 4 figures. This is the version accepted by PRL and includes updated limit

Physico-chemical foundations underpinning microarray and next-generation sequencing experiments

Hybridization of nucleic acids on solid surfaces is a key process involved in high-throughput technologies such as microarrays and, in some cases, next-generation sequencing (NGS). A physical understanding of the hybridization process helps to determine the accuracy of these technologies. The goal of a widespread research program is to develop reliable transformations between the raw signals reported by the technologies and individual molecular concentrations from an ensemble of nucleic acids. This research has inputs from many areas, from bioinformatics and biostatistics, to theoretical and experimental biochemistry and biophysics, to computer simulations. A group of leading researchers met in Ploen Germany in 2011 to discuss present knowledge and limitations of our physico-chemical understanding of high-throughput nucleic acid technologies. This meeting inspired us to write this summary, which provides an overview of the state-of-the-art approaches based on physico-chemical foundation to modeling of the nucleic acids hybridization process on solid surfaces. In addition, practical application of current knowledge is emphasized

Geographic and temporal morphological stasis in the latest Cretaceous ammonoid Discoscaphites iris from the U.S. Gulf and Atlantic Coastal Plains

We examine temporal and spatial variation in morphology of the ammonoid cephalopod Discoscaphites iris using a large dataset from multiple localities in the Late Cretaceous (Maastrichtian) of the United States Gulf and Atlantic Coastal Plains, spanning a distance of 2000 km along the paleoshoreline. Our results suggest that the fossil record of D. iris is consistent with no within species net accumulation of phyletic evolutionary change across morphological traits or the lifetime of this species. Correlations between some traits and paleoenvironmental conditions as well as changes in the coefficient of variation may support limited population-scale ecophenotypic plasticity, however where stratigraphic data are available, no directional changes in morphology occur prior to the Cretaceous/Paleogene (K/Pg) boundary. This is consistent with models of 'dynamic' evolutionary stasis. Combined with knowledge of life history traits and paleoecology of scaphitid ammonoids, specifically a short planktonic phase after hatching followed by transition to a nektobenthic adult stage, these data suggest that scaphitids had significant potential for rapid morphological change in conjunction with limited dispersal capacity. It is therefore likely that evolutionary mode in the Scaphitidae (and potentially across the broader ammonoid clade) follows a model of cladogenesis wherein a dynamic morphological stasis is periodically interrupted by more substantial evolutionary change at speciation events. Finally, the lack of temporal changes in our data suggest that global environmental changes (such as those possibly related to the emplacement of the Deccan Traps Large Igneous Province) had a limited effect on the morphology of North American ammonoid faunas during the latest Cretaceous prior to the K/Pg mass extinction event.Missing morphometric values are highlighted with NA in the dataset.Funding provided by: National Science FoundationCrossref Funder Registry ID: http://dx.doi.org/10.13039/100000001Award Number: 1924807Funding provided by: American Museum of Natural History and Richard Gilder Graduate School*Crossref Funder Registry ID: Award Number:We assembled a large morphometric dataset consisting of 328 individual fossil specimens of the scaphitid ammonoid cephalopod Discoscaphites iris collected from nine localities in Texas, Missouri, Mississippi, and New Jersey, representing a ~2000 km transect from SW to NE and encompassing the full geographic range of this species. Morphometric parameters were measured on well-preserved adult specimens of two dimorphs (Macroconchs - presumably the female, and microconch, presumably the male). We took up to seven morphometric measurements, and calculated ratios that captured the size, shape, and degree of compression of each of these ammonoid shells from each different locality. We evaluated the coefficient of variation (the standard deviation divided by the mean) for size and shape ratios as well as compression ratios at each locality. We used non-parametric statistical tests [Mann-Whitney U] to evaluate the significance of changes in mean morphological trait values between localities. To correct for multiple comparisons we applied a Bonferroni correction and also controlled for the false discovery rate. We also explored relationships between morphological traits and several environmental variables using linear modelling. All analyses were conducted in the R programming environment

Epigenetic memory in induced pluripotent stem cells.

Somatic cell nuclear transfer and transcription-factor-based reprogramming revert adult cells to an embryonic state, and yield pluripotent stem cells that can generate all tissues. Through different mechanisms and kinetics, these two reprogramming methods reset genomic methylation, an epigenetic modification of DNA that influences gene expression, leading us to hypothesize that the resulting pluripotent stem cells might have different properties. Here we observe that low-passage induced pluripotent stem cells (iPSCs) derived by factor-based reprogramming of adult murine tissues harbour residual DNA methylation signatures characteristic of their somatic tissue of origin, which favours their differentiation along lineages related to the donor cell, while restricting alternative cell fates. Such an 'epigenetic memory' of the donor tissue could be reset by differentiation and serial reprogramming, or by treatment of iPSCs with chromatin-modifying drugs. In contrast, the differentiation and methylation of nuclear-transfer-derived pluripotent stem cells were more similar to classical embryonic stem cells than were iPSCs. Our data indicate that nuclear transfer is more effective at establishing the ground state of pluripotency than factor-based reprogramming, which can leave an epigenetic memory of the tissue of origin that may influence efforts at directed differentiation for applications in disease modelling or treatment

Lineage-based identification of cellular states and expression programs

We present a method, LineageProgram, that uses the developmental lineage relationship of observed gene expression measurements to improve the learning of developmentally relevant cellular states and expression programs. We find that incorporating lineage information allows us to significantly improve both the predictive power and interpretability of expression programs that are derived from expression measurements from in vitro differentiation experiments. The lineage tree of a differentiation experiment is a tree graph whose nodes describe all of the unique expression states in the input expression measurements, and edges describe the experimental perturbations applied to cells. Our method, LineageProgram, is based on a log-linear model with parameters that reflect changes along the lineage tree. Regularization with L1 that based methods controls the parameters in three distinct ways: the number of genes change between two cellular states, the number of unique cellular states, and the number of underlying factors responsible for changes in cell state. The model is estimated with proximal operators to quickly discover a small number of key cell states and gene sets. Comparisons with existing factorization, techniques, such as singular value decomposition and non-negative matrix factorization show that our method provides higher predictive power in held, out tests while inducing sparse and biologically relevant gene sets.National Institutes of Health (U.S.) (P01-NS055923)National Institutes of Health (U.S.) (1-UL1-RR024920

"Hook"-calibration of GeneChip-microarrays: Chip characteristics and expression measures

<p>Abstract</p> <p>Background</p> <p>Microarray experiments rely on several critical steps that may introduce biases and uncertainty in downstream analyses. These steps include mRNA sample extraction, amplification and labelling, hybridization, and scanning causing chip-specific systematic variations on the raw intensity level. Also the chosen array-type and the up-to-dateness of the genomic information probed on the chip affect the quality of the expression measures. In the accompanying publication we presented theory and algorithm of the so-called hook method which aims at correcting expression data for systematic biases using a series of new chip characteristics.</p> <p>Results</p> <p>In this publication we summarize the essential chip characteristics provided by this method, analyze special benchmark experiments to estimate transcript related expression measures and illustrate the potency of the method to detect and to quantify the quality of a particular hybridization. It is shown that our single-chip approach provides expression measures responding linearly on changes of the transcript concentration over three orders of magnitude. In addition, the method calculates a detection call judging the relation between the signal and the detection limit of the particular measurement. The performance of the method in the context of different chip generations and probe set assignments is illustrated. The hook method characterizes the RNA-quality in terms of the 3'/5'-amplification bias and the sample-specific calling rate. We show that the proper judgement of these effects requires the disentanglement of non-specific and specific hybridization which, otherwise, can lead to misinterpretations of expression changes. The consequences of modifying probe/target interactions by either changing the labelling protocol or by substituting RNA by DNA targets are demonstrated.</p> <p>Conclusion</p> <p>The single-chip based hook-method provides accurate expression estimates and chip-summary characteristics using the natural metrics given by the hybridization reaction with the potency to develop new standards for microarray quality control and calibration.</p

puma: a Bioconductor package for propagating uncertainty in microarray analysis

BACKGROUND: Most analyses of microarray data are based on point estimates of expression levels and ignore the uncertainty of such estimates. By determining uncertainties from Affymetrix GeneChip data and propagating these uncertainties to downstream analyses it has been shown that we can improve results of differential expression detection, principal component analysis and clustering. Previously, implementations of these uncertainty propagation methods have only been available as separate packages, written in different languages. Previous implementations have also suffered from being very costly to compute, and in the case of differential expression detection, have been limited in the experimental designs to which they can be applied. RESULTS: puma is a Bioconductor package incorporating a suite of analysis methods for use on Affymetrix GeneChip data. puma extends the differential expression detection methods of previous work from the 2-class case to the multi-factorial case. puma can be used to automatically create design and contrast matrices for typical experimental designs, which can be used both within the package itself but also in other Bioconductor packages. The implementation of differential expression detection methods has been parallelised leading to significant decreases in processing time on a range of computer architectures. puma incorporates the first R implementation of an uncertainty propagation version of principal component analysis, and an implementation of a clustering method based on uncertainty propagation. All of these techniques are brought together in a single, easy-to-use package with clear, task-based documentation. CONCLUSION: For the first time, the puma package makes a suite of uncertainty propagation methods available to a general audience. These methods can be used to improve results from more traditional analyses of microarray data. puma also offers improvements in terms of scope and speed of execution over previously available methods. puma is recommended for anyone working with the Affymetrix GeneChip platform for gene expression analysis and can also be applied more generally

Pre-processing and differential expression analysis of Agilent microRNA arrays using the AgiMicroRna Bioconductor library

<p>Abstract</p> <p>Background</p> <p>The main research tool for identifying microRNAs involved in specific cellular processes is gene expression profiling using microarray technology. Agilent is one of the major producers of microRNA arrays, and microarray data are commonly analyzed by using R and the functions and packages collected in the Bioconductor project. However, an analytical package that integrates the specific characteristics of microRNA Agilent arrays has been lacking.</p> <p>Results</p> <p>This report presents the new bioinformatic tool <it>AgiMicroRNA </it>for the pre-processing and differential expression analysis of Agilent microRNA array data. The software is implemented in the open-source statistical scripting language R and is integrated in the Bioconductor project (<url>http://www.bioconductor.org</url>) under the GPL license. For the pre-processing of the microRNA signal, <it>AgiMicroRNA </it>incorporates the <it>robust multiarray average algorithm</it>, a method that produces a summary measure of the microRNA expression using a linear model that takes into account the probe affinity effect. To obtain a normalized microRNA signal useful for the statistical analysis, <it>AgiMicroRna </it>offers the possibility of employing either the processed signal estimated by the <it>robust multiarray average algorithm </it>or the processed signal produced by the Agilent image analysis software. The <it>AgiMicroRNA </it>package also incorporates different graphical utilities to assess the quality of the data. <it>AgiMicroRna </it>uses the linear model features implemented in the <it>limma </it>package to assess the differential expression between different experimental conditions and provides links to the <it>miRBase </it>for those microRNAs that have been declared as significant in the statistical analysis.</p> <p>Conclusions</p> <p><it>AgiMicroRna </it>is a rational collection of Bioconductor functions that have been wrapped into specific functions in order to ease and systematize the pre-processing and statistical analysis of Agilent microRNA data. The development of this package contributes to the Bioconductor project filling the gap in microRNA array data analysis.</p