476 research outputs found
Generalization of Word Retrieval Following Semantic Feature Treatment
The purpose of this research was to analyze generalization effects following semantic feature treatment (SFT) for aphasia. The effectiveness of SFT at improving accuracy and speed of word retrieval, generalization to untreated words and discourse tasks and the influence of shared features was examined. The three participants improved in retrieval accuracy of treated words. Accuracy of untreated words improved for two participants; retrieval accuracy for words with shared features improved slightly more than for words with no-shared features. Two participants showed variable generalization to discourse tasks and improved speed of accurate responses. Clinical implications and future research directions are discussed
Systems developmental biology: the use of ontologies in annotating models and in identifying gene function within and across species
Systems developmental biology is an approach to the study of embryogenesis that attempts to analyze complex developmental processes through integrating the roles of their molecular, cellular, and tissue participants within a computational framework. This article discusses ways of annotating these participants using standard terms and IDs now available in public ontologies (these are areas of hierarchical knowledge formalized to be computationally accessible) for tissues, cells, and processes. Such annotations bring two types of benefit. The first comes from using standard terms: This allows linkage to other resources that use them (e.g., GXD, the gene-expression [G-E] database for mouse development). The second comes from the annotation procedure itself: This can lead to the identification of common processes that are used in very different and apparently unrelated events, even in other organisms. One implication of this is the potential for identifying the genes underpinning common developmental processes in different tissues through Boolean analysis of their G-E profiles. While it is easiest to do this for single organisms, the approach is extendable to analyzing similar processes in different organisms. Although the full computational infrastructure for such an analysis has yet to be put in place, two examples are briefly considered as illustration. First, the early development of the mouse urogenital system shows how a line of development can be graphically formalized using ontologies. Second, Boolean analysis of the G-E profiles of the mesenchyme-to-epithelium transitions that take place during mouse development suggest Lhx1, Foxc1, and Meox1 as candidate transcription factors for mediating this process
Pre-M Phase-promoting Factor Associates with Annulate Lamellae in Xenopus Oocytes and Egg Extracts
We have used complementary biochemical and in vivo approaches to study the compartmentalization of M phase-promoting factor (MPF) in prophase Xenopus eggs and oocytes. We first examined the distribution of MPF (Cdc2/CyclinB2) and membranous organelles in high-speed extracts of Xenopus eggs made during mitotic prophase. These extracts were found to lack mitochondria, Golgi membranes, and most endoplasmic reticulum (ER) but to contain the bulk of the pre-MPF pool. This pre-MPF could be pelleted by further centrifugation along with components necessary to activate it. On activation, Cdc2/CyclinB2 moved into the soluble fraction. Electron microscopy and Western blot analysis showed that the pre-MPF pellet contained a specific ER subdomain comprising "annulate lamellae" (AL): stacked ER membranes highly enriched in nuclear pores. Colocalization of pre-MPF with AL was demonstrated by anti-CyclinB2 immunofluorescence in prophase oocytes, in which AL are positioned close to the vegetal surface. Green fluorescent protein-CyclinB2 expressed in oocytes also localized at AL. These data suggest that inactive MPF associates with nuclear envelope components just before activation. This association may explain why nuclei and centrosomes stimulate MPF activation and provide a mechanism for targeting of MPF to some of its key substrates
BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata
As the volume and complexity of data sets archived at NCBI grow rapidly, so does the need to gather and organize the associated metadata. Although metadata has been collected for some archival databases, previously, there was no centralized approach at NCBI for collecting this information and using it across databases. The BioProject database was recently established to facilitate organization and classification of project data submitted to NCBI, EBI and DDBJ databases. It captures descriptive information about research projects that result in high volume submissions to archival databases, ties together related data across multiple archives and serves as a central portal by which to inform users of data availability. Concomitantly, the BioSample database is being developed to capture descriptive information about the biological samples investigated in projects. BioProject and BioSample records link to corresponding data stored in archival repositories. Submissions are supported by a web-based Submission Portal that guides users through a series of forms for input of rich metadata describing their projects and samples. Together, these databases offer improved ways for users to query, locate, integrate and interpret the masses of data held in NCBI's archival repositories. The BioProject and BioSample databases are available at http://www.ncbi.nlm.nih.gov/bioproject and http://www.ncbi.nlm.nih.gov/biosample, respectively
Measurements of double-helicity asymmetries in inclusive production in longitudinally polarized collisions at GeV
We report the double helicity asymmetry, , in inclusive
production at forward rapidity as a function of transverse momentum
and rapidity . The data analyzed were taken during
GeV longitudinally polarized collisions at the Relativistic Heavy Ion
Collider (RHIC) in the 2013 run using the PHENIX detector. At this collision
energy, particles are predominantly produced through gluon-gluon
scatterings, thus is sensitive to the gluon polarization
inside the proton. We measured by detecting the decay
daughter muon pairs within the PHENIX muon spectrometers in the
rapidity range . In this kinematic range, we measured the
to be ~(stat)~~(syst). The
can be expressed to be proportional to the product of the
gluon polarization distributions at two distinct ranges of Bjorken : one at
moderate range where recent RHIC data of jet and
double helicity spin asymmetries have shown evidence for significant gluon
polarization, and the other one covering the poorly known small- region . Thus our new results could be used to further
constrain the gluon polarization for .Comment: 335 authors, 10 pages, 4 figures, 3 tables, 2013 data. Version
accepted for publication by Phys. Rev. D. Plain text data tables for the
points plotted in figures for this and previous PHENIX publications are (or
will be) publicly available at http://www.phenix.bnl.gov/papers.htm
Inclusive cross section and double-helicity asymmetry for production at midrapidity in collisions at GeV
PHENIX measurements are presented for the cross section and double-helicity
asymmetry () in inclusive production at midrapidity from
collisions at ~GeV from data taken in 2012 and 2013 at
the Relativistic Heavy Ion Collider. The next-to-leading-order
perturbative-quantum-chromodynamics theory calculation is in excellent
agreement with the presented cross section results. The calculation utilized
parton-to-pion fragmentation functions from the recent DSS14 global analysis,
which prefer a smaller gluon-to-pion fragmentation function. The
results follow an increasingly positive asymmetry trend with
and with respect to the predictions and are in excellent
agreement with the latest global analysis results. This analysis incorporated
earlier results on and jet , and suggested a positive
contribution of gluon polarization to the spin of the proton for the
gluon momentum fraction range . The data presented here extend to a
currently unexplored region, down to , and thus provide additional
constraints on the value of . The results confirm the evidence for
nonzero using a different production channel in a complementary
kinematic region.Comment: 413 authors, 8 pages, 4 figures. v2 is version accepted as PRD Rapid
Communication. Plain text data tables for the points plotted in figures for
this and previous PHENIX publications are (or will be) publicly available at
http://www.phenix.bnl.gov/papers.htm
meson production in Au collisions at GeV
The PHENIX experiment has measured meson production in Au
collisions at GeV using the dimuon and dielectron decay
channels. The meson is measured in the forward (backward) -going
(Au-going) direction, () in the transverse-momentum
() range from 1--7 GeV/, and at midrapidity in the
range below 7 GeV/. The meson invariant yields and
nuclear-modification factors as a function of , rapidity, and centrality
are reported. An enhancement of meson production is observed in the
Au-going direction, while suppression is seen in the -going direction, and
no modification is observed at midrapidity relative to the yield in
collisions scaled by the number of binary collisions. Similar behavior was
previously observed for inclusive charged hadrons and open heavy flavor
indicating similar cold-nuclear-matter effects.Comment: 484 authors, 16 pages, 12 figures, 6 tables. v1 is the version
accepted for publication in Phys. Rev. C. Data tables for the points plotted
in the figures are given in the paper itsel
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