241 research outputs found
dalmatian: A Package for Fitting Double Hierarchical Linear Models in R via JAGS and nimble
Traditional regression models, including generalized linear mixed models, focus on understanding the deterministic factors that affect the mean of a response variable. Many biological studies seek to understand non-deterministic patterns in the variance or dispersion of a phenotypic or ecological response variable. We describe a new R package, dalmatian, that provides methods for fitting double hierarchical generalized linear models incorporating fixed and random predictors of both the mean and variance. Models are fit via Markov chain Monte Carlo sampling implemented in either JAGS or nimble and the package provides simple functions for monitoring the sampler and summarizing the results. We illustrate these functions through an application to data on food delivery by breeding pied flycatchers (Ficedula hypoleuca). Our intent is that this package makes it easier for practitioners to implement these models without having to learn the intricacies of Markov chain Monte Carlo methods
The use of operational event sequence diagrams and work domain analysis techniques for the specification of the crewing configuration of a single-pilot commercial aircraft
Advanced optical imaging in living embryos
Developmental biology investigations have evolved from static studies of embryo anatomy and into dynamic studies of the genetic and cellular mechanisms responsible for shaping the embryo anatomy. With the advancement of fluorescent protein fusions, the ability to visualize and comprehend how thousands to millions of cells interact with one another to form tissues and organs in three dimensions (xyz) over time (t) is just beginning to be realized and exploited. In this review, we explore recent advances utilizing confocal and multi-photon time-lapse microscopy to capture gene expression, cell behavior, and embryo development. From choosing the appropriate fluorophore, to labeling strategy, to experimental set-up, and data pipeline handling, this review covers the various aspects related to acquiring and analyzing multi-dimensional data sets. These innovative techniques in multi-dimensional imaging and analysis can be applied across a number of fields in time and space including protein dynamics to cell biology to morphogenesis
Blood Glucose Levels Regulate Pancreatic β-Cell Proliferation during Experimentally-Induced and Spontaneous Autoimmune Diabetes in Mice
Type 1 diabetes mellitus is caused by immune-mediated destruction of pancreatic beta-cells leading to insulin deficiency, impaired intermediary metabolism, and elevated blood glucose concentrations. While at autoimmune diabetes onset a limited number of beta-cells persist, the cells' regenerative potential and its regulation have remained largely unexplored. Using two mouse autoimmune diabetes models, this study examined the proliferation of pancreatic islet ss-cells and other endocrine and non-endocrine subsets, and the factors regulating that proliferation.We adapted multi-parameter flow cytometry techniques (including DNA-content measurements and 5'-bromo-2'-deoxyuridine [BrdU] incorporation) to study pancreatic islet single cell suspensions. These studies demonstrate that beta-cell proliferation rapidly increases at diabetes onset, and that this proliferation is closely correlated with the diabetic animals' elevated blood glucose levels. For instance, we show that when normoglycemia is restored by exogenous insulin or islet transplantation, the beta-cell proliferation rate returns towards low levels found in control animals, yet surges when hyperglycemia recurs. In contrast, other-than-ss endocrine islet cells did not exhibit the same glucose-dependent proliferative responses. Rather, disease-associated alterations of BrdU-incorporation rates of delta-cells (minor decrease), and non-endocrine islet cells (slight increase) were not affected by blood glucose levels, or were inversely related to glycemia control after diabetes onset (alpha-cells).We conclude that murine beta-cells' ability to proliferate in response to metabolic need (i.e. rising blood glucose concentrations) is remarkably well preserved during severe, chronic beta-cell autoimmunity. These data suggest that timely control of the destructive immune response after disease manifestation could allow spontaneous regeneration of sufficient beta-cell mass to restore normal glucose homeostasis
Photodisintegration of He into p+t
The two-body photodisintegration of He into a proton and a triton has
been studied using the CEBAF Large-Acceptance Spectrometer (CLAS) at Jefferson
Laboratory. Real photons produced with the Hall-B bremsstrahlung-tagging system
in the energy range from 0.35 to 1.55 GeV were incident on a liquid He
target. This is the first measurement of the photodisintegration of He
above 0.4 GeV. The differential cross sections for the He
reaction have been measured as a function of photon-beam energy and
proton-scattering angle, and are compared with the latest model calculations by
J.-M. Laget. At 0.6-1.2 GeV, our data are in good agreement only with the
calculations that include three-body mechanisms, thus confirming their
importance. These results reinforce the conclusion of our previous study of the
three-body breakup of He that demonstrated the great importance of
three-body mechanisms in the energy region 0.5-0.8 GeV .Comment: 13 pages submitted in one tgz file containing 2 tex file and 22
postscrip figure
photoproduction on the proton for photon energies from 0.675 to 2.875 GeV
Differential cross sections for the reaction have been
measured with the CEBAF Large Acceptance Spectrometer (CLAS) and a tagged
photon beam with energies from 0.675 to 2.875 GeV. The results reported here
possess greater accuracy in the absolute normalization than previous
measurements. They disagree with recent CB-ELSA measurements for the process at
forward scattering angles. Agreement with the SAID and MAID fits is found below
1 GeV. The present set of cross sections has been incorporated into the SAID
database, and exploratory fits have been extended to 3 GeV. Resonance couplings
have been extracted and compared to previous determinations.Comment: 18 pages, 48 figure
Exclusive electroproduction on the proton at CLAS
The reaction has been measured, using the 5.754
GeV electron beam of Jefferson Lab and the CLAS detector. This represents the
largest ever set of data for this reaction in the valence region. Integrated
and differential cross sections are presented. The , and
dependences of the cross section are compared to theoretical calculations based
on -channel meson-exchange Regge theory on the one hand and on quark handbag
diagrams related to Generalized Parton Distributions (GPDs) on the other hand.
The Regge approach can describe at the 30% level most of the features
of the present data while the two GPD calculations that are presented in this
article which succesfully reproduce the high energy data strongly underestimate
the present data. The question is then raised whether this discrepancy
originates from an incomplete or inexact way of modelling the GPDs or the
associated hard scattering amplitude or whether the GPD formalism is simply
inapplicable in this region due to higher-twists contributions, incalculable at
present.Comment: 29 pages, 29 figure
First Measurement of Beam-Recoil Observables Cx and Cz in Hyperon Photoproduction
Spin transfer from circularly polarized real photons to recoiling hyperons
has been measured for the reactions and
. The data were obtained using the CLAS
detector at Jefferson Lab for center-of-mass energies between 1.6 and 2.53
GeV, and for . For the , the
polarization transfer coefficient along the photon momentum axis, , was
found to be near unity for a wide range of energy and kaon production angles.
The associated transverse polarization coefficient, , is smaller than
by a roughly constant difference of unity. Most significantly, the {\it
total} polarization vector, including the induced polarization ,
has magnitude consistent with unity at all measured energies and production
angles when the beam is fully polarized. For the this simple
phenomenology does not hold. All existing hadrodynamic models are in poor
agreement with these results.Comment: 28 pages, 18 figures, Submitted to Physical Review
The Whereabouts of 2D Gels in Quantitative Proteomics
Two-dimensional gel electrophoresis has been instrumental in the development
of proteomics. Although it is no longer the exclusive scheme used for
proteomics, its unique features make it a still highly valuable tool,
especially when multiple quantitative comparisons of samples must be made, and
even for large samples series. However, quantitative proteomics using 2D gels
is critically dependent on the performances of the protein detection methods
used after the electrophoretic separations. This chapter therefore examines
critically the various detection methods (radioactivity, dyes, fluorescence,
and silver) as well as the data analysis issues that must be taken into account
when quantitative comparative analysis of 2D gels is performed
Anti-diabetic effect of a preparation of vitamins, minerals and trace elements in diabetic rats: a gender difference
BACKGROUND: Although multivitamin products are widely used as dietary supplements to maintain health or as special medical food in certain diseases, the effects of these products were not investigated in diabetes mellitus, a major cardiovascular risk factor. Therefore, here we investigated if a preparation of different minerals, vitamins, and trace elements (MVT) for human use affects the severity of experimental diabetes. METHODS: Two days old neonatal Wistar rats from both genders were injected with 100 mg/kg of streptozotocin or its vehicle to induce diabetes. At week 4, rats were fed with an MVT preparation or vehicle for 8 weeks. Well established diagnostic parameters of diabetes, i.e. fasting blood glucose and oral glucose tolerance test were performed at week 4, 8 and 12. Moreover, serum insulin and blood HbA1c were measured at week 12. RESULTS: An impaired glucose tolerance has been found in streptozotocin-treated rats in both genders at week 4. In males, fasting blood glucose and HbA1c were significantly increased and glucose tolerance and serum insulin was decreased at week 12 in the vehicle-treated diabetic group as compared to the vehicle-treated non-diabetic group. All of the diagnostic parameters of diabetes were significantly improved by MVT treatment in male rats. In females, streptozotocin treatment resulted in a less severe prediabetic-like phenotype as only glucose tolerance and HbA1c were altered by the end of the study in the vehicle-treated diabetic group as compared to the vehicle-treated non-diabetic group. MVT treatment failed to improve the diagnostic parameters of diabetes in female streptozotocin-treated rats. CONCLUSION: This is the first demonstration that MVT significantly attenuates the progression of diabetes in male rats with chronic experimental diabetes. Moreover, we have confirmed that females are less sensitive to STZ-induced diabetes and MVT preparation did not show protection against prediabetic state. This may suggest a gender difference in the pathogenesis of diabetes
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