575 research outputs found
Using satellite imagery and historical maps to study the original contours of Lalbagh Botanical Garden
The Lalbagh Botanical Garden in Bangalore,
one of the country’s oldest botanical
gardens, has a long history. In 1760,
Hyder Ali established a garden here,
which was later expanded by his son
Tipu Sultan. After Tipu was defeated and
killed in 1799, the stewardship of
Lalbagh passed through several hands
before finally being taken over by the
then Government of Mysore and made
the Government Gardens.
It is generally believed that the garden
that Hyder Ali set up in 1760 was located
north of and adjacent to the Lalbagh
tank. For example, maps published by
the Department of Horticulture, Government
of Karnataka depict the garden
between 1760 and 1856 covering a
roughly rectangular patch of about 40
acres adjacent to the tank.
Using a combination of historical
maps, old paintings and recent remotely
sensed images, we have examined the
actual boundaries of the garden as it was
in the period of Tipu
Pharmacological screening using an FXN-EGFP cellular genomic reporter assay for the therapy of Friedreich ataxia
Copyright @ 2013 Li et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.Friedreich ataxia (FRDA) is an autosomal recessive disorder characterized by neurodegeneration and cardiomyopathy. The presence of a GAA trinucleotide repeat expansion in the first intron of the FXN gene results in the inhibition of gene expression and an insufficiency of the mitochondrial protein frataxin. There is a correlation between expansion length, the amount of residual frataxin and the severity of disease. As the coding sequence is unaltered, pharmacological up-regulation of FXN expression may restore frataxin to therapeutic levels. To facilitate screening of compounds that modulate FXN expression in a physiologically relevant manner, we established a cellular genomic reporter assay consisting of a stable human cell line containing an FXN-EGFP fusion construct, in which the EGFP gene is fused in-frame with the entire normal human FXN gene present on a BAC clone. The cell line was used to establish a fluorometric cellular assay for use in high throughput screening (HTS) procedures. A small chemical library containing FDA-approved compounds and natural extracts was screened and analyzed. Compound hits identified by HTS were further evaluated by flow cytometry in the cellular genomic reporter assay. The effects on FXN mRNA and frataxin protein levels were measured in lymphoblast and fibroblast cell lines derived from individuals with FRDA and in a humanized GAA repeat expansion mouse model of FRDA. Compounds that were established to increase FXN gene expression and frataxin levels included several anti-cancer agents, the iron-chelator deferiprone and the phytoalexin resveratrol.Muscular Dystrophy Association (USA), the National Health and Medical Research Council (Australia), the Friedreich’s Ataxia Research Alliance (USA), the Brockhoff Foundation (Australia), the Friedreich Ataxia Research Association (Australasia), Seek A Miracle (USA) and the Victorian Government’s Operational Infrastructure Support Program
Interplay between pleiotropy and secondary selection determines rise and fall of mutators in stress response
Dramatic rise of mutators has been found to accompany adaptation of bacteria
in response to many kinds of stress. Two views on the evolutionary origin of
this phenomenon emerged: the pleiotropic hypothesis positing that it is a
byproduct of environmental stress or other specific stress response mechanisms
and the second order selection which states that mutators hitchhike to fixation
with unrelated beneficial alleles. Conventional population genetics models
could not fully resolve this controversy because they are based on certain
assumptions about fitness landscape. Here we address this problem using a
microscopic multiscale model, which couples physically realistic molecular
descriptions of proteins and their interactions with population genetics of
carrier organisms without assuming any a priori fitness landscape. We found
that both pleiotropy and second order selection play a crucial role at
different stages of adaptation: the supply of mutators is provided through
destabilization of error correction complexes or fluctuations of production
levels of prototypic mismatch repair proteins (pleiotropic effects), while rise
and fixation of mutators occur when there is a sufficient supply of beneficial
mutations in replication-controlling genes. This general mechanism assures a
robust and reliable adaptation of organisms to unforeseen challenges. This
study highlights physical principles underlying physical biological mechanisms
of stress response and adaptation
The holographic principle
There is strong evidence that the area of any surface limits the information
content of adjacent spacetime regions, at 10^(69) bits per square meter. We
review the developments that have led to the recognition of this entropy bound,
placing special emphasis on the quantum properties of black holes. The
construction of light-sheets, which associate relevant spacetime regions to any
given surface, is discussed in detail. We explain how the bound is tested and
demonstrate its validity in a wide range of examples.
A universal relation between geometry and information is thus uncovered. It
has yet to be explained. The holographic principle asserts that its origin must
lie in the number of fundamental degrees of freedom involved in a unified
description of spacetime and matter. It must be manifest in an underlying
quantum theory of gravity. We survey some successes and challenges in
implementing the holographic principle.Comment: 52 pages, 10 figures, invited review for Rev. Mod. Phys; v2:
reference adde
Corner contributions to holographic entanglement entropy
The entanglement entropy of three-dimensional conformal field theories
contains a universal contribution coming from corners in the entangling
surface. We study these contributions in a holographic framework and, in
particular, we consider the effects of higher curvature interactions in the
bulk gravity theory. We find that for all of our holographic models, the corner
contribution is only modified by an overall factor but the functional
dependence on the opening angle is not modified by the new gravitational
interactions. We also compare the dependence of the corner term on the new
gravitational couplings to that for a number of other physical quantities, and
we show that the ratio of the corner contribution over the central charge
appearing in the two-point function of the stress tensor is a universal
function for all of the holographic theories studied here. Comparing this
holographic result to the analogous functions for free CFT's, we find fairly
good agreement across the full range of the opening angle. However, there is a
precise match in the limit where the entangling surface becomes smooth, i.e.,
the angle approaches , and we conjecture the corresponding ratio is a
universal constant for all three-dimensional conformal field theories. In this
paper, we expand on the holographic calculations in our previous letter
arXiv:1505.04804, where this conjecture was first introduced.Comment: 62 pages, 6 figures, 1 table; v2: minor modifications to match
published version, typos fixe
Enriching for correct prediction of biological processes using a combination of diverse classifiers
<p>Abstract</p> <p>Background</p> <p>Machine learning models (classifiers) for classifying genes to biological processes each have their own unique characteristics in what genes can be classified and to what biological processes. No single learning model is qualitatively superior to any other model and overall precision for each model tends to be low. The classification results for each classifier can be complementary and synergistic suggesting the benefit of a combination of algorithms, but often the prediction probability outputs of various learning models are neither comparable nor compatible for combining. A means to compare outputs regardless of the model and data used and combine the results into an improved comprehensive model is needed.</p> <p>Results</p> <p>Gene expression patterns from NCI's panel of 60 cell lines were used to train a Random Forest, a Support Vector Machine and a Neural Network model, plus two over-sampled models for classifying genes to biological processes. Each model produced unique characteristics in the classification results. We introduce the Precision Index measure (PIN) from the maximum posterior probability that allows assessing, comparing and combining multiple classifiers. The class specific precision measure (PIC) is introduced and used to select a subset of predictions across all classes and all classifiers with high precision. We developed a single classifier that combines the PINs from these five models in prediction and found that the PIN Combined Classifier (PINCom) significantly increased the number of correctly predicted genes over any single classifier. The PINCom applied to test genes that were not used in training also showed substantial improvement over any single model.</p> <p>Conclusions</p> <p>This paper introduces novel and effective ways of assessing predictions by their precision and recall plus a method that combines several machine learning models and capitalizes on synergy and complementation in class selection, resulting in higher precision and recall. Different machine learning models yielded incongruent results each of which were successfully combined into one superior model using the PIN measure we developed. Validation of the boosted predictions for gene functions showed the genes to be accurately predicted.</p
Logarithmic Corrections to Extremal Black Hole Entropy from Quantum Entropy Function
We evaluate the one loop determinant of matter multiplet fields of N=4
supergravity in the near horizon geometry of quarter BPS black holes, and use
it to calculate logarithmic corrections to the entropy of these black holes
using the quantum entropy function formalism. We show that even though
individual fields give non-vanishing logarithmic contribution to the entropy,
the net contribution from all the fields in the matter multiplet vanishes. Thus
logarithmic corrections to the entropy of quarter BPS black holes, if present,
must be independent of the number of matter multiplet fields in the theory.
This is consistent with the microscopic results. During our analysis we also
determine the complete spectrum of small fluctuations of matter multiplet
fields in the near horizon geometry.Comment: LaTeX file, 52 pages; v2: minor corrections, references adde
Beclin-1 Expression is a Predictor of Clinical Outcome in Patients with Esophageal Squamous Cell Carcinoma and Correlated to Hypoxia-Inducible Factor (HIF)-1α Expression
In the present study, we examined the relationship between Beclin-1 expression and HIF-1α expression in esophageal squamous cell carcinoma(ESCC). There was a loss of Beclin-1 protein expression in 33% of ESCCs. Beclin-1 expression significantly correlated with depth of invasion, lymph node metastasis and clinical stage. Among the 54 patients, The survival rate of the Beclin-1-positive group was better than that of the Beclin-1-negative group. Twenty-five of the 54 (46%) tumor specimens showed high levels of HIF-1α immunoreactivity. Beclin-1 expression was associated with HIF-1α expression. The survival rate of patients with Beclin-1-positive and HIF-1α-low tumors was significantly higher than that of the other groups. These results suggest that Beclin-1 and HIF-1α expression are important determinants of survival in ESCCs
Stability and inheritance of endosperm-specific expression of two transgenes in progeny from crossing independently transformed barley plants
To study stability and inheritance of two different transgenes in barley, we crossed a homozygous T8 plant, having uidA (or gus) driven by the barley endosperm-specific B1-hordein promoter (localized in the near centromeric region of chromosome 7H) with a second homozygous T4 plant, having sgfp(S65T) driven by the barley endosperm-specific D-hordein promoter (localized on the subtelomeric region of chromosome 2H). Both lines stably expressed the two transgenes in the generations prior to the cross. Three independently crossed F1 progeny were analyzed by PCR for both uidA and sgfp(S65T) in each plant and functional expression of GUS and GFP in F2 seeds followed a 3:1 Mendelian segregation ratio and transgenes were localized by FISH to the same location as in the parental plants. FISH was used to screen F2 plants for homozygosity of both transgenes; four homozygous plants were identified from the two crossed lines tested. FISH results showing presence of transgenes were consistent with segregation ratios of expression of both transgenes, indicating that the two transgenes were expressed without transgene silencing in homozygous progeny advanced to the F3 and F4 generations. Thus, even after crossing independently transformed, homozygous parental plants containing a single, stably expressed transgene, progeny were obtained that continued to express multiple transgenes through generation advance. Such stability of transgenes, following outcrossing, is an important attribute for trait modification and for gene flow studies
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