308 research outputs found
Bellybutton: Accessible and Customizable Deep-Learning Image Segmentation
The conversion of raw images into quantifiable data can be a major hurdle in
experimental research, and typically involves identifying region(s) of
interest, a process known as segmentation. Machine learning tools for image
segmentation are often specific to a set of tasks, such as tracking cells, or
require substantial compute or coding knowledge to train and use. Here we
introduce an easy-to-use (no coding required), image segmentation method, using
a 15-layer convolutional neural network that can be trained on a laptop:
Bellybutton. The algorithm trains on user-provided segmentation of example
images, but, as we show, just one or even a portion of one training image can
be sufficient in some cases. We detail the machine learning method and give
three use cases where Bellybutton correctly segments images despite substantial
lighting, shape, size, focus, and/or structure variation across the regions(s)
of interest. Instructions for easy download and use, with further details and
the datasets used in this paper are available at
pypi.org/project/Bellybuttonseg.Comment: 6 Pages 3 Figure
Describing astronomy identity of upper primary and middle school students through structural equation modeling
We describe how young students situate themselves with respect to astronomy through an identity framework that features four dimensions: interest, utility value, confidence, and conceptual knowledge. Overall, about 900 Italian students, from 5th to 9th grade (9-14 years old), were involved in the study. We tested our model using confirmatory factor analysis and structural equation modeling. Differences between girls and boys and across school levels were also investigated. Results show that interest has both a direct and an indirect effect on astronomy identity. The indirect effect of interest on identity is mediated by utility value. Moreover, confidence mediates the effect of interest on conceptual knowledge. Concerning differences between girls and boys, we found that the effect of interest on identity is greater for girls than for boys and that the utility value mediates the effect of interest on identity for boys but not for girls. Finally, our findings show also that the students' interest in astronomy and confidence in their performance decrease with age, with a potential negative impact on conceptual knowledge and future career choice in astronomy. The astronomy identity framework can be employed to examine the role of affective variables on performance and persistence in astronomy and to improve the design of teaching-learning activities that can potentially stimulate a lasting interest in astronomy
Design, synthesis and biological evaluation of novel bicyclo[1.1.1]pentane-basedx-acidic amino acids as glutamate receptors ligands
A novel series of bicyclo[1.1.1]pentane-based x-acidic amino acids, including (2S)- and (2R)-3-(30-carboxybicyclo[
1.1.1]pentyl)alanines (8 and 9), (2S)- and (2R)-2-(30-carboxymethylbicyclo[1.1.1]pentyl)glycines
(10 and 11), and (2S)- and (2R)-3-(30-phosphonomethylbicyclo[1.1.1]pentyl)glycines (12 and 13),
were synthesized and evaluated as glutamate receptor ligands. Among them, (2R)-3-(30-phosphonomethylbicyclo[
1.1.1]pentyl)glycine (13) showed relatively high affinity and selectivity at the NMDA
receptor. The results are also discussed in light of pharmacophoric modelling studies of NMDA agonists
and antagonists
Activated Random Walkers: Facts, Conjectures and Challenges
We study a particle system with hopping (random walk) dynamics on the integer
lattice . The particles can exist in two states, active or
inactive (sleeping); only the former can hop. The dynamics conserves the number
of particles; there is no limit on the number of particles at a given site.
Isolated active particles fall asleep at rate , and then remain
asleep until joined by another particle at the same site. The state in which
all particles are inactive is absorbing. Whether activity continues at long
times depends on the relation between the particle density and the
sleeping rate . We discuss the general case, and then, for the
one-dimensional totally asymmetric case, study the phase transition between an
active phase (for sufficiently large particle densities and/or small )
and an absorbing one. We also present arguments regarding the asymptotic mean
hopping velocity in the active phase, the rate of fixation in the absorbing
phase, and survival of the infinite system at criticality. Using mean-field
theory and Monte Carlo simulation, we locate the phase boundary. The phase
transition appears to be continuous in both the symmetric and asymmetric
versions of the process, but the critical behavior is very different. The
former case is characterized by simple integer or rational values for critical
exponents (, for example), and the phase diagram is in accord with
the prediction of mean-field theory. We present evidence that the symmetric
version belongs to the universality class of conserved stochastic sandpiles,
also known as conserved directed percolation. Simulations also reveal an
interesting transient phenomenon of damped oscillations in the activity
density
The physiological effects of hypobaric hypoxia versus normobaric hypoxia: a systematic review of crossover trials
Much hypoxia research has been carried out at high altitude in a hypobaric hypoxia (HH) environment. Many research teams seek to replicate high-altitude conditions at lower altitudes in either hypobaric hypoxic conditions or normobaric hypoxic (NH) laboratories. Implicit in this approach is the assumption that the only relevant condition that differs between these settings is the partial pressure of oxygen (PO2), which is commonly presumed to be the principal physiological stimulus to adaptation at high altitude. This systematic review is the first to present an overview of the current available literature regarding crossover studies relating to the different effects of HH and NH on human physiology. After applying our inclusion and exclusion criteria, 13 studies were deemed eligible for inclusion. Several studies reported a number of variables (e.g. minute ventilation and NO levels) that were different between the two conditions, lending support to the notion that true physiological difference is indeed present. However, the presence of confounding factors such as time spent in hypoxia, temperature, and humidity, and the limited statistical power due to small sample sizes, limit the conclusions that can be drawn from these findings. Standardisation of the study methods and reporting may aid interpretation of future studies and thereby improve the quality of data in this area. This is important to improve the quality of data that is used for improving the understanding of hypoxia tolerance, both at altitude and in the clinical setting
The role of resveratrol on skeletal muscle cell differentiation and myotube hypertrophy during glucose restriction
Glucose restriction (GR) impairs muscle cell differentiation and evokes myotube atrophy. Resveratrol treatment in skeletal
muscle cells improves inflammatory-induced reductions in skeletal muscle cell differentiation. We therefore hypothesised
that resveratrol treatment would improve muscle cell differentiation and myotube hypertrophy in differentiating C2C12
myoblasts and mature myotubes during GR. Glucose restriction at 0.6 g/L (3.3 mM) blocked differentiation and myotube
hypertrophy versus high-glucose (4.5 g/L or 25 mM) differentiation media (DM) conditions universally used for myoblast
culture. Resveratrol (10 μM) treatment increased SIRT1 phosphorylation in DM conditions, yet did not improve differentiation
when administered to differentiating myoblasts in GR conditions. Resveratrol did evoke increases in hypertrophy of mature
myotubes under DM conditions with corresponding elevated Igf-I and Myhc7 gene expression, coding for the ‘slow’ type I
MYHC protein isoform. Inhibition of SIRT1 via EX-527 administration (100 nM) also reduced myotube diameter and area
in DM conditions and resulted in lower gene expression of Myhc 1, 2 and 4 coding for ‘intermediate’ and ‘faster’ IIx, IIa
and IIb protein isoforms, respectively. Resveratrol treatment did not appear to modulate phosphorylation of energy-sensing
protein AMPK or protein translation initiator P70S6K. Importantly, in mature myotubes, resveratrol treatment was able to
ameliorate reduced myotube growth in GR conditions over an acute 24-h period, but not over 48–72 h. Overall, resveratrol
evoked myotube hypertrophy in DM conditions while favouring ‘slower’ Myhc gene expression and acutely ameliorated
impaired myotube growth observed during glucose restriction
Black hole thermodynamical entropy
As early as 1902, Gibbs pointed out that systems whose partition function
diverges, e.g. gravitation, lie outside the validity of the Boltzmann-Gibbs
(BG) theory. Consistently, since the pioneering Bekenstein-Hawking results,
physically meaningful evidence (e.g., the holographic principle) has
accumulated that the BG entropy of a black hole is
proportional to its area ( being a characteristic linear length), and
not to its volume . Similarly it exists the \emph{area law}, so named
because, for a wide class of strongly quantum-entangled -dimensional
systems, is proportional to if , and to if
, instead of being proportional to (). These results
violate the extensivity of the thermodynamical entropy of a -dimensional
system. This thermodynamical inconsistency disappears if we realize that the
thermodynamical entropy of such nonstandard systems is \emph{not} to be
identified with the BG {\it additive} entropy but with appropriately
generalized {\it nonadditive} entropies. Indeed, the celebrated usefulness of
the BG entropy is founded on hypothesis such as relatively weak probabilistic
correlations (and their connections to ergodicity, which by no means can be
assumed as a general rule of nature). Here we introduce a generalized entropy
which, for the Schwarzschild black hole and the area law, can solve the
thermodynamic puzzle.Comment: 7 pages, 2 figures. Accepted for publication in EPJ
The pathology of familial breast cancer: Immunohistochemistry and molecular analysis
Extensive studies of BRCA1- and BRCA2-associated breast tumours have been carried out in the few years since the identification of these familial breast cancer predisposing genes. The morphological studies suggest that BRCA1 tumours differ from BRCA2 tumours and from sporadic breast cancers. Recent progress in immunohistochemistry and molecular biology techniques has enabled in-depth investigation of molecular pathology of these tumours. Studies to date have investigated issues such as steroid hormone receptor expression, mutation status of tumour suppressor genes TP53 and c-erbB2, and expression profiles of cell cycle proteins p21, p27 and cyclin D(1). Despite relative paucity of data, strong evidence of unique biological characteristics of BRCA1-associated breast cancer is accumulating. BRCA1-associated tumours appear to show an increased frequency of TP53 mutations, frequent p53 protein stabilization and absence of imunoreactivity for steroid hormone receptors. Further studies of larger number of samples of both BRCA1- and BRCA2-associated tumours are necessary to clarify and confirm these observations
Efficient CRISPR/Cas9 genome editing in a salmonid fish cell line using a lentivirus delivery system
The present study was funded by were funded by the Biotechnology and Biological Sciences Research Council (BB/R008612/1, BB/S004343/1 to RH and RG; grant BB/R008973/1 to SM and CD) and the Institute Strategic Programme Grants (BBS/E/D/20002172, BBS/E/D/30002275 and BBS/E/D/10002070, to RH and RG). The funders had no roles in the study design, data collection and analysis, decision to publish or preparation of the manuscript.Peer reviewedPublisher PD
Exendin-4 Improves Steatohepatitis by Increasing Sirt1 Expression in High-Fat Diet-Induced Obese C57BL/6J Mice
The effects of exendin-4 on Sirt1 expression as a mechanism of reducing fatty liver have not been previously reported. Therefore, we investigated whether the beneficial effects of exendin-4 treatment on fatty liver are mediated via Sirt1 in high-fat (HF) diet-induced obese C57BL/6J mice and related cell culture models. Exendin-4 treatment decreased body weight, serum free fatty acid (FA), and triglyceride levels in HF-induced obese C57BL/6J mice. Histological analysis showed that exendin-4 reversed HF-induced hepatic accumulation of lipids and inflammation. Exendin-4 treatment increased mRNA and protein expression of Sirt1 and its downstream factor, AMPK, in vivo and also induced genes associated with FA oxidation and glucose metabolism. In addition, a significant increase in the hepatic expression of Lkb1 and Nampt mRNA was observed in exendin-4-treated groups. We also observed increased expression of phospho-Foxo1 and GLUT2, which are involved in hepatic glucose metabolism. In HepG2 and Huh7 cells, mRNA and protein expressions of GLP-1R were increased by exendin-4 treatment in a dose-dependent manner. Exendin-4 enhanced protein expression of Sirt1 and phospho-AMPKα in HepG2 cells treated with 0.4 mM palmitic acid. We also found that Sirt1 was an upstream regulator of AMPK in hepatocytes. A novel finding of this study was the observation that expression of GLP-1R is proportional to exendin-4 concentration and exendin-4 could attenuate fatty liver through activation of Sirt1
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