116 research outputs found
Automated Measurement of Vascular Calcification in Femoral Endarterectomy Patients Using Deep Learning
Atherosclerosis, a chronic inflammatory disease affecting the large arteries,
presents a global health risk. Accurate analysis of diagnostic images, like
computed tomographic angiograms (CTAs), is essential for staging and monitoring
the progression of atherosclerosis-related conditions, including peripheral
arterial disease (PAD). However, manual analysis of CTA images is
time-consuming and tedious. To address this limitation, we employed a deep
learning model to segment the vascular system in CTA images of PAD patients
undergoing femoral endarterectomy surgery and to measure vascular calcification
from the left renal artery to the patella. Utilizing proprietary CTA images of
27 patients undergoing femoral endarterectomy surgery provided by Prisma Health
Midlands, we developed a Deep Neural Network (DNN) model to first segment the
arterial system, starting from the descending aorta to the patella, and second,
to provide a metric of arterial calcification. Our designed DNN achieved 83.4%
average Dice accuracy in segmenting arteries from aorta to patella, advancing
the state-of-the-art by 0.8%. Furthermore, our work is the first to present a
robust statistical analysis of automated calcification measurement in the lower
extremities using deep learning, attaining a Mean Absolute Percentage Error
(MAPE) of 9.5% and a correlation coefficient of 0.978 between automated and
manual calcification scores. These findings underscore the potential of deep
learning techniques as a rapid and accurate tool for medical professionals to
assess calcification in the abdominal aorta and its branches above the patella.
The developed DNN model and related documentation in this project are available
at GitHub page at https://github.com/pip-alireza/DeepCalcScoring.Comment: Published in MDPI Diagnostic journal, the code can be accessed via
the GitHub link in the pape
Singularity Free (Homogeneous Isotropic) Universe in Graviton-Dilaton Models
We present a class of graviton-dilaton models in which a homogeneous
isotropic universe, such as our observed one, evolves with no singularity at
any time. Such models may stand on their own as interesting models for
singularity free cosmology, and may be studied further accordingly. They may
also arise from string theory. We discuss critically a few such possibilities.Comment: 11 pages. Latex file. Revised in response to referees' Comments.
Results remain same. To appear in Phys. Rev. Let
TransONet: Automatic Segmentation of Vasculature in Computed Tomographic Angiograms Using Deep Learning
Pathological alterations in the human vascular system underlie many chronic
diseases, such as atherosclerosis and aneurysms. However, manually analyzing
diagnostic images of the vascular system, such as computed tomographic
angiograms (CTAs) is a time-consuming and tedious process. To address this
issue, we propose a deep learning model to segment the vascular system in CTA
images of patients undergoing surgery for peripheral arterial disease (PAD).
Our study focused on accurately segmenting the vascular system (1) from the
descending thoracic aorta to the iliac bifurcation and (2) from the descending
thoracic aorta to the knees in CTA images using deep learning techniques. Our
approach achieved average Dice accuracies of 93.5% and 80.64% in test dataset
for (1) and (2), respectively, highlighting its high accuracy and potential
clinical utility. These findings demonstrate the use of deep learning
techniques as a valuable tool for medical professionals to analyze the health
of the vascular system efficiently and accurately. Please visit the GitHub page
for this paper at https://github.com/pip-alireza/TransOnet.Comment: Accepted for the 2023 International Conference on Computational
Science and Computational Intelligence (CSCI), Las Vegas, US
Statistical Mechanical Theory of a Closed Oscillating Universe
Based on Newton's laws reformulated in the Hamiltonian dynamics combined with
statistical mechanics, we formulate a statistical mechanical theory supporting
the hypothesis of a closed oscillating universe. We find that the behaviour of
the universe as a whole can be represented by a free entropic oscillator whose
lifespan is nonhomogeneous, thus implying that time is shorter or longer
according to the state of the universe itself given through its entropy. We
conclude that time reduces to the entropy production of the universe and that a
nonzero entropy production means that local fluctuations could exist giving
rise to the appearance of masses and to the curvature of the space
Energy-Momentum Localization for a Space-Time Geometry Exterior to a Black Hole in the Brane World
In general relativity one of the most fundamental issues consists in defining
a generally acceptable definition for the energy-momentum density. As a
consequence, many coordinate-dependent definitions have been presented, whereby
some of them utilize appropriate energy-momentum complexes. We investigate the
energy-momentum distribution for a metric exterior to a spherically symmetric
black hole in the brane world by applying the Landau-Lifshitz and Weinberg
prescriptions. In both the aforesaid prescriptions, the energy thus obtained
depends on the radial coordinate, the mass of the black hole and a parameter
, while all the momenta are found to be zero. It is shown that for
a special value of the parameter , the Schwarzschild space-time
geometry is recovered. Some particular and limiting cases are also discussed.Comment: 10 pages, sections 1 and 3 slightly modified, references modified and
adde
On the energy of charged black holes in generalized dilaton-axion gravity
In this paper we calculate the energy distribution of some charged black
holes in generalized dilaton-axion gravity. The solutions correspond to charged
black holes arising in a Kalb-Ramond-dilaton background and some existing
non-rotating black hole solutions are recovered in special cases. We focus our
study to asymptotically flat and asymptotically non-flat types of solutions and
resort for this purpose to the M{\o}ller prescription. Various aspects of
energy are also analyzed.Comment: LaTe
Trans-Translation in Helicobacter pylori: Essentiality of Ribosome Rescue and Requirement of Protein Tagging for Stress Resistance and Competence
BACKGROUND: The ubiquitous bacterial trans-translation is one of the most studied quality control mechanisms. Trans-translation requires two specific factors, a small RNA SsrA (tmRNA) and a protein co-factor SmpB, to promote the release of ribosomes stalled on defective mRNAs and to add a specific tag sequence to aberrant polypeptides to direct them to degradation pathways. Helicobacter pylori is a pathogen persistently colonizing a hostile niche, the stomach of humans. PRINCIPAL FINDINGS: We investigated the role of trans-translation in this bacterium well fitted to resist stressful conditions and found that both smpB and ssrA were essential genes. Five mutant versions of ssrA were generated in H. pylori in order to investigate the function of trans-translation in this organism. Mutation of the resume codon that allows the switch of template of the ribosome required for its release was essential in vivo, however a mutant in which this codon was followed by stop codons interrupting the tag sequence was viable. Therefore one round of translation is sufficient to promote the rescue of stalled ribosomes. A mutant expressing a truncated SsrA tag was viable in H. pylori, but affected in competence and tolerance to both oxidative and antibiotic stresses. This demonstrates that control of protein degradation through trans-translation is by itself central in the management of stress conditions and of competence and supports a regulatory role of trans-translation-dependent protein tagging. In addition, the expression of smpB and ssrA was found to be induced upon acid exposure of H. pylori. CONCLUSIONS: We conclude to a central role of trans-translation in H. pylori both for ribosome rescue possibly due to more severe stalling and for protein degradation to recover from stress conditions frequently encountered in the gastric environment. Finally, the essential trans-translation machinery of H. pylori is an excellent specific target for the development of novel antibiotics
Energy Distribution for Non-commutative Radiating Schwarzschild Black Holes
The aim of this article is the calculation of the energy-momentum for a
non-commutative radiating Schwarzschild black hole in order to obtain the
expressions for energy. We make the calculations with the Einstein and M\oller
prescriptions. We show that the expressions for energy in both the
prescriptions depend on the mass , parameter and radial coordinate.
We make some comparisons between the results. Our results show that the
Einstein prescription is a more powerful concept than the M\oller prescription.Comment: 5 pages and 6 figures. Revised version submitted in Int.J.Theor.Phys.
after minor revisio
Integrated transcriptomic and proteomic analysis of the global response of Wolbachia to doxycycline-induced stress
The bacterium Wolbachia (order Rickettsiales), representing perhaps the most abundant vertically transmitted microbe worldwide, infects arthropods and filarial nematodes. In arthropods, Wolbachia can induce reproductive alterations and interfere with the transmission of several arthropod-borne pathogens. In addition, Wolbachia is an obligate mutualist of the filarial parasites that cause lymphatic filariasis and onchocerciasis in the tropics. Targeting Wolbachia with tetracycline antibiotics leads to sterilisation and ultimately death of adult filariae. However, several weeks of treatment are required, restricting the implementation of this control strategy. To date, the response of Wolbachia to stress has not been investigated, and almost nothing is known about global regulation of gene expression in this organism. We exposed an arthropod Wolbachia strain to doxycycline in vitro, and analysed differential expression by directional RNA-seq and label-free, quantitative proteomics. We found that Wolbachia responded not only by modulating expression of the translation machinery, but also by upregulating nucleotide synthesis and energy metabolism, while downregulating outer membrane proteins. Moreover, Wolbachia increased the expression of a key component of the twin-arginine translocase (tatA) and a phosphate ABC transporter ATPase (PstB); the latter is associated with decreased susceptibility to antimicrobials in free-living bacteria. Finally, the downregulation of 6S RNA during translational inhibition suggests that this small RNA is involved in growth rate control. Despite its highly reduced genome, Wolbachia shows a surprising ability to regulate gene expression during exposure to a potent stressor. Our findings have general relevance for the chemotherapy of obligate intracellular bacteria and the mechanistic basis of persistence in the Rickettsiales
Cancer metabolism: current perspectives and future directions
Cellular metabolism influences life and death decisions. An emerging theme in cancer biology is that metabolic regulation is intricately linked to cancer progression. In part, this is due to the fact that proliferation is tightly regulated by availability of nutrients. Mitogenic signals promote nutrient uptake and synthesis of DNA, RNA, proteins and lipids. Therefore, it seems straight-forward that oncogenes, that often promote proliferation, also promote metabolic changes. In this review we summarize our current understanding of how ‘metabolic transformation' is linked to oncogenic transformation, and why inhibition of metabolism may prove a cancer′s ‘Achilles' heel'. On one hand, mutation of metabolic enzymes and metabolic stress sensors confers synthetic lethality with inhibitors of metabolism. On the other hand, hyperactivation of oncogenic pathways makes tumors more susceptible to metabolic inhibition. Conversely, an adequate nutrient supply and active metabolism regulates Bcl-2 family proteins and inhibits susceptibility to apoptosis. Here, we provide an overview of the metabolic pathways that represent anti-cancer targets and the cell death pathways engaged by metabolic inhibitors. Additionally, we will detail the similarities between metabolism of cancer cells and metabolism of proliferating cells
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