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result(s) for
"Matin, S."
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Earthquake-Induced Building-Damage Mapping Using Explainable AI (XAI)
by
Pradhan, Biswajeet
,
Matin, Sahar S.
in
building-damage mapping
,
explainable AI
,
feature analysis
2021
Building-damage mapping using remote sensing images plays a critical role in providing quick and accurate information for the first responders after major earthquakes. In recent years, there has been an increasing interest in generating post-earthquake building-damage maps automatically using different artificial intelligence (AI)-based frameworks. These frameworks in this domain are promising, yet not reliable for several reasons, including but not limited to the site-specific design of the methods, the lack of transparency in the AI-model, the lack of quality in the labelled image, and the use of irrelevant descriptor features in building the AI-model. Using explainable AI (XAI) can lead us to gain insight into identifying these limitations and therefore, to modify the training dataset and the model accordingly. This paper proposes the use of SHAP (Shapley additive explanation) to interpret the outputs of a multilayer perceptron (MLP)—a machine learning model—and analyse the impact of each feature descriptor included in the model for building-damage assessment to examine the reliability of the model. In this study, a post-event satellite image from the 2018 Palu earthquake was used. The results show that MLP can classify the collapsed and non-collapsed buildings with an overall accuracy of 84% after removing the redundant features. Further, spectral features are found to be more important than texture features in distinguishing the collapsed and non-collapsed buildings. Finally, we argue that constructing an explainable model would help to understand the model’s decision to classify the buildings as collapsed and non-collapsed and open avenues to build a transferable AI model.
Journal Article
Targeting MET and AXL overcomes resistance to sunitinib therapy in renal cell carcinoma
2016
Antiangiogenic therapy resistance occurs frequently in patients with metastatic renal cell carcinoma (RCC). The purpose of this study was to understand the mechanism of resistance to sunitinib, an antiangiogenic small molecule, and to exploit this mechanism therapeutically. We hypothesized that sunitinib-induced upregulation of the prometastatic MET and AXL receptors is associated with resistance to sunitinib and with more aggressive tumor behavior. In the present study, tissue microarrays containing sunitinib-treated and untreated RCC tissues were stained with MET and AXL antibodies. The low malignant RCC cell line 786-O was chronically treated with sunitinib and assayed for AXL, MET, epithelial–mesenchymal transition (EMT) protein expression and activation. Co-culture experiments were used to examine the effect of sunitinib pretreatment on endothelial cell growth. The effects of AXL and MET were evaluated in various cell-based models by short hairpin RNA or inhibition by cabozantinib, the multi-tyrosine kinases inhibitor that targets vascular endothelial growth factor receptor, MET and AXL. Xenograft mouse models tested the ability of cabozantinib to rescue sunitinib resistance. We demonstrated that increased AXL and MET expression was associated with inferior clinical outcome in patients. Chronic sunitinib treatment of RCC cell lines activated both AXL and MET, induced EMT-associated gene expression changes, including upregulation of Snail and β-catenin, and increased cell migration and invasion. Pretreatment with sunitinib enhanced angiogenesis in 786-0/human umbilical vein endothelial cell co-culture models. The suppression of AXL or MET expression and the inhibition of AXL and MET activation using cabozantinib both impaired chronic sunitinib treatment-induced prometastatic behavior in cell culture and rescued acquired resistance to sunitinib in xenograft models. In summary, chronic sunitinib treatment induces the activation of AXL and MET signaling and promotes prometastatic behavior and angiogenesis. The inhibition of AXL and MET activity may overcome resistance induced by prolonged sunitinib therapy in metastatic RCC.
Journal Article
Symmetry Breaking of B2N(−, 0, +): An Aspect of the Electric Potential and Atomic Charges
by
Moradiyeh, Nahid
,
Ahmadin, Hashem
,
Monajjemi, Majid
in
atomic charges
,
Boron Compounds - chemistry
,
Boron Nitride compounds
2015
In this study, the three forms of B2N(−, 0, +)—radical, anion and cation—have been compared in terms of electric potential and atomic charges, ESP, rather than the well-known cut of the potential energy surface (PES). We have realized that the double minimum of the BNB radical is related to the lack of the correct permutational symmetry of the wave function and charge distribution. The symmetry breaking (SB) for B2N(0, +) exhibits energy barrier in the region of (5–150) cm−1. The SB barrier goes through a dynamic change with no centrosymmetric form which depends on the wave function or charge distribution. In spite of A ˜ 2 Σ g + exited state, the B ˜ 2 ∏ g excited configuration contributes to the ground state ( B ˜ 2 ∏ g − X ˜ 2 Σ u + ) for forming radicals. The SB did not occur for the anion form (B2N(−)) in any electrostatic potential and charges distribution. Finally, we have modified the Columbic term of the Schrödinger equation to define the parameters “αα' and ββ'” in order to investigate the SBs subject.
Journal Article
MicroRNA profiling in clear cell renal cell carcinoma tissues potentially links tumorigenesis and recurrence with obesity
2017
Background:
Twenty to 40% localised RCC patients may experience recurrence after curative surgery. Limited miRNA predictors have been identified for ccRCC recurrence.
Methods:
Through a multi-phase study design, we analysed miRNAs in tissues obtained from 203 ccRCC patients. Paired
t
-test was used for tumour–normal comparisons and Cox regression model was performed to compute hazard ratios (HRs) and corresponding 95% CIs.
Results:
A 17-miRNA signature was identified that can concordantly classify >95% of tumour/adjacent normal samples. Significant enrichment was found as 6 out of 17 miRNAs were associated with obesity (binomial probability=0.001). Decreased levels of miR-204-5p and miR-139-5p were each associated with an approximately three-fold increased risk of recurrence (
P
<0.01). Risk score was generated based on expressions of miR-204-5p and miR-139-5p, and the trend test was significant in both discovery and validation sets (
P
for trend
<0.05). Striking MST reduction was observed for patients with a high-risk score (high
vs
low: discovery, 9.4
vs
>97.7 months; validation, 20.8
vs
>70.3 months). Expressions of miR-204-5p were also associated with body mass index (
β
=5.64,
P
<0.001). Significant inverse correlations were observed and validated between miR-204-5p and 13 obesity-related genes (
r
<0,
P
<0.01).
Conclusions:
We identified 17 miRNAs dysregulated in ccRCC tissues and showed that low expressions of miR-204-5p and miR-139-5p were associated with the higher risk of recurrence. The link between miR-204-5p and ccRCC recurrence may be partially mediated by regulating the expression of targeted obesity-related genes.
Journal Article
Composite Graphene-Containing Porous Materials from Carbon for Capacitive Deionization of Water
by
Khamizov, Ruslan Kh
,
Kurnosov, Dmitry A.
,
Ashurov, Matin S.
in
aerogel
,
capacitive deionization
,
Carbon - chemistry
2020
New techniques were developed for the synthesis of monolithic highly porous composite aerogels (hydrogels) from reduced graphene oxide and carbon nanotubes, as well as graphene-containing composites based on mesoporous activated carbon. Simple operations for hydrophilization of synthesized samples were proposed. New electrode materials for electrosorption and deionization of water were fabricated. The resulting materials were investigated and tested in electrochemical cells for membrane capacitive deionization (MCDI).
Journal Article
The effect of conjugated linoleic acid on oxidative stress and matrix metalloproteinases 2 and 9 in patients with COPD
by
Matin, Somaieh
,
Nemati, Ali
,
Rezagholizadeh, Lotfollah
in
Analysis
,
Antioxidants
,
Antioxidants (Nutrients)
2018
Natural antioxidants in foods may be used in prevention and treatment of oxidative stress and inflammation in COPD. Therefore, this study aimed to evaluate the effect of conjugated linoleic acid (CLA) supplement as natural antioxidants on oxidative stress levels, and MMP2 and MMP9 serum levels in COPD patients.
This clinical trial study was conducted on 90 (supplement group=45 and control group=45) COPD patients in Ardabil city, Iran, in 2015. After obtaining written consent, general information was collected from each patient using a validated and reliable questionnaire. Supplement group received 3.2 g of CLA and those in the control group were given 3.2 g of placebo for 6 weeks on a daily basis. Fasting blood samples were taken from all of the patients for testing of malondialdehyde (MDA), MMP2, and MMP9 levels at the beginning and end of the study. Data were analyzed using Kolmogorov-Smirnov test, independent samples
-test, paired sample
-test, chi-square test, and ANOVA.
There were no significant differences between the two groups with regard to mean age, smoking status, and serum level of MDA at the beginning of the study. In the supplement group, the serum level of MDA decreased significantly at the end of the 6th week compared to that in the beginning of the study (
=0.0004), while in the placebo group, the difference was found to be insignificant. The serum level of MMP9 decreased significantly in the supplement group, while in the placebo group its level increased significantly as compared to that at the beginning of the study (
<0.05). The serum levels of MMP2 indicated no significant differences between the two groups neither at the beginning nor at the end of the study.
These findings indicated that CLA supplementation may be helpful for COPD patients through inhibiting the production of oxidative stress and controlling MMP9 serum levels.
Journal Article
A Nano Catalyst of CoFe2o4@ B18N18 as a Novel Material
2017
In this work the properties of CoFe2O4@ B18N18have been illustrated as a novel catalyst to compare with well-known catalyst “Fe3O4@Silica”.It has been shown that CoFe2O4 magnetite particle can be use as important catalyst inside the B18N18 ring. In our previous papers amazing result about the BnNn properties have been calculated, exhibited (Struct.Chem., 23, 551-580, (2012); J. Phys. Chem A, 117, 1670-1684, (2013); J. Phys. Chem. C, 114, 15315,(2010)and discussed. In present work it has been shown there is a non-covalent attraction between CoFe2O4 and B18N18 coated molecules. In the system of CoFe2O4@B18N18 catalyst, the magnetic nanoparticles (MNPs)as a core part causes important change in the electronic structure of B18N18 as a shell which some compounds are specific-sensitive functional groups for this system such as OH, CHO,NH2 and were subjected to the some organic reaction.The Physical-chemistry properties such asenergy densities, potential energy densities, electron densities, ELF, LOL,eta index, ellipticity of electron density and ECPforCoFe2O4@ B18N18 shell have been calculated and simulated in related reactions for those groups-functionalized. Our Calculation indicates that the B18N18 is much better surfaces for CoFe2O4 rather than silica surfaces.
Journal Article
Automated Bone Segmentation and Surface Evaluation of a Small Animal Model of Post-Traumatic Osteoarthritis
by
Coughlin, Thomas R.
,
Lendhey, Matin S.
,
Kennedy, Oran D.
in
Animal models
,
Animals
,
Automation
2017
MicroCT imaging allows for noninvasive microstructural evaluation of mineralized bone tissue, and is essential in studies of small animal models of bone and joint diseases. Automatic segmentation and evaluation of articular surfaces is challenging. Here, we present a novel method to create knee joint surface models, for the evaluation of PTOA-related joint changes in the rat using an atlas-based diffeomorphic registration to automatically isolate bone from surrounding tissues. As validation, two independent raters manually segment datasets and the resulting segmentations were compared to our novel automatic segmentation process. Data were evaluated using label map volumes, overlap metrics, Euclidean distance mapping, and a time trial. Intraclass correlation coefficients were calculated to compare methods, and were greater than 0.90. Total overlap, union overlap, and mean overlap were calculated to compare the automatic and manual methods and ranged from 0.85 to 0.99. A Euclidean distance comparison was also performed and showed no measurable difference between manual and automatic segmentations. Furthermore, our new method was 18 times faster than manual segmentation. Overall, this study describes a reliable, accurate, and automatic segmentation method for mineralized knee structures from microCT images, and will allow for efficient assessment of bony changes in small animal models of PTOA.
Journal Article
The effect of conjugated linoleic acid supplementation on the nutritional status of COPD patients
2016
COPD patients are susceptible to anorexia, reduction of caloric intake, weight loss, and malnutrition. One of the possible mechanisms is the increase of inflammatory markers such as interleukin 1β (IL
), is highly correlated with anorexia. Considering the anti-inflammatory role of conjugated linoleic acid (CLA), this study aimed to investigate the effect of CLA supplementation on the nutritional status of COPD patients.
In a double-blind clinical trial, 93 COPD patients who volunteered to participate in the study and who filled out a written consent form, were randomly assigned to control or supplementation groups. The patients in the supplementation group received 3.2 g of CLA on a daily basis for 6 weeks, while those in the control group received placebo on a daily basis for 6 weeks. For IL
assessment, the patients' anthropometric indices and appetite score were checked and their blood samples were collected both before and after the treatment. Moreover, in order to investigate the changes in the caloric intake trend during the study, their dietary intake levels were assessed using 24-hour dietary recall, 3 days a week at the onset, in the 4th week, and at the end of the study. Eventually, 90 patients completed the study.
The results demonstrated a significant increase in appetite score (
=0.001), average caloric intake (
=0.01), and macronutrient intake (
<0.05), while a significant decrease was observed in the serum level of IL
among the patients of the supplementation group (
=0.008). Meanwhile, although the supplementation group's body mass index was also higher on completion, compared to their own initial state as well as to that in the control group, the differences were not significant (
=0.13).
The findings of this research indicate that the consumption of CLA supplementation can be effective in regulating the appetite and improving the nutritional status of patients suffering from COPD through adjusting the serum level of IL
.
Journal Article
Predicted distribution of High Nature Value farmland in the Republic of Ireland
by
Sullivan, C. A.
,
Green, S.
,
Ó hUallacháin, D.
in
Agricultural land
,
Biodiversity
,
Conservation
2016
High Nature Value (HNV) farmland is typically characterised by low-intensity farming associated with high biodiversity and species of conservation concern. Mapping the occurrence and distribution of such farmland are useful for appropriate targeting of conservation measures and supporting associated rural communities. We mapped the likely distribution of HNV farmland in the Republic of Ireland using a linear regression model incorporating established European indicators, adapted for Ireland and weightings based on expert opinion. The indicators used were semi-natural habitat cover, stocking density, hedgerow density, river and stream density and soil diversity, with highest weightings placed on the first two indicators (40% and 30%, respectively). The map provides information on the likely occurrence and distribution of HNV farmland in each electoral division as a reference point for future monitoring of the distribution of HNV farmland in the Republic of Ireland in order to assist with planning and policy development for the rural environment.
Journal Article