Microsecond molecular dynamics simulations revealed the inhibitory potency of amiloride analogs against SARS-CoV-2 E viroporin

Jaber, Abdullah All,Chowdhury, Zeshan Mahmud,Bhattacharjee, Arittra,Mourin, Muntahi,Keya, Chaman Ara,Bhuyan, Zaied Ahmed Korea Genome Organization 2021 Genomics & informatics Vol.19 No.4

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) encodes small envelope protein (E) that plays a major role in viral assembly, release, pathogenesis, and host inflammation. Previous studies demonstrated that pyrazine ring containing amiloride analogs inhibit this protein in different types of coronavirus including SARS-CoV-1 small envelope protein E (SARS-CoV-1 E). SARS-CoV-1 E has 93.42% sequence identity with SARS-CoV-2 E and shared a conserved domain NS3/small envelope protein (NS3_envE). Amiloride analog hexamethylene amiloride (HMA) can inhibit SARS-CoV-1 E. Therefore, we performed molecular docking and dynamics simulations to explore whether amiloride analogs are effective in inhibiting SARS-CoV-2 E. To do so, SARS-CoV-1 E and SARS-CoV-2 E proteins were taken as receptors while HMA and 3-amino-5-(azepan-1-yl)-N-(diaminomethylidene)-6-pyrimidin-5-ylpyrazine-2-carboxamide (3A5NP2C) were selected as ligands. Molecular docking simulation showed higher binding affinity scores of HMA and 3A5NP2C for SARS-CoV-2 E than SARS-CoV-1 E. Moreover, HMA and 3A5NP2C engaged more amino acids in SARS-CoV-2 E. Molecular dynamics simulation for 1 ㎲ (1,000 ns) revealed that these ligands could alter the native structure of the proteins and their flexibility. Our study suggests that suitable amiloride analogs might yield a prospective drug against coronavirus disease 2019.

The Three-Bite Technique: A Novel Method of Dog Ear Correction

Jaber, Omar,Vischio, Marta,Faga, Angela,Nicoletti, Giovanni Korean Society of Plastic and Reconstructive Surge 2015 Archives of Plastic Surgery Vol.42 No.2

The closure of any circular or asymmetric wound can result in puckering or an excess of tissue known as a 'dog ear'. Understanding the mechanism of dog ear formation is a fundamental requirement necessary to facilitate an appropriate treatment. Many solutions have been reported in the literature, but in all cases, the correction entails the extension of the scar and the sacrifice of the dermal plexus. Here, we propose a novel technique of dog ear correction by using a three-bite suture that sequentially pierces the deep fascial plane and each dog ear's margin, thus allowing for flattening the dog ear by anchoring the over-projecting tissue to the deep plane. The three-bite technique proved to be a fast, easy, and versatile method of immediate dog ear correction without extending the scar, while maintaining a full and complete local skin blood supply.

Contrasting changes in the abundance and diversity of Northern Iranian birds assemblages from 2011 to 2015

Jaber Aazami,RamazanAli Nafar 국립중앙과학관 2018 Journal of Asia-Pacific Biodiversity Vol.11 No.3

Birds are distributed in wide range based on flight power and structural changes in their composition. So, the ecological diversity and density can be indicative of the environmental changes. This study was conducted for the first time in the north of Iran to quantify and compare the temporal abundance in the taxonomic diversity of bird assemblages. Data were collected by the Iranian Environmental Protection Agency from 22 key sampling sites from 2011 to 2015 in Golestan Province. During the 5-years period, 13 abundance and diversity metrics with the average abundances of 123 species for each site were calculated. In terms of the number of birds in a particular species, mallard and greater flamingo were the most abundant species, and Anatidae family was the most abundant bird family in all monitoring data. Based on ecological indicators, the most diversity in species has been observed in 2012.

MPPT Control and Architecture for PV Solar Panel with Sub-Module Integrated Converters

Jaber A. Abu Qahouq,Yuncong Jiang,Mohamed Orabi 전력전자학회 2014 JOURNAL OF POWER ELECTRONICS Vol.14 No.6

Photovoltaic (PV) solar systems with series-connected module integrated converters (MICs) are receiving increased attention because of their ability to create high output voltage while performing local maximum power point tracking (MPPT) control for individual solar panels, which is a solution for partial shading effects in PV systems at panel level. To eliminate the partial shading effects in PV system more effectively, sub-MICs are utilized at the cell level or grouped cell level within a PV solar panel. This study presents the results of a series-output-connection MPPT (SOC-MPPT) controller for sub-MIC architecture using a single sensor at the output and a single digital MPPT controller (sub-MIC SOC-MPPT controller and architecture). The sub-MIC SOC-MPPT controller and architecture are investigated based on boost type sub-MICs. Experimental results under steady-state and transient conditions are presented to verify the performance of the controller and the effectiveness of the architecture.

Modified Digital Pulse Width Modulator for Power Converters with a Reduced Modulation Delay

Jaber Abu Qahouq,VaraPrasad Arikatla,Thanukamalam Arunachalam 전력전자학회 2012 JOURNAL OF POWER ELECTRONICS Vol.12 No.1

This paper presents a digital pulse width modulator (DPWM) with a reduced digital modulation delay (a transport delay of the modulator) during the transient response of power converters. During the transient response operation of a power converter, as a result of dynamic variations such as load step-up or step-down, the closed loop controller will continuously adjust the duty cycle in order to regulate the output voltage. The larger the modulation delays, the larger the undesired output voltage deviation from the reference point. The three conventional DPWM techniques exhibit significant leading-edge and/or trailing-edge modulation delays. The DPWM technique proposed in this paper, which results in modulation delay reductions, is discussed, experimentally tested and compared with conventional modulation techniques.

Molecular flows through nanopore: can we use continuum approach

Jaber Al Hossain,김보흥 대한기계학회 2023 대한기계학회 춘추학술대회 Vol.2023 No.5

Safety and Efficacy of an Intensified and Repeated Transcranial Direct Current Stimulation Targeting Supplementary Motor Area and Dorsolateral Prefrontal Cortex in Trichotillomania (Hair Pulling Disorder): A Case Report

Jaber Alizadehgoradel,Asghar Pouresmali,Mina Taherifard 대한정신약물학회 2024 CLINICAL PSYCHOPHARMACOLOGY AND NEUROSCIENCE Vol.22 No.1

Trichotillomania (or hair pulling disorder) is a habitual condition in which patients constantly pull their hair. Although psychotherapies such as behavioral therapy and pharmacotherapy have shown relative effectiveness for trichotillomania, some patients fail to respond to these interventions or show only partial responses. Recently, noninvasive brain stimulation techniques such as transcranial direct current stimulation have shown promise in the treatment of psychiatric disorders. We designed a new protocol that included intensified and repeated during 16 sessions, every other day, 2 sessions one day, current intensity of 2 mA for 20 minutes, which regions dorsolateral prefrontal cortex (DLPFC) and supplementary motor area (SMA): Anodal (F3) and cathodal (SMA) were selected as stimulation target areas. The results showed that after the electrical stimulation intervention and also in the follow-up phase, there was a significant improvement in hair pulling behavior and psychiatric evaluations such as depression and anxiety. Therefore, there are many hopes in the effectiveness of the protocol used (intensified and repeated DLPFC and SMA areas) in the treatment of trichotillomania disorder, although there is a need for a future experimental study with a larger group of patients.

Genome-Wide Characterization and Expression Profiling of Plant-Specific PLATZ Transcription Factor Family Genes in Brassica rapa L.

Jaber Bin Azim,Md. Fahim Hassan Khan,Lutful Hassan,Arif Hasan Khan Robin 한국육종학회 2020 Plant Breeding and Biotechnology Vol.8 No.1

Plant AT-rich sequence and zinc-binding (PLATZ) proteins constitute a plant-specific transcription factor family with two conserved zinc-dependent DNA-binding domains. The PLATZ proteins operate significant functions in regulating plant development and resistance. To date, PLATZ genes have been studied only in a few model plants, including Arabidopsis, rice, maize and soybean, but not yet in any Brassica species. We identified 24 Brassica rapa PLATZ gene family (BrPLATZ) genes through genome-wide characterization and profiled their expression using available RNA-Sequencing data. We divided 153 PLATZ proteins from eight plant species into seven groups based on sequence alignment and phylogeny. The BrPLATZ genes were generally conserved in groups with similar motif and exon-intron distribution. The 24 BrPLATZ genes were located in eight of the ten B. rapa chromosomes, with segmental duplication detected in 20 paralogs. Analysis of Ka/Ks ratios revealed that the duplicated genes were under purifying selection. Cis-elements analysis implied that BrPLATZ genes are diverse in functions including tissue-specific, stress and hormone responsive expressions. Furthermore, expression profiling based on RNA-sequencing data revealed that the BrPLATZ genes were expressed in various tissues, with most genes preferentially expressed in flower and silique compared to other tissues. Systematic analysis revealed structural and functional diversity among BrPLATZ proteins, which indicated the possibility of diverse functions of BrPLATZ genes in development and stress resistance. The characterization of PLATZ gene family members may aid in the selection of appropriate candidate genes responsible for biological functions in B. rapa and relevant species.

Comparative evaluation of statistically downscaling Tropical Rainfall Measuring Mission (TRMM) and Global Precipitation Measurement (GPM) mission precipitation data: evidence from a typical semi-arid to arid environment

Jaber Salahuddin M. 대한공간정보학회 2021 Spatial Information Research Vol.29 No.3

This study aimed at comparing the performance of statistically downscaling Tropical Rainfall Measuring Mission (TRMM) 3B43 Version 7 and Global Precipitation Measurement (GPM) 3IMERGM Version 6 precipitation data from 25 km and 10 km resolutions, respectively, to 1 km resolution using Moderate Resolution Imaging Spectroradiometer (MODIS) MOD13A3 Version 6 Normalized Difference Vegetation Index (NDVI) data. Simple linear regression (SLR) and geographically weighted regression (GWR) were applied in a typical semi-arid to arid country—Jordan—using data for the year 2015. It was observed that all statistically downscaled outputs exhibited almost similar spatial distribution patterns. These patterns captured the typical decreasing behavior of precipitation in the country from northwest to south and east. They also provided more spatial detail of precipitation information than their raw counterparts. Unscaled and scaled validation measures of bias, precision, and accuracy relied on precipitation data for the year 2015 obtained from 137 rain gauges distributed all over the country revealed that: (1) GWR produced better results than SLR, (2) statistically downscaling GPM 3IMERGM Version 6 precipitation data outperformed statistically downscaling TRMM 3B43 Version 7 precipitation data, and (3) although, all statistically downscaled precipitation outputs overestimated rain gauge precipitation data, this overestimation was larger in the statistically downscaled TRMM 3B43 Version 7 precipitation outputs than in the statistically downscaled GPM 3IMERGM Version 6 precipitation outputs.

Improved Executive Functions and Reduced Craving in Youths with Methamphetamine Addiction: Evidence from Combined Transcranial Direct Current Stimulation with Mindfulness Treatment

Jaber Alizadehgoradel,Saeed Imani,Vahid Nejati,Marie-Anne Vanderhasselt,Behnam Molaei,Mohammad Ali Salehinejad,Shirin Ahmadi,Mina Taherifard 대한정신약물학회 2021 CLINICAL PSYCHOPHARMACOLOGY AND NEUROSCIENCE Vol.19 No.4

Objective: Transcranial direct current stimulation (tDCS) and mindfulness practices have been proposed as a potential approach to improve executive functions (EFs) and reduce craving in persons with substance use disorders. Based on the neural mechanisms of action of each of these interventions, the combination of both non-pharmacological interventions might have additive effects. In the current study, the effects of tDCS combined with mindfulness-based substance abuse treatment (MBSAT) to improve EFs and reduce craving were investigated in early abstinent methamphetamine abuse. Methods: Eighty (youths aged between 18 and 21) early-abstinent methamphetamine users were randomly assigned to the research groups (tDCS group [n = 20], mindfulness group [n = 20], combined mindfulness-tDCS group [n = 20], and sham group [n = 20]). Active tDCS (1.5 mA,20 min, 12 sessions) or sham tDCS was appliedover the left dorsolateral prefrontal cortex and the MBSAT protocol was used over twelve 50-min sessions. Results: Both in the post-test phase (immediately after the intervention) and follow-up phase (one month after the intervention), performance in most EFs tasks significantly improved in the combination group which received real tDCS + MBSAT, as compared to baseline values and sham stimulation group. Similarly, a significant reduction in craving was observed after intervention inall treatment groups, but not the sham stimulation group. Interestingly, the increase in EFs and the reduction in craving post versus pre tDCS + MBSAT intervention were correlated. Conclusion: Findings from the current study provide initial support for the clinical effectiveness of combination tDCS + MBSAT, possibly influencing cognitive/affective processes.