Publications by authors named "Muhammad Arif"

390 Publications

Brain Tumor Detection and Classification by MRI Using Biologically Inspired Orthogonal Wavelet Transform and Deep Learning Techniques.

J Healthc Eng 2022 10;2022:2693621. Epub 2022 Jan 10.

Faculty of Electrical Engineering and Computer Science, Stefan cel Mare University of Suceava, Suceava, Romania.

Radiology is a broad subject that needs more knowledge and understanding of medical science to identify tumors accurately. The need for a tumor detection program, thus, overcomes the lack of qualified radiologists. Using magnetic resonance imaging, biomedical image processing makes it easier to detect and locate brain tumors. In this study, a segmentation and detection method for brain tumors was developed using images from the MRI sequence as an input image to identify the tumor area. This process is difficult due to the wide variety of tumor tissues in the presence of different patients, and, in most cases, the similarity within normal tissues makes the task difficult. The main goal is to classify the brain in the presence of a brain tumor or a healthy brain. The proposed system has been researched based on Berkeley's wavelet transformation (BWT) and deep learning classifier to improve performance and simplify the process of medical image segmentation. Significant features are extracted from each segmented tissue using the gray-level-co-occurrence matrix (GLCM) method, followed by a feature optimization using a genetic algorithm. The innovative final result of the approach implemented was assessed based on accuracy, sensitivity, specificity, coefficient of dice, Jaccard's coefficient, spatial overlap, AVME, and FoM.
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http://dx.doi.org/10.1155/2022/2693621DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8763556PMC
January 2022

Coal fines migration: A holistic review of influencing factors.

Adv Colloid Interface Sci 2021 Dec 29;301:102595. Epub 2021 Dec 29.

Petroleum Engineering Discipline, School of Engineering, Edith Cowan University, 270 Joondalup Dr, Joondalup 6027, WA, Australia; Centre for Sustainable Energy and Resources, Edith Cowan University, 270 Joondalup Drive, Joondalup 6027, Western Australia, Australia.

Coal fines can substantially influence coal seam gas reservoir permeability, thus impeding the flow of gas in coal microstructure. The coal fines generation and migration are influenced by several factors, wherein coal fines are generally hydrophobic and aggregate in natural coal seam gas (CSG) under prevailing conditions of pH, salinity, temperature and pressure. This aggregation behaviour can damage the coal matrix and cleat system permeabilities, leading to a considerable reduction of proppant pack conductivity (i.e. fracture conductivity). Several datasets have been reported within the literature on this subject in the last decade. However, a more up-to-date discussion of this area is key to understanding coal fines migration and associated knowledge. Thus, in this review, we conduct a systematic investigation of coal fines and their influencing factors. Here, coal fines are introduced, followed by an initial holistic investigation of their generation, plugging, movement, redistribution and production. Then, in order to enhance current understandings of the subject matter, a parametric evaluation of the factors noted earlier is conducted, based on recently published literature. Subsequently, the published mathematical and analytical models for fines generation are reviewed. Finally, the implications and challenges associated with coal fines mitigation are discussed.
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http://dx.doi.org/10.1016/j.cis.2021.102595DOI Listing
December 2021

Preparation, urease inhibition mechanisms, and anti- activities of hesperetin-7-rhamnoglucoside.

Curr Res Microb Sci 2022 29;3:100103. Epub 2021 Dec 29.

Department of Biochemistry and Molecular Biology, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, PR China.

This work investigated the effects of the bioflavonoid hesperetin-7-rhamnoglucoside isolated from fruit peel on (). Separation and purity, crystalline state, and urease inhibition assays were carried out. Then, molecular docking and molecular dynamics (MD) simulations were conducted with urease as the target protein. Hesp was isolated from citrus peel with a purity of 95.14 µg mg of dry raw material. X-ray diffraction analysis, hydrogen-1 nuclear magnetic resonance, Fourier transform infrared spectroscopy, and differential scanning calorimetry revealed that pure Hesp had the same crystallinity rating as the Hesp standard. The kinetic inhibition study demonstrated that Hesp inhibited urease in a competitive and concentration-dependent manner with jack bean urease. In addition, bioimaging studies with laser scanning confocal microscopy and scanning electron microscopy illustrated that Hesp interacted with bacterial cells and induced membrane disruption by creating holes in the outer membranes of the bacterial cells, resulting in the leakage of amino acids. Importantly, molecular docking and 20 ns MD simulations revealed that Hesp inhibited the target protein through slow-binding inhibition and hydrogen bond interactions with active site residues, namely, Gly11 (O⋯H distance = 2.2 Å), Gly13 (O⋯H distance = 2.4 Å), Ser12 (O⋯H distance = 3.3 Å), Lys14 (O⋯H distance = 3.3 Å), and Arg179 (O⋯H distance = 2.7 Å). This work presents novel anti- agents from natural sources.
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http://dx.doi.org/10.1016/j.crmicr.2021.100103DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8732090PMC
December 2021

Classification of Clinically Significant Prostate Cancer on Multi-Parametric MRI: A Validation Study Comparing Deep Learning and Radiomics.

Cancers (Basel) 2021 Dec 21;14(1). Epub 2021 Dec 21.

Department of Radiology and Nuclear Medicine, Erasmus MC, 3015 GD Rotterdam, The Netherlands.

The computer-aided analysis of prostate multiparametric MRI (mpMRI) could improve significant-prostate-cancer (PCa) detection. Various deep-learning- and radiomics-based methods for significant-PCa segmentation or classification have been reported in the literature. To be able to assess the generalizability of the performance of these methods, using various external data sets is crucial. While both deep-learning and radiomics approaches have been compared based on the same data set of one center, the comparison of the performances of both approaches on various data sets from different centers and different scanners is lacking. The goal of this study was to compare the performance of a deep-learning model with the performance of a radiomics model for the significant-PCa diagnosis of the cohorts of various patients. We included the data from two consecutive patient cohorts from our own center ( = 371 patients), and two external sets of which one was a publicly available patient cohort ( = 195 patients) and the other contained data from patients from two hospitals ( = 79 patients). Using multiparametric MRI (mpMRI), the radiologist tumor delineations and pathology reports were collected for all patients. During training, one of our patient cohorts ( = 271 patients) was used for both the deep-learning- and radiomics-model development, and the three remaining cohorts ( = 374 patients) were kept as unseen test sets. The performances of the models were assessed in terms of their area under the receiver-operating-characteristic curve (AUC). Whereas the internal cross-validation showed a higher AUC for the deep-learning approach, the radiomics model obtained AUCs of 0.88, 0.91 and 0.65 on the independent test sets compared to AUCs of 0.70, 0.73 and 0.44 for the deep-learning model. Our radiomics model that was based on delineated regions resulted in a more accurate tool for significant-PCa classification in the three unseen test sets when compared to a fully automated deep-learning model.
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http://dx.doi.org/10.3390/cancers14010012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8749796PMC
December 2021

Development of an Probe to Track SARS-CoV-2 Infection in Rhesus Macaques.

Front Immunol 2021 24;12:810047. Epub 2021 Dec 24.

Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States.

Infection with the novel coronavirus, SARS-CoV-2, results in pneumonia and other respiratory symptoms as well as pathologies at diverse anatomical sites. An outstanding question is whether these diverse pathologies are due to replication of the virus in these anatomical compartments and how and when the virus reaches those sites. To answer these outstanding questions and study the spatiotemporal dynamics of SARS-CoV-2 infection a method for tracking viral spread is needed. We developed a novel, fluorescently labeled, antibody-based probe system using the anti-spike monoclonal antibody CR3022 and demonstrated that it could successfully identify sites of SARS-CoV-2 infection in a rhesus macaque model of COVID-19. Our results showed that the fluorescent signal from our antibody-based probe could differentiate whole lungs of macaques infected for 9 days from those infected for 2 or 3 days. Additionally, the probe signal corroborated the frequency and density of infected cells in individual tissue blocks from infected macaques. These results provide proof of concept for the use of antibody-based probes to study SARS-CoV-2 infection dynamics in rhesus macaques.
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http://dx.doi.org/10.3389/fimmu.2021.810047DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8739270PMC
January 2022

Comparative effectiveness of routine physical therapy with and without instrument assisted soft tissue mobilization in patients with neck pain due to upper crossed syndrome.

J Pak Med Assoc 2021 Oct;71(10):2304-2308

University Institute of Physical Therapy, The University of Lahore, Lahore, Pakistan.

Objectives: To determine the effectiveness of routine physical therapy with and without instrument-assisted soft tissue mobilisation on pain intensity and range of motion in patients with neck pain due to upper crossed syndrome.

Methods: The randomised controlled trial was conducted from January to March 2020, and comprised diagnosed male patients aged 18-40 years of upper crossed syndrome complaining of neck pain visiting the Agile Physical Therapy and Rehabilitation Complex and the National Orthopaedic Hospital, Bahawalpur, Pakistan. The subjects were randomised into control group A which received routine physical therapy and experimental group B which received instrument-assisted soft tissue mobilization along with routine physical therapy. The inclinometer was used to measure range of motion and the numeric pain rating scale for pain measurement. Data was analysed using SPSS 22.

Results: Of the 60 subjects, there were 30(50%) in group A with a mean age of 31.50±6.388 years and 30(50%) in group B with a mean age of 32.60±5.55 years. Pain rating at baseline in group B compared to group A show significant difference (p=0.01). Neck range of motion, including flexion, neck right bending, and neck left bending showed significant differences between the groups (p<0.05). The results for neck extension showed that both techniques were equally effective (p>0.05).

Conclusions: Instrument-assisted soft tissue mobilisation with combination of stretching exercises was found to be more effective in the management of neck pain in upper crossed syndrome compared to routine physical therapy.

Registration Number: IRCT20190912044754N1.
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http://dx.doi.org/10.47391/JPMA.03-415DOI Listing
October 2021

Prediction of disease-associated nsSNPs by integrating multi-scale ResNet models with deep feature fusion.

Brief Bioinform 2022 Jan;23(1)

School of Computer Science and Engineering, Nanjing University of Science and Technology, 200 Xiaolingwei, Nanjing, 210094, China.

More than 6000 human diseases have been recorded to be caused by non-synonymous single nucleotide polymorphisms (nsSNPs). Rapid and accurate prediction of pathogenic nsSNPs can improve our understanding of the principle and design of new drugs, which remains an unresolved challenge. In the present work, a new computational approach, termed MSRes-MutP, is proposed based on ResNet blocks with multi-scale kernel size to predict disease-associated nsSNPs. By feeding the serial concatenation of the extracted four types of features, the performance of MSRes-MutP does not obviously improve. To address this, a second model FFMSRes-MutP is developed, which utilizes deep feature fusion strategy and multi-scale 2D-ResNet and 1D-ResNet blocks to extract relevant two-dimensional features and physicochemical properties. FFMSRes-MutP with the concatenated features achieves a better performance than that with individual features. The performance of FFMSRes-MutP is benchmarked on five different datasets. It achieves the Matthew's correlation coefficient (MCC) of 0.593 and 0.618 on the PredictSNP and MMP datasets, which are 0.101 and 0.210 higher than that of the existing best method PredictSNP1. When tested on the HumDiv and HumVar datasets, it achieves MCC of 0.9605 and 0.9507, and area under curve (AUC) of 0.9796 and 0.9748, which are 0.1747 and 0.2669, 0.0853 and 0.1335, respectively, higher than the existing best methods PolyPhen-2 and FATHMM (weighted). In addition, on blind test using a third-party dataset, FFMSRes-MutP performs as the second-best predictor (with MCC and AUC of 0.5215 and 0.7633, respectively), when compared with the other four predictors. Extensive benchmarking experiments demonstrate that FFMSRes-MutP achieves effective feature fusion and can be explored as a useful approach for predicting disease-associated nsSNPs. The webserver is freely available at http://csbio.njust.edu.cn/bioinf/ffmsresmutp/ for academic use.
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http://dx.doi.org/10.1093/bib/bbab530DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8769912PMC
January 2022

MutTMPredictor: Robust and accurate cascade XGBoost classifier for prediction of mutations in transmembrane proteins.

Comput Struct Biotechnol J 2021 19;19:6400-6416. Epub 2021 Nov 19.

School of Computer Science and Engineering, Nanjing University of Science and Technology, 200 Xiaolingwei, Nanjing 210094, China.

Transmembrane proteins have critical biological functions and play a role in a multitude of cellular processes including cell signaling, transport of molecules and ions across membranes. Approximately 60% of transmembrane proteins are considered as drug targets. Missense mutations in such proteins can lead to many diverse diseases and disorders, such as neurodegenerative diseases and cystic fibrosis. However, there are limited studies on mutations in transmembrane proteins. In this work, we first design a new feature encoding method, termed weight attenuation position-specific scoring matrix (WAPSSM), which builds upon the protein evolutionary information. Then, we propose a new mutation prediction algorithm (cascade XGBoost) by leveraging the idea learned from consensus predictors and gcForest. Multi-level experiments illustrate the effectiveness of WAPSSM and cascade XGBoost algorithms. Finally, based on WAPSSM and other three types of features, in combination with the cascade XGBoost algorithm, we develop a new transmembrane protein mutation predictor, named MutTMPredictor. We benchmark the performance of MutTMPredictor against several existing predictors on seven datasets. On the 546 mutations dataset, MutTMPredictor achieves the accuracy () of 0.9661 and the Matthew's Correlation Coefficient () of 0.8950. While on the 67,584 dataset, MutTMPredictor achieves an of 0.7523 and area under curve () of 0.8746, which are 0.1625 and 0.0801 respectively higher than those of the existing best predictor (fathmm). Besides, MutTMPredictor also outperforms two specific predictors on the Pred-MutHTP datasets. The results suggest that MutTMPredictor can be used as an effective method for predicting and prioritizing missense mutations in transmembrane proteins. The MutTMPredictor webserver and datasets are freely accessible at http://csbio.njust.edu.cn/bioinf/muttmpredictor/ for academic use.
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http://dx.doi.org/10.1016/j.csbj.2021.11.024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8649221PMC
November 2021

Tunneling-induced groundwater depletion limits long-term growth dynamics of forest trees.

Sci Total Environ 2022 Mar 13;811:152375. Epub 2021 Dec 13.

Chongqing Key Laboratory of Karst Environment & School of Geographical Sciences, Southwest University, Chongqing 400715, China.

Human interventions such as tunnel construction have caused groundwater depletion, which substantially affected the functions of forest tree species and their communities. However, the extent to which tunneling-induced groundwater depletion (TIGD) degrades their function levels at various spatial-temporal scales under varying climate conditions remains still unclear. Researchers used stand-scale dendrological records to track and extract the effects of TIGD associated with a single or series of tunneling events (three tunneling events during 1999-2001, 2006-2008, and 2010-2013) on short- and long-term growth levels of two dominant drought-tolerant tree species across (karst and non-karst) landscapes affected by tunnel construction and landscapes not subjected to tunnel construction in a mountainous forest ecosystem located in the southwest of China. The results showed that growth responses of both trees stand to TIGD, and the TIGD-linked water losses of other available water sources were negative and widespread across tunnel-affected landscapes, particularly in the karst landscapes known as delicate landscapes. Tree stands with faster (more vigorous) growth rates showed more significant adverse growth levels in response to either tunneling-induced or drought-induced water stresses. Also, they showed the highest recovered growth levels in response to favorable climatic conditions. Moreover, the growth level in the tunnel-affected forest never fully recovered during six years of very wet weather (2012-2018) after the construction of the final (third) tunnel in 2010-2013. Current research shows that tunnel construction has a cumulatively detrimental impact on the long-term survival of the forest. Even with the mediation of long-term very wet circumstances, it can substantially restrict the development dynamics of the forest compared to drought.
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http://dx.doi.org/10.1016/j.scitotenv.2021.152375DOI Listing
March 2022

Dietary application of Lactococcus lactis alleviates toxicity and regulates gut microbiota in Cyprinus carpio on exposure to heavy metals mixture.

Fish Shellfish Immunol 2022 Jan 27;120:190-201. Epub 2021 Nov 27.

MOE, Key Laboratory of Cell Activities and Stress Adaptations, Lanzhou University, Lanzhou City, 730000, Gansu Province, PR China. Electronic address:

Heavy metals (HMs) contaminated fish is a threat to humans when consumed. Dietary probiotics have evolved as a successful HMs removal approach. In this study, probiotics Enterococcus (EC) sp. and Lactococcus (LC) sp. were evaluated for toxicity alleviation and gut microbiota maintenance in Cyprinus carpio (single and combined approach) on Cr, Cd, and Cu mixture (0.8 mg/L and 1.6 mg/L) exposure (28 days). HMs removal, oxidative stress, cytokines response, histology, and gut microbiota were investigated. LC alone showed remarkable HMs removal for Cr (62.28%-87.57%), Cd (89%-90.42%), and Cu (72%-88%) than LC + EC. Probiotics up-regulated superoxide dismutase and total protein levels, while decreased the activity of malondialdehyde than the control. Pro-inflammatory cytokine (TNF-α) and chemokine (IL-8) expressions were higher at 1.6 mg/L concentration, whereas anti-inflammatory cytokine (IL-10) was higher in the 0.8 mg/L group. LC mitigated the histological alterations of gills, kidneys, and intestines, particularly at the lower concentration. Sequencing results revealed that Proteobacteria (44%-61%) was the most dominant phylum in all groups, followed by Fusobacteria (34%-36%) at 0.8 mg/L and Firmicutes (19%-34%) at 1.6 mg/L. The current study presented LC and EC potential separately and in combination to countermeasure HMs mixture induced toxicity and gut microbial dysbiosis, in which the conjoint group was less effective.
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http://dx.doi.org/10.1016/j.fsi.2021.11.038DOI Listing
January 2022

Next generation plasma proteome profiling of COVID-19 patients with mild to moderate symptoms.

EBioMedicine 2021 Dec 27;74:103723. Epub 2021 Nov 27.

Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden. Electronic address:

Background: COVID-19 has caused millions of deaths globally, yet the cellular mechanisms underlying the various effects of the disease remain poorly understood. Recently, a new analytical platform for comprehensive analysis of plasma protein profiles using proximity extension assays combined with next generation sequencing has been developed, which allows for multiple proteins to be analyzed simultaneously without sacrifice on accuracy or sensitivity.

Methods: We analyzed the plasma protein profiles of COVID-19 patients (n = 50) with mild and moderate symptoms by comparing the protein levels in newly diagnosed patients with the protein levels in the same individuals after 14 days.

Findings: The study has identified more than 200 proteins that are significantly elevated during infection and many of these are related to cytokine response and other immune-related functions. In addition, several other proteins are shown to be elevated, including SCARB2, a host cell receptor protein involved in virus entry. A comparison with the plasma protein response in patients with severe symptoms shows a highly similar pattern, but with some interesting differences.

Interpretation: The study presented here demonstrates the usefulness of "next generation plasma protein profiling" to identify molecular signatures of importance for disease progression and to allow monitoring of disease during recovery from the infection. The results will facilitate further studies to understand the molecular mechanism of the immune-related response of the SARS-CoV-2 virus.

Funding: This work was financially supported by Knut and Alice Wallenberg Foundation.
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http://dx.doi.org/10.1016/j.ebiom.2021.103723DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8626206PMC
December 2021

Response of Annual Herbaceous Plant Leaching and Decomposition to Periodic Submergence in Mega-Reservoirs: Changes in Litter Nutrients and Soil Properties for Restoration.

Biology (Basel) 2021 Nov 5;10(11). Epub 2021 Nov 5.

Key Laboratory of Eco-Environments in the Three Gorges Reservoir Region (Ministry of Education), Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, College of Life Sciences, Southwest University, Chongqing 400715, China.

Litter decomposition is an important soil nutrient source that promotes vegetation in deteriorated riparian zones worldwide. The periodic submergence and sediment burial effects on two prominent annual herbaceous plants ( and ) are little known in mega-reservoir settings. Our study focuses on the mass and carbon loss and nutrient release from and litter and changes in soil properties, which are important for riparian zone rehabilitation in the Three Gorges Dam Reservoir, China. This study adopted the litter bag method to explore the nutrient change characteristics and changes in soil properties at different sediment burial depths under flooding scenarios. Three burial depths (0 cm, 5 cm, and 10 cm) were used for these two plants, and the experiment lasted for 180 days. The results revealed that the litter decay rate was high at first in the incubation experiment, and the nutrient loss rate followed the pattern of K > P > N > C. The relationship between % C remaining and % mass remaining was nearly 1:1, and the total amount of P exhibited a leaching-enrichment-release state in the decomposition process. Nutrients were changed significantly in the soil and overlying water at the first decomposition stage. Still, the total soil nutrient change was insignificant at the end, except for the 10 cm burial of . Moreover, oxidation-reduction potential was the main factor in the litter decomposition process at different burial depths. This study indicated that sediment deposition reduced litter mass loss, slowed down the release of N and P, and retained more C, but promoted the release of K. Conclusively, in litter decomposition under waterlogging, the total soil nutrient content changed little. However, litter does more to the soil than that. Therefore, it is necessary to study the residual soil litter's continuous output after the water level declines for restoration purposes.
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http://dx.doi.org/10.3390/biology10111141DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8614921PMC
November 2021

Revealing the Molecular Mechanisms of Alzheimer's Disease Based on Network Analysis.

Int J Mol Sci 2021 Oct 26;22(21). Epub 2021 Oct 26.

Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London SE1 9RT, UK.

The complex pathology of Alzheimer's disease (AD) emphasises the need for comprehensive modelling of the disease, which may lead to the development of efficient treatment strategies. To address this challenge, we analysed transcriptome data of post-mortem human brain samples of healthy elders and individuals with late-onset AD from the Religious Orders Study and Rush Memory and Aging Project (ROSMAP) and Mayo Clinic (MayoRNAseq) studies in the AMP-AD consortium. In this context, we conducted several bioinformatics and systems medicine analyses including the construction of AD-specific co-expression networks and genome-scale metabolic modelling of the brain in AD patients to identify key genes, metabolites and pathways involved in the progression of AD. We identified and as examples of commonly altered marker genes in AD patients. Moreover, we found alterations in energy metabolism, represented by reduced oxidative phosphorylation and ATPase activity, as well as the depletion of hexanoyl-CoA, pentanoyl-CoA, (2E)-hexenoyl-CoA and numerous other unsaturated fatty acids in the brain. We also observed that neuroprotective metabolites (e.g., vitamins, retinoids and unsaturated fatty acids) tend to be depleted in the AD brain, while neurotoxic metabolites (e.g., β-alanine, bilirubin) were more abundant. In summary, we systematically revealed the key genes and pathways related to the progression of AD, gained insight into the crucial mechanisms of AD and identified some possible targets that could be used in the treatment of AD.
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http://dx.doi.org/10.3390/ijms222111556DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8584243PMC
October 2021

Prolonged ventricular pause associated with ticagrelor use: A case report.

Clin Case Rep 2021 Oct 25;9(10):e05017. Epub 2021 Oct 25.

Cardiology Department, Heart Hospital Hamad Medical Corporation Doha Qatar.

Case: We report a case of a 76-year-old female who presented with non-ST elevation myocardial infarction and developed a 22-second ventricular pause with ticagrelor that did not recur after shifting to clopidogrel. Based on the Naranjo algorithm, the likelihood that our patient's prolonged ventricular pause was due to ticagrelor exposure was probable.

Conclusion: Ticagrelor use is associated with prolonged ventricular pauses, warranting close monitoring, particularly during the first week of therapy.
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http://dx.doi.org/10.1002/ccr3.5017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8543052PMC
October 2021

A network-based approach reveals the dysregulated transcriptional regulation in non-alcoholic fatty liver disease.

iScience 2021 Nov 5;24(11):103222. Epub 2021 Oct 5.

Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden.

Non-alcoholic fatty liver disease (NAFLD) is a leading cause of chronic liver disease worldwide. We performed network analysis to investigate the dysregulated biological processes in the disease progression and revealed the molecular mechanism underlying NAFLD. Based on network analysis, we identified a highly conserved disease-associated gene module across three different NAFLD cohorts and highlighted the predominant role of key transcriptional regulators associated with lipid and cholesterol metabolism. In addition, we revealed the detailed metabolic differences between heterogeneous NAFLD patients through integrative systems analysis of transcriptomic data and liver-specific genome-scale metabolic model. Furthermore, we identified transcription factors (TFs), including SREBF2, HNF4A, SREBF1, YY1, and KLF13, showing regulation of hepatic expression of genes in the NAFLD-associated modules and validated the TFs using data generated from a mouse NAFLD model. In conclusion, our integrative analysis facilitates the understanding of the regulatory mechanism of these perturbed TFs and their associated biological processes.
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http://dx.doi.org/10.1016/j.isci.2021.103222DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8529555PMC
November 2021

Interactive effect of different salinity sources and their formulations on plant growth, ionic homeostasis and seed quality of maize.

Chemosphere 2022 Mar 25;291(Pt 1):132678. Epub 2021 Oct 25.

Department of Environment and Soil Sciences, University of Lleida, Avinguda Alcalde Rovira Roure 191, 25198, Lleida, Spain. Electronic address:

Soil salinity is one of the most pernicious environmental hazards affecting crop growth and productivity in arid and semi-arid climates. In saline soils, the crop plants encounter nutrients deficient conditions mainly due to antagonistic affinity of sodium (Na) and chloride (Cl). The accumulation of salts in the rhizosphere restricts plant growth, the severity of which depends on the source and concentration of the salt. Therefore, we hypothesized that sodium containing salts could have toxic effects on maize plants either in a single or in combined form. To evaluate the interactive effect of sodium salts on plant growth, ionic homeostasis, and seed quality attributes, a pot study was performed using maize as a test plant at the research area of the College of Agriculture, University of Sargodha. Selected salts including, NaCl, NaSO and their combination (NaCl + NaSO), were applied in equal ratio for different salinity levels (7, 10, 13 and 16 dS m) and the untreated control. The results show that all the measured growth, yield, biochemical and quality attributes of maize were negatively affected with increasing concentration of all the salt sources; however, severity of these effects were more intense when NaCl was applied at all salinity levels. It is concluded that all salts (NaCl, NaSO and NaCl + NaSO) had negative effects on biochemical, qualitative, growth and yield characteristics of maize plant. Most importantly, NaCl was found to be more harmful compared to NaSO and mixtures of both salts due to the dominance of Na+ and Clions. Among all salinity levels, the more detrimental effects of NaCl occurred at salinity level of 16 dS m.
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http://dx.doi.org/10.1016/j.chemosphere.2021.132678DOI Listing
March 2022

Combined metabolic activators therapy ameliorates liver fat in nonalcoholic fatty liver disease patients.

Mol Syst Biol 2021 Oct;17(10):e10459

Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden.

Nonalcoholic fatty liver disease (NAFLD) refers to excess fat accumulation in the liver. In animal experiments and human kinetic study, we found that administration of combined metabolic activators (CMAs) promotes the oxidation of fat, attenuates the resulting oxidative stress, activates mitochondria, and eventually removes excess fat from the liver. Here, we tested the safety and efficacy of CMA in NAFLD patients in a placebo-controlled 10-week study. We found that CMA significantly decreased hepatic steatosis and levels of aspartate aminotransferase, alanine aminotransferase, uric acid, and creatinine, whereas found no differences on these variables in the placebo group after adjustment for weight loss. By integrating clinical data with plasma metabolomics and inflammatory proteomics as well as oral and gut metagenomic data, we revealed the underlying molecular mechanisms associated with the reduced hepatic fat and inflammation in NAFLD patients and identified the key players involved in the host-microbiome interactions. In conclusion, we showed that CMA can be used to develop a pharmacological treatment strategy in NAFLD patients.
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http://dx.doi.org/10.15252/msb.202110459DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8724764PMC
October 2021

Responses of Ecological Stoichiometric Characteristics of Carbon, Nitrogen, and Phosphorus to Periodic Submergence in Mega-Reservoir: Growth of and .

Plants (Basel) 2021 Sep 28;10(10). Epub 2021 Sep 28.

Key Laboratory of Eco-Environments in the Three Gorges Reservoir Region (Ministry of Education), Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, College of Life Sciences, Southwest University, Chongqing 400715, China.

Ecological stoichiometric studies can be useful for managing the deteriorated riparian zones of mega-reservoirs in which nutrients significantly impact the balanced vegetation cover. The present study aims to explore the effects of periodic submergence on the stoichiometric ecological characteristics of carbon (C), nitrogen (N), and phosphorus (P), as well as the growth conditions of two leading conifer species ( and ) in the hydro-fluctuation zone of the Three Gorges Reservoir (TGR) region, China. The stoichiometrical contents of C, N, and P in fine roots, leaves, and branches, and the growth conditions of and were measured in July 2019. The results showed that periodic submergence affected the stoichiometric characteristics and growth conditions of these two woody species, and the impact was restrained, but both grew well. The effects of inundation on the C, N, and P ecological stoichiometric characteristics differed in different parts of trees. In general, the C contents showed the following pattern: leaves > branches > fine roots. The N and P content showed the following pattern: leaves > fine roots > branches, while the C/N and C/P ratios showed an opposite trend to that of N and P. The N and P content in all parts of (with means of 17.18 and 1.70 g/kg for leaves, 4.80 and 0.57 g/kg for branches, and 6.88 and 1.10 g/kg for fine roots, respectively) and (with means of 14.56 and 1.87 g/kg for leaves, 5.03 and 0.63 g/kg for branches, and 8.17 and 1.66 g/kg for fine roots, respectively) were higher than the national average level (with means of 14.14 and 1.11 g/kg for leaves, 3.04 and 0.31 g/kg for branches, and 4.85 and 0.47 g/kg for fine roots, respectively). Except for N and P contents in the leaves of , there was a significant correlation between N and P elements in other parts ( < 0.05). Nevertheless, the N/P ratio (10.15, 8.52, 6.44, and 7.93, 8.12, 5.20 in leaves, branches, and fine roots of and , respectively) was lower than the critical ratio of 14. The growth conditions of and were significantly negatively correlated with their leaf C contents and significantly positively correlated with their fine root N and P contents. This study showed that and could maintain their normal growth needs by properly allocating nutrients between different organs to adapt to the long periodic submergence in the hydro-fluctuation zone of the TGR region.
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http://dx.doi.org/10.3390/plants10102040DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8540895PMC
September 2021

Systems Analysis Reveals Ageing-Related Perturbations in Retinoids and Sex Hormones in Alzheimer's and Parkinson's Diseases.

Biomedicines 2021 Sep 24;9(10). Epub 2021 Sep 24.

Faculty of Dentistry, Oral and Craniofacial Sciences, King's College London, London SE1 9RT, UK.

Neurodegenerative diseases, including Alzheimer's (AD) and Parkinson's diseases (PD), are complex heterogeneous diseases with highly variable patient responses to treatment. Due to the growing evidence for ageing-related clinical and pathological commonalities between AD and PD, these diseases have recently been studied in tandem. In this study, we analysed transcriptomic data from AD and PD patients, and stratified these patients into three subclasses with distinct gene expression and metabolic profiles. Through integrating transcriptomic data with a genome-scale metabolic model and validating our findings by network exploration and co-analysis using a zebrafish ageing model, we identified retinoids as a key ageing-related feature in all subclasses of AD and PD. We also demonstrated that the dysregulation of androgen metabolism by three different independent mechanisms is a source of heterogeneity in AD and PD. Taken together, our work highlights the need for stratification of AD/PD patients and development of personalised and precision medicine approaches based on the detailed characterisation of these subclasses.
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http://dx.doi.org/10.3390/biomedicines9101310DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8533098PMC
September 2021

Analysis of newly developed fractal-fractional derivative with power law kernel for MHD couple stress fluid in channel embedded in a porous medium.

Sci Rep 2021 Oct 21;11(1):20858. Epub 2021 Oct 21.

Center of Excellence in Theoretical and Computational Science (TaCS-CoE), Faculty of Science, King Mongkut's University of Technology Thonburi (KMUTT), 126 Pracha Uthit Rd., Bang Mod, Thung Khru, Bangkok, 10140, Thailand.

Fractal-fractional derivative is a new class of fractional derivative with power Law kernel which has many applications in real world problems. This operator is used for the first time in such kind of fluid flow. The big advantage of this operator is that one can formulate models describing much better the systems with memory effects. Furthermore, in real world there are many problems where it is necessary to know that how much information the system carries. To explain the memory in a system fractal-fractional derivatives with power law kernel is analyzed in the present work. Keeping these motivation in mind in the present paper new concept of fractal-fractional derivative for the modeling of couple stress fluid (CSF) with the combined effect of heat and mass transfer have been used. The magnetohydrodynamics (MHD) flow of CSF is taken in channel with porous media in the presence of external pressure. The constant motion of the left plate generates the CSF motion while the right plate is kept stationary. The non-dimensional fractal-fractional model of couple stress fluid in Riemann-Liouville sense with power law is solved numerically by using the implicit finite difference method. The obtained solutions for the present problem have been shown through graphs. The effects of various parameters are shown through graphs on velocity, temperature and concentration fields. The velocity, temperature and concentration profiles of the MHD CSF in channel with porous media decreases for the greater values of both fractional parameter [Formula: see text] and fractal parameter [Formula: see text] respectively. From the graphical results it can be noticed that the fractal-fractional solutions are more general as compared to classical and fractional solutions of CSF motion in channel. Furthermore, the fractal-fractional model of CSF explains good memory effect on the dynamics of couple stress fluid in channel as compared to fractional model of CSF. Finally, the skin friction, Nusselt number and Sherwood number are evaluated and presented in tabular form.
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http://dx.doi.org/10.1038/s41598-021-00163-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8531019PMC
October 2021

Occurrence and risk assessment of antibiotics in the surface water of Chaohu Lake and its tributaries in China.

Sci Total Environ 2022 Feb 18;807(Pt 3):151040. Epub 2021 Oct 18.

CAS Key Laboratory of Crust-Mantle Materials and the Environment, School of Earth and Space Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China.

The extensive use of antibiotics for treating humans, animals, and plants has resulted in the contamination of aquatic environments, posing a potential threat to public health and aquatic life; hence, this topic is of great concern worldwide. Lakes are considered to be antibiotic-rich reservoirs because many of the antibiotics discharged from rivers enter lakes. Chaohu Lake is one of the top five freshwater lakes in China. This study aims to provide a current evaluation of the antibiotics present in the surface water of the Chaohu Lake basin. To this end, the occurrences of 18 antibiotics categorized into 5 different groups were investigated in the study area, and the impact of inflowing rivers on their distribution was assessed. The results showed that the concentrations of 14 antibiotics in water samples ranged from 0 to 892 ng/L, and that antibiotics were detected at most sampling sites. Among them, the Nanfeihe and Shiwulihe rivers, which are close to the city, contributed the most to antibiotic pollution, indicating the widespread occurrence of antibiotics in the study area. A risk assessment based on the risk quotient method indicated that ofloxacin, ciprofloxacin, sulfamethoxazole, erythromycin, and norfloxacin in the lake water posed a high ecological risk to algae, while sulfamethazine posed a high risk to plants (RQ >1).
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http://dx.doi.org/10.1016/j.scitotenv.2021.151040DOI Listing
February 2022

Potential utility of nano-based treatment approaches to address the risk of .

Expert Rev Anti Infect Ther 2021 Oct 17:1-18. Epub 2021 Oct 17.

Department of Biochemistry and Molecular Biology, College of Marine Life Sciences, Ocean University of China, Qingdao, China.

Introduction: () has occupied a significant place among infectious pathogens and it has been documented as a leading challenge due to its higher resistance to the commonly used drugs, higher adaptability, and lower targeting specificity of the available drugs.

Areas Covered: New treatment strategies are urgently needed in order to improve the current advancement in modern medicine. Nanocarriers have gained an advantage of drug encapsulation and high retention time in the stomach with a prolonged drug release rate at the targeted site. This article aims to highlight the recent advances in nanotechnology with special emphasis on metallic, polymeric, lipid, membrane coated, and target-specific nanoparticles (NPs), as well as, natural products for treating infection. We discussed a comprehensive approach to understand infection and elicits to rethink about the increasing threat posed by and its treatment strategies.

Expert Opinion: To address these issues, nanotechnology has got huge potential to combat infection and has made great progress in the field of biomedicine. Moreover, combinatory studies of natural products and probiotics in conjugation with NPs have proven efficiency against infection, with an advantage of lower cytotoxicity, minimal side effects, and stronger antibacterial potential.[Figure: see text].
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http://dx.doi.org/10.1080/14787210.2022.1990041DOI Listing
October 2021

Bacteria-targeting chitosan/carbon dots nanocomposite with membrane disruptive properties improve eradication rate of .

J Biomater Sci Polym Ed 2021 12 23;32(18):2423-2447. Epub 2021 Oct 23.

College of Marine Life Science, Ocean University Of China, Qingdao, P.R. China.

We designed a bacteria-targeting and membrane disrupting nanocomposite for successful antibiotic treatment of () infections in the present study. The antibacterial nanocomposite was prepared from thiolated-ureido-chitosan (Cys-U-CS) and anionic poly (malic acid) (PMLA) electrostatic interaction decorated with dual functional ammonium citrate carbon quantum dots (CDs). Cys-U-CS serves as a targeting building block for attaching antibacterial nanocomposite onto bacterial cell surface through Urel-mediated protein channel. Simultaneously, membrane disrupting CDs generate ROS and lyse the bacterial outer membrane, allowing antibiotics to enter the intracellular cytoplasm. As a result, Cys-U-CS/[email protected] nanocomposite (UCPM-NPs) loaded with the antibiotic amoxicillin (AMX) not only effectively target and kill bacteria Urel-mediated adhesion but also efficiently retain in the stomach where reside, serving as an effective drug carrier for abrupt on-site release of AMX into the bacterial cytoplasm. Furthermore, since thiolated-chitosan has a mucoadhesive property, UCPM-NPs may adhere to the stomach mucus layer and pass through it swiftly. According to our results, bacterial targeting is crucial for guaranteeing successful antibiotic treatment. The bacteria targeting UCPM-NPs with membrane disruptive ability may establish a promising drug delivery system for the effective targeted delivery of antibiotics to treat infections.
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http://dx.doi.org/10.1080/09205063.2021.1972559DOI Listing
December 2021

Empagliflozin: HPLC based analytical method development and application to pharmaceutical raw material and dosage form.

Pak J Pharm Sci 2021 May;34(3(Supplementary)):1081-1087

Department of Pharmaceutics, Faculty of Pharmacy, University of Karachi, Karachi, Pakistan.

The current investigation is based on efficient method development for the quantification of empagliflozin in raw and pharmaceutical dosage forms, as no pharmacopoeial method for the drug is available so far. The developed analytical method was validated as per ICH guidelines. C18 column with mobile phase (pH 4.8) consisted of 0.1% trifluoroacetic acid solution and acetonitrile (70:30 v/v) was used for drug analysis. The calibration plot showed good linear regression (r2>0.999) over the concentration of 0.025-30 μg mL. The LOD and LOQ were found to be 0.020 μg mL and 0.061 μg mL, respectively. The percentage recovery was estimated between 98.0 to 100.13%. Accuracy and precision data were found to be less than 2%, indicating the suitability of method for routine analysis in pharmaceutical industries. Moreover, the drug solution was found to be stable in refrigerator and ambient room temperature with mean % accuracy of >98%. Empagliflozin contents were also tested in both the raw API and marketed tablet brands using this newly developed method. The mean assay of raw empagliflozin and tablet brands were ranged from 99.29%±1.12 to 100.95%±1.69 and 97.18%±1.59 to 98.92%±1.00 respectively. Based on these findings, the present investigated approach is suitable for quantification of empagliflozin in raw and pharmaceutical dosage forms.
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May 2021

1,3-di-4-piperidylpropane derivatives as potential acetyl cholinesterase antagonists: Molecular docking, synthesis, and biological evaluation.

Pak J Pharm Sci 2021 May;34(3):855-860

Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Hamdard University, Karachi, Pakistan.

Acetylcholine esterase (AChE) is a key biological target responsible for the management of cholinergic transmission, and its inhibitors are used for the therapy of Alzheimer's disease. In the present study, a small library of molecules with 1,3-di-4-piperidylpropane nucleus were docked on AChE. The selected compounds were synthesized and evaluated for their enzyme inhibition. P25 and P17 expressed significantly higher AChE inhibition than standards with IC50 values of 0.591μM and 0.625μM, respectively. Binding mode of derivatives in the active site of AChE revealed dual binding of molecules in peripheral anionic site (PAS) and catalytic anionic site (CAS) of enzyme cavity.
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May 2021

Alteration in soil arsenic dynamics and toxicity to sunflower (Helianthus annuus L.) in response to phosphorus in different textured soils.

Chemosphere 2022 Jan 28;287(Pt 4):132406. Epub 2021 Sep 28.

Department of Environment and Soil Sciences, University of Lleida, Avinguda Alcalde Rovira Roure 191, 25198, Lleida, Spain. Electronic address:

Being analogue to arsenic (As), phosphorus (P) may affect As dynamics in soil and toxicity to plants depending upon many soil and plant factors. Two sets of experiments were conducted to determine the effect of P on As fractionation in soils, its accumulation by plants and subsequent impact on growth, yield and physiological characteristics of sunflower (Helianthus annuus L.). Experimental plan comprised of two As levels (60 and 120 mg As kg soil), four P (0-5-10-20 g phosphate rock kg soil) and three textural types (sandy, loamy and clayey) with three replications. Among different As fractions determined, labile, calcium-bound, organic matter-bound and residual As increased while iron-bound and aluminum-bound As decreased with increasing P in all the three textural types. Labile-As percentage increased in the presence of P by 16.9-48.0% at As60 while 36.0-68.1% at As120 in sandy, 19.1-64.0% at As60 while 11.5-52.3% at As120 in loamy, and 21.8-58.2% at As60 while 22.3-70.0% at As120 in clayey soil compared to respective As treatment without P. Arsenic accumulation in plant tissues at both contamination levels declined with P addition as evidenced by lower bioconcentration factor. Phosphorus mitigated the As-induced oxidative stress expressed in term of reduced hydrogen peroxide, malondialdehyde while increased glutathione, and consequently improved the achene yield. Although, P increased As solubility in soil but restricted its translocation to plant, leading to reversal of oxidative damage, and improved sunflower growth and yield in all the three soil textural types, more profound effect at highest P level and in sandy texture.
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http://dx.doi.org/10.1016/j.chemosphere.2021.132406DOI Listing
January 2022

Autozygosity mapping in consanguineous Pakistani families identifies nine non-overlapping novel linkage intervals for autosomal recessive non-syndromic mental retardation (AR-NSMR); shows genetic heterogeneity for AR-NSMR.

J Pak Med Assoc 2021 09;71(9):2250-2254

Department of Biotechnology, Abdul Wali Khan University, Mardan, Pakistan.

Psychological disturbance (PD) or cerebral dysfunction (CD) covers several clinical areas, and has defining features of mental retardation. Recently, we conducted a study to investigate heritable heterogeneity in Pakistani consanguineous couples with recessive autosomal intellectual abnormalities. A cohort of three consanguineous families with multiple birth defects, belonging two to district lower Dir and one to district Lodhra, were selected for molecular analysis. All the affected individuals in the cohort showed autosomal recessive non-syndromic mental disturbances. DNA was extracted and subjected to Single tagged sequence (STS) marker analyses to all known non-syndromic autosomal recessive mental retardation (NS-ARMR) genes, while autozygosity mapping was performed by advanced SNP techniques. Fragment analyses of the NS-ARMR disease genes CRBN, CC2D2A, PRSS12, GRIK2, TUSC3, and CC2D1A using polymorphic STS markers confirmed these to be contender genes for the alteration. Mapping of autozygosity in all the study subjects using genome study revealed nine novel linkage intervals, i.e. four intervals for MR4, two intervals for MR8 and three intervals for MR13. In spite of being a monogenic condition, autosomal recessive mental retardation shows genetic heterogeneity and several genes are involved in different families; hence, there is a chance for involvement of separate gene in each family.
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http://dx.doi.org/10.47391/JPMA.206DOI Listing
September 2021

Can Bacterial Endophytes Be Used as a Promising Bio-Inoculant for the Mitigation of Salinity Stress in Crop Plants?-A Global Meta-Analysis of the Last Decade (2011-2020).

Microorganisms 2021 Sep 2;9(9). Epub 2021 Sep 2.

Center Agriculture Food Environment (C3A), University of Trento, Via E. Mach 1, 38098 San Michele all'Adige, Italy.

Soil salinity is a major problem affecting crop production worldwide. Lately, there have been great research efforts in increasing the salt tolerance of plants through the inoculation of plant growth-promoting endophytic bacteria. However, their ability to promote plant growth under no-stress and salinity-stress conditions remains largely uncertain. Here, we carried out a global meta-analysis to quantify the plant growth-promoting effects (improvement of morphological attributes, photosynthetic capacity, antioxidative ability, and ion homeostasis) of endophytic bacteria in plants under no-stress and salinity-stress conditions. In addition, we elucidated the underlying mechanisms of growth promotion in salt-sensitive (SS) and salt-tolerant (ST) plants derived from the interaction with endophytic bacteria under no-stress and salinity-stress conditions. Specifically, this work encompassed 42 peer-reviewed articles, a total of 77 experiments, and 24 different bacterial genera. On average, endophytic bacterial inoculation increased morphological parameters. Moreover, the effect of endophytic bacteria on the total dry biomass, number of leaves, root length, shoot length, and germination rate was generally greater under salinity-stress conditions than no-stress conditions. On a physiological level, the relative better performance of the bacterial inoculants under the salinity-stress condition was associated with the increase in total chlorophyll and chlorophyll-b, as well as with the decrease of 1-aminocylopropane-1-carboxylate concentration. Moreover, under the salinity-stress condition, bacterial inoculation conferred a significantly higher increase in root K concentration and decrease in leaf Na concentration than under the no-stress condition. In SS plants, bacterial inoculation induced a higher increase in chlorophyll-b and superoxide dismutase activity, as well as a higher decrease in abscisic acid content, than in ST plants. Under salinity-stress, endophytic bacterial inoculation increased root K concentration in both SS and ST plants but decreased root Na concentration only in ST plants. Overall, this meta-analysis suggests that endophytic bacterial inoculation is beneficial under both no salinity-stress and salinity-stress conditions, but the magnitude of benefit is definitely higher under salinity-stress conditions and varies with the salt tolerance level of plants.
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http://dx.doi.org/10.3390/microorganisms9091861DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8467090PMC
September 2021

Do soil conservation practices exceed their relevance as a countermeasure to greenhouse gases emissions and increase crop productivity in agriculture?

Sci Total Environ 2022 Jan 15;805:150337. Epub 2021 Sep 15.

Department of Soil Science, Faculty of Agriculture, Bahauddin Zakariya University, Multan, Punjab, Pakistan.

Globally, agriculture sector is the significant source of greenhouse gases (GHGs) emissions into the atmosphere. To achieve the goal of limiting or mitigating these emissions, a rigorous abatement strategy with an additional focus on improving crop productivity is now imperative. Replacing traditional agriculture with soil conservation-based farming can have numerous ecological benefits. However, most assessments only consider improvements in soil properties and crop productivity, and often preclude the quantitative impact analysis on GHGs emissions. Here, we conducted a meta-analysis to evaluate crop productivity (i.e., biomass, grain, total yield) and GHGs emissions (i.e., CO, NO, CH) for three major soil conservation practices i.e., no-tillage, manures, and biochar. We also examined the yield potential of three major cereal crops (i.e., wheat, rice, maize) and their significance in mitigating GHGs emissions. None of the manures were able to reduce GHGs emissions, with poultry manure being the largest contributor to all GHGs emissions. However, pig-manure had the greatest impact on crop yield while emitting the least CO emissions Use of biochar showed a strong coupling effect between reduction of GHGs (i.e., CH by -37%; NO by -25%; CO by -5%) and the increase in crop productivity. In contrast, no-tillage resulted in higher GHGs emissions with only a marginal increase in grain yield. Depending on crop type, all cereal crops showed varied degrees of GHGs mitigation under biochar application, with wheat responding most strongly due to the additional yield increment. The addition of biochar significantly reduced CO and NO emissions under both rainfed and irrigated conditions, although CH reductions were identical in both agroecosystems. Interestingly, the use of biochar resulted in a greater yield benefit in rainfed than in irrigated agriculture. Despite significant GHGs emissions, manure application contributed to higher crop yields, regardless of soil type or agroecosystem. Moreover, no-tillage showed a significant reduction in CH and NO emissions under rainfed and irrigated conditions. Notably , biochar application in coarse while no-till in fine textured soils contributed to NO mitigation. Most importantly, effectiveness of no-tillage as a countermeasure to GHGs emissions while providing yield benefits is inconsistent. Overall, the decision to use farm manures should be reconsidered due to higher GHGs emissions. We conclude that the use of biochar could be an ideal way to reduce GHGs emissions. However, further understanding of the underlying mechanisms and processes affecting GHGs emissions is needed to better understand the feedback effects in conservation agriculture.
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http://dx.doi.org/10.1016/j.scitotenv.2021.150337DOI Listing
January 2022
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