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Bagging with CTD–A Novel signature for the Hierarchical Prediction of secreted Protein Trafcking in Eukaryotes

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Genomics, Proteomics & Bioinformatics 2013年第6期11卷 385-390页

作者： Geetha Govindan Achuthsankar s.nair Department of Computational Biology and Bioinformatics University of Kerala

Protein trafficking or protein sorting in eukaryotes is a complicated process and is carried out based on the information contaified in the protein. Many methods reported prediction of the subcellular location of proteins from sequence information. However, most of these prediction methods use a flat structure or parallel architecture to perform prediction. In this work, we introduce ensemble classifiers with features that are extracted directly from full length protein sequences to predict locations in the protein-sorting pathway hierarchically. sequence driven features, sequence mapped features and sequence autocorrelation features were tested with ensemble learners and their performances were compared. When evaluated by independent data testing, ensemble based-bagging algorithms with sequence feature composition, transition and distribution （CTD） successfully classified two datasets with accuracies greater than 90%. We compared our results with similar published methods, and our method equally performed with the others at two levels in the secreted pathway. This study shows that the feature CTD extracted from protein sequences is effective in capturing biological features among compartments in secreted pathways.

关键词： sequence driven features sequence mapped features Autocorrelation Ensemble classifiter Protein sorting

A combination of learning and non-learning based method for enhancement, compression and reconstruction of underwater images

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Aquaculture and Fisheries 2022年第2期7卷 201-210页

作者： Rashmi s.nair sandanam Domnic Department of Computer Applications National Institute of TechnologyTiruchirappalliTamil Nadu620015India

Complex nature of underwater environment poses biggest challenge towards image acquisition and transmission of underwater *** paper proposes an integrated approach which consists of a non-learning enhancement method with deep Convolutional Neural Networks(CNN)for compression and reconstruction of the *** proposed method does color and contrast correction for image *** enhanced images are down-sampled using 9-layer CNN followed by Discrete Wavelet Transform(DWT).The decompression is done by using Inverse ***,the sub-pixel up-sampled image is de-blurred using a three-layer *** Dense CNN(RD-CNN)is used to improve the quality of the reconstructed image after *** quality of the reconstructed images is measured using Peak signal to Noise Ratio(PsNR)and structural similarity Index Metric(ssIM).The proposed model provides better image enhancement,compression,and reconstruction quality than the existing state-of-the-art methods and super Resolution CNN(sRCNN)respectively.

关键词： Convolutional neural network Discrete wavelet transform Residual dense convolutional neural network Peak signal to noise ratio structural similarity index metric super resolution CNN

structural,magnetic and antibacterial properties of manganese-substituted magnetite ferrofluids

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International Journal of Minerals,Metallurgy and Materials 2023年第7期30卷 1417-1426页

作者： Blessy Babukutty Deepalekshmi Ponnamma swapna s.nair Jiya Jose saritha G.Bhat sabu Thomas Department of Physics Central University of KeralaKasargod 671314India Materials science and Technology Program College of Arts and SciencesQatar UniversityP.O.Box 2713DohaQatar Department of Biotechnology Cochin University of Science and TechnologyKalamasseryKeralaIndia Department of Chemistry Mahatma Gandhi UniversityKottayam 686560KeralaIndia

Manganese-substituted magnetite ferrofluids(FFs)Mnx Fe_(1-x)Fe_(2)O_(4)(x=0–0.8)were prepared in this work through a chemical coprecipitation *** controlled growth of FF nanomaterials for antibacterial activities is challenging,and therefore,very few reports are available on the *** research focuses on stabilizing aqueous FFs with the tetramethylammonium hydroxide surfactant to achieve high *** characterization reveals nanoparticles of 5–11 nm formed by the chemical reaction and nanocrystalline nature,as evident from structural ***-substituted magnetic FFs are analyzed for their structural,functional,and antibacterial performance according to the Mn-substituent *** studies show a high blue shift for Mn^(2+)-substituted Mnx Fe_(1-x)Fe_(2)O_(4)with the theoretical correlation of optical band gaps with the Mn *** superparamagnetic nature of substituted FFs causes zero coercivity and remanence,which consequently influence the particle size,cation distribution,and spin *** structural and functional performance of the FFs is correlated with the antibacterial activity,finally demonstrating the highest inhibition zone formation for Mnx Fe_(1-x)Fe_(2)O_(4)FFs.

关键词： manganese ferrofluids homogeneity antibacterial stability

Electroconductivity,a regenerative engineering approach to reverse rotator cuff muscle degeneration

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Regenerative Biomaterials 2023年第1期10卷 1693-1712页

作者： Nikoo saveh-shemshaki Mohammed A.Barajaa Takayoshi Otsuka Elnaz s.Mirdamadi Lakshmi s.nair Cato T.Laurencin The Cato T.Laurencin Institute for Regenerative Engineering University of ConnecticutFarmingtonCT 06030USA Department of Biomedical Engineering University of ConnecticutStorrsCT 06269USA Department of Biomedical Engineering Imam Abdulrahman Bin Faisal UniversityDammam 31451Saudi Arabia Department of Orthopedic surgery University of Connecticut Health CenterFarmingtonCT 06030USA Department of Materials science and Engineering University of ConnecticutStorrsCT 06269USA Department of Chemical&Biomolecular Engineering University of ConnecticutStorrsCT 06269USA

Inhalation-administrated drugs remain an interesting possibility of addressing pulmonary *** drug delivery to the lungs allows one to obtain high concentration in the site of action with limited systemic distribution,leading to a more effective therapy with reduced required doses and side *** the other hand,there are several difficulties in obtaining a formulation that would meet all the criteria related to physicochemical,aerodynamic and biological properties,which is the reason why only very few of the investigated systems can reach the clinical trial phase and proceed to everyday use as a ***,we focused on powders consisting of polysaccharides,lipids,proteins or natural and synthetic polymers in the form of microparticles that are delivered by inhalation to the lungs as drug *** summarized the most common trends in research today to provide the best dry powders in the right fraction for inhalation that would be able to release the drug before being removed by natural *** review article addresses the most common manufacturing methods with novel modifications,pros and cons of different materials,drug loading capacities with release profiles,and biological properties such as cytocompatibility,bactericidal or anticancer properties.

关键词： pulmonary therapies drug delivery systems to lungs microparticles inhalers dry powder inhalers

Construction of Vertical Wind Profile from satellite-Derived Winds for Objective Analysis of Wind Field

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Advances in Atmospheric sciences 1992年第2期9卷 237-246页

作者： P.N.Mahajan D.R.Talwalkar s.nair s.Rajamani Indian Institute of Tropical Meteorology Pune-411008Indian Institute of Tropical Meteorology Pune-411008Indian Institute of Tropical Meteorology Pune-411008Indian Institute of Tropical Meteorology Pune-411008

During summer Monex-79, a variety of observing systems viz. research ships, research aircrafts, constant pressure balloons and geostationary satellite etc. were deployed, besides the regular conventional observations. The purpose of these additional systems was to make the best possible data for the studies on various aspects of monsoon circulation. The present study is aimed at the construction of vertical wind profile using cloud motion vectors obtained from GOEs (I-O) satellite and to examine whether the constructed wind profiles improves the representation of the monsoon system, flow pattern etc. in the objective analysis. For this purpose, climatological normals of the wind field are considered as the initial guess and the objective analyses of the wind field are made with, first using only data from conventional observations over land areas, subsequently including the constructed winds from cloud motion vectors. These analyses are then compared with the standard analyses of wind field obtained from Quick Look Atlas by T. N. Krishnamurti et al. (1979).It is inferred that satellite estimated mean wind profiles show good agreement with the mean wind profiles of the research ships with RMs errors less than 5 mps below 500 hPa and less than 8 mps above 500 hPa. It is further inferred that the inclusion of constructed winds shows a positive impact on the objective analysis and improvement is seen to be more marked in the data-sparse region of the Arabian sea. Analyses which include the constructed winds show better agreement with the standard analysis, than the analyses obtained using only conventional winds. Thus, results of our study suggest that the wind profiles constructed using cloud motion vectors are of potential use in objective analysis to depict the major circulation features over the Indian region.

关键词： Construction of Vertical Wind Profile from satellite-Derived Winds for Objective Analysis of Wind Field Wind

Revisiting cerebral endothelial cells in Alzheimer’s disease

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Neural Regeneration Research 2025年第10期20卷 2911-2912页

作者： Amira s.Hanafy Department of Neurosurgery University Hospital BonnBonnGermany

Alzheimer’s disease(AD)is the most common neurodegenerative disorder characterized by slow and progressive decline of cognitive and memory *** only approximately 5%of the cases,AD is familial,as often predisposed by genetic mutations(Hoogmartens et al.,2021),while sporadic AD accounts for approximately 95%of the *** amyloid cascade hypothesis is one of the fundamental hypotheses put out to explain AD pathogenesis as dysregulated homeostasis of amyloid-β(Aβ)peptides that leads to the accumulation of Aβplaques in the parenchyma,an anatomical hallmark of AD.

关键词： Alzheimer Aβ cerebral

A systematic review of progenitor survival and maturation in Parkinsonian models

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Neural Regeneration Research 2025年第11期20卷 3172-3178页

作者： Giulia Comini Eilís Dowd Pharmacology&Therapeutics and Galway Neuroscience Center University of GalwayGalwayIreland

stem cell-based brain repair is a promising emergent therapy for Parkinson's disease based on years of foundational research using human fetal donors as a cell *** current therapeutic options for patients,this approach has the potential to provide longterm stem cell–derived reconstruction and restoration of the dopaminergic input to denervated regions of the brain allowing for restoration of certain functions to *** ultimate clinical success of stem cell–derived brain repair will depend on both the safety and efficacy of the approach and the latter is dependent on the ability of the transplanted cells to survive and differentiate into functional dopaminergic neurons in the Parkinsonian *** the pre-clinical literature suggests that there is considerable variability in survival and differentiation between studies,the aim of this systematic review was to assess these parameters in human stem cell-derived dopaminergic progenitor transplant studies in animal models of Parkinson's disease.A defined systematic search of the PubMed database was completed to identify relevant studies published up to March *** screening,76 articles were included in the analysis from which 178 separate transplant studies were *** these,graft survival could be assessed in 52 studies and differentiation in 129 ***,we found that graft survival ranged froms transplanted,with a median of 51%of transplanted cells surviving in the brain;while dopaminergic differentiation of the cells ranged from 0% to 46% of cells transplanted with a median of 3%.This systematic review suggests that there is considerable scope for improvement in the differentiation of stem cell-derived dopaminergic progenitors to maximize the therapeutic potential of this approach for patients.

关键词： cell replacement therapy differentiation embryonic stem cells graft induced pluripotent stem cells Parkinson's disease survival transplant

Deciphering the mechanobiology of microglia in traumatic brain injury with advanced microsystems

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Neural Regeneration Research 2025年第8期20卷 2304-2306页

作者： Anthony Procès sylvain Gabriele Univ.Grenoble Alpes InsermU1216Grenoble Institut des NeurosciencesGrenobleFrance Mechanobiology&Biomaterials Group CIRMAPResearch Institute for BiosciencesUniversity of MonsMonsBelgium

Advanced microsystems in traumatic brain injury research:Traumatic brain injury(TBI)results from a mechanical insult to the brain,leading to neuronal and axonal damage and subsequently causing a secondary *** minutes ... 详细信息

关键词： traumatic injury damage

Emerging structures and dynamic mechanisms ofγ-secretase for Alzheimer’s disease

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Neural Regeneration Research 2025年第1期20卷 174-180页

作者： Yinglong Miao Michael s.Wolfe Computational Medicine Program and Department of Pharmacology University of North Carolina–Chapel HillChapel HillNCUSA Department of Medicinal Chemistry University of KansasLawrenceKSUSA

γ-secretase,called“the proteasome of the membrane,”is a membrane-embedded protease complex that cleaves 150+peptide substrates with central roles in biology and medicine,including amyloid precursor protein and the Notch family of cell-surface *** inγ-secretase and amyloid precursor protein lead to early-onset familial Alzheimer’s disease.γ-secretase has thus served as a critical drug target for treating familial Alzheimer’s disease and the more common late-onset Alzheimer’s disease as ***,critical gaps remain in understanding the mechanisms of processive proteolysis of substrates,the effects of familial Alzheimer’s disease mutations,and allosteric modulation of substrate cleavage byγ-*** this review,we focus on recent studies of structural dynamic mechanisms ofγ-*** mechanisms,including the“Fit-stay-Trim,”“sliding-Unwinding,”and“Tilting-Unwinding,”have been proposed for substrate proteolysis of amyloid precursor protein byγ-secretase based on all-atom molecular dynamics *** an incorrect registry of the Notch1 substrate was identified in the cryo-electron microscopy structure of Notch1-boundγ-secretase,molecular dynamics simulations on a resolved model of Notch1-boundγ-secretase that was reconstructed using the amyloid precursor protein-boundγ-secretase as a template successfully capturedγ-secretase activation for proper cleavages of both wildtype and mutant Notch,being consistent with biochemical experimental *** approach could be potentially applied to decipher the processing mechanisms of various substrates byγ-*** addition,controversy over the effects of familial Alzheimer’s disease mutations,particularly the issue of whether they stabilize or destabilizeγ-secretase-substrate complexes,is ***,an outlook is provided for future studies ofγ-secretase,including pathways of substrate binding and product release,effects of modulators on familial Alzheimer’s disease mutations

关键词： Alzheimer’s disease amyloid precursor protein cryo-EM structures drug design intramembrane proteolysis molecular dynamics Notch