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MARS and RNAcmap3:The Master Database of All Possible RNA Sequences Integrated with RNAcmap for RNA Homology Search

Genomics, Proteomics & Bioinformatics 2024年第1期22卷 143-150页

作者： Ke Chen Thomas Litfin jaswinder singh Jian Zhan Yaoqi Zhou Institute of Systems and Physical Biology Shenzhen Bay LaboratoryShenzhen 518055China Peking University Shenzhen Graduate School Shenzhen 518055China University of Science and Technology of China Hefei 230026China Suzhou Institute for Advanced Research University of Science and Technology of ChinaSuzhou 215123China Institute for Glycomics Griffith UniversitySouthportQLD 4222Australia

sequences found in the huge,integrated database of protein sequences(Big Fantastic Database).In contrast,the existing nucleotide databases were not consolidated to facilitate wider and deeper homology ***,we built a comprehensive database by incorporating the non-coding RNA(ncRNA)sequences from RNAcentral,the transcriptome assembly and metagenome assembly from metagenomics RAST(MG-RAST),the genomic sequences from Genome Warehouse(GWH),and the genomic sequences from MGnify,in addition to the nucleotide(nt)database and its subsets in National Center of Biotechnology Information(NCBI).The resulting Master database of All possible RNA sequences(MARS)is 20-fold larger than NCBI’s nt database or 60-fold larger than *** new dataset along with a new split-search strategy allows a substantial improvement in homology search over existing state-of-the-art *** also yields more accurate and more sensitive multiple sequence alignments(MSAs)than manually curated MSAs from Rfam for the majority of structured RNAs mapped to *** results indicate that MARS coupled with the fully automatic homology search tool RNAcmap will be useful for improved structural and functional inference of ncRNAs and RNA language models based on *** is accessible at https://***/omix/release/OMIX003037,and RNAcmap3 is accessible at http://***/download/.

关键词： RNA sequence database Homology search Secondary structure MARS RNAcmap3

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Fabrication characteristics and tribological behavior of Al/SiC/Gr hybrid aluminum matrix composites: A review

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Friction 2016年第3期4卷 191-207页

作者： jaswinder singh University Institute of Engineering and Technology Panjab University SSG Regional Centre Hoshiarpur Punjab 146023 India

Improvement in surface properties and retainment of bulk properties are essential requirements for the design of components for wear resistance applications. This paper summarizes various features of Al/SiC/Gr hybrid composites that can be employed in different tribological applications. The study has revealed that the processing route plays a significant role in obtaining a homogeneous structure of these composites. In powder metallurgy, the selection of sizes of the matrix and reinforcement powders is crucial, whereas the wettability between the reinforcement particles and molten alloy is a major challenge in liquid metallurgy. The incorporation of SiC particles increases the mechanical strength and wear performance of Al composites. However, ejection of these particles can reduce the wear performance of Al composites under severe conditions. The addition of Gr particles helps in the formation of a thick and extensive tribolayer on the wear surface. This layer reduces direct contact between the rubbing surfaces, thereby decreasing the wear rate under certain conditions. Morphological analysis of worn surfaces has confirmed that the hybrid composites exhibit superior wear properties than the pure Al alloy and the ceramic-reinforced composite. However, increase in the Gr content beyond a limiting value can deteriorate the tribological properties of these composites. Therefore, true optimization of a tribosystem (of the hybrid composite and counterface) can be achieved by selecting appropriate reinforcement contents.

关键词： metal matrix composites (MMCs) sliding wear solid lubricant particles scanning electron microscopy (SEM) casting/sintering

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Sequence-based genetic mapping of Ds-tagged insertions to characterize malting-related traits in barley

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The Crop Journal 2017年第1期5卷 11-20页

作者： Surinder singh jaswinder singh Department of Food and Bioproduct Sciences University of Saskatchewan 51 Campus Drive Plant Science Department 21 111 Rue LakeshoreSt Anne de BellevueMc Gill University

Among various functional genomics tools used to characterize genes in plants, transposonbased mutagenesis approaches offer great potential, especially in barley and wheat, which possess large genomes and in which genetic transformation is not routine. Two Ds transposon flanking sequences(TNPs), TNP-29(27.4 c M(centi Morgan)) and TNP-79(70.3 c M), were mapped in the vicinity of a malting quality QTL located on chromosome 4H of barley. Reactivation of the Ds transposon sequence from these TNP lines led to the identification of genes in the malting QTL regions. Several Ds(dissociation) lines were generated by crossing TNP-29 and TNP-79 with an Ac TPase(activator) expressing line(25-B), and F2 progenies were subsequently screened for Ds insertions at new locations. To further characterize these Ds mutants, we mapped the new Ds flanking sequences on a barley genetic map and found that 29% of Ds were located in regions associated with the malting QTL located on chromosome 4H and in close proximity to other important malting-associated QTL across the barley chromosome. Using a sequence based approach, a linkage map was generated that confirmed the position of Ds loci in the barley genome map. Locating these Ds loci on the barley map opens avenues to dissect important malting QTL for facilitating identification of candidate malting genes.

关键词： Transposon tagging Linkage mapping Malting QTL Barley

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Transposon-based genetic diversity assessment in wild and cultivated barley

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The Crop Journal 2017年第4期5卷 296-304页

作者： Surinder singh Prabhjot singh Nandha jaswinder singh Department of Plant Science McGill University 21111 Lakeshore Road Sainte-Anne-de-Bellevue Quebec H9X 3V9 Canada Department of Plant Sciences University of Saskatchewan 51 campus drive Saskatoon SK S7N 5A8 Canada

Transposable element-based molecular markers can be utilized to investigate genetic diversity and to create genetic linkage *** this study,Class I and class II transposons were employed to obtain a comparative account of genetic diversity between wild and cultivated barley *** types of PCR-based techniques were used:IMP(Inter MITE Polymorphism),IRAP(Inter-Retrotransposon Amplified Polymorphism)and REMAP(Retrotransposon-Microsatellite Amplified Polymorphism).Specific primer pairs for IMP,IRAP,and REMAP detected a total of 200 bands with an average of 20 bands per *** mean polymorphic information content(PIC)and discrimination power(D)values in all 47 genotypes from these three types of transposon-based polymorphisms were 0.910 and0.935,*** Pair Group Method with Arithmetic mean(UPGMA)-based cluster analysis classified all 47 genotypes,both wild and cultivated,into separate groups consistent with their geographical *** followed by chromosome location of polymorphic bands enables precise gene introgression from wild gene pool to cultivated *** highly polymorphic nature of these marker systems makes them suitable for use in varietal identification and MAS-based breeding programs in barley and other cereals.

关键词： IMP REMAP IRAP Polymorphic information content (PIC) Discrimination power (D)

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Roman to Gurmukhi Social Media Text Normalization

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International Journal of Intelligent Computing and Cybernetics 2020年第4期13卷 407-435页

作者： Jagroop Kaur jaswinder singh Department of Computer Science and Engineering Punjabi UniversityPatialaIndia

Purpose-Normalization is an important step in all the natural language processing applications that are handling social media *** text from social media poses a different kind of problems that are not present in regular ***,a considerable amount of work has been done in this direction,but mostly in the English *** who do not speak English code mixed the text with their native language and posted text on social media using the Roman *** kind of text further aggravates the problem of *** paper aims to discuss the concept of normalization with respect to code-mixed social media text,and a model has been proposed to normalize such ***/methodology/approach-The system is divided into two phases-candidate generation and most probable sentence *** generation task is treated as machine translation task where the Roman text is treated as source language and Gurmukhi text is treated as the target *** translation system has been proposed to generate candidate *** candidates are generated,the second phase uses the beam search method for selecting the most probable sentence based on hidden Markov ***-Character error rate(CER)and bilingual evaluation understudy(BLEU)score are *** proposed system has been compared with Akhar software and RB\_R2G system,which are also capable of transliterating Roman text to *** performance of the system outperforms Akhar *** CER and BLEU scores are 0.268121 and 0.6807939,respectively,for ill-formed *** limitations/implications-It was observed that the system produces dialectical variations of a word or the word with minor errors like diacritic *** checker can improve the output of the system by correcting these minor *** experimentation is needed for optimizing language identifier,which will further help in improving the *** language model also seeks further ***

关键词： Social media text Text normalization Code-mixed text Deep neural network Language model

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Fabrication characteristics and tensile strength of novel Al2024/SiC/red mud composites processed via stir casting route

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Transactions of Nonferrous Metals Society of China 2017年第12期27卷 2573-2586页

作者： jaswinder singh Amit CHAUHAN University Institute of Engineering and Technology PUSSGRC Hoshiarpur Punjab 146023 India University Institute of Engineering and Technology Panjab University Chandigarh 160014 India

The stir casting technique was used to fabricate aluminum2024matrix hybrid composites reinforced with SiC(5%,mass fraction)and red mud(5%-20%,mass fraction)*** developed composites were characterized by using scanning electron microscopy(SEM)and electron dispersive spectrum(EDS)***,Taguchi’s approach of experimental design was used to examine the tensile strength of the hybrid composites(with minimum number of experiments).It was found that the reinforcing particles were well dispersed and adequately bonded in the hybrid *** density and porosity of the hybrid composites were reduced with the increase in reinforcement *** tensile strength of the composites increased with the increase in the red mud content and the ageing *** developed model indicated that the red mud content had the highest influence on the tensile strength response followed by the ageing ***,it was found that Al2024/SiC/red mud composites exhibited superior tensile strength(about34%higher)in comparison to the Al2024alloy under optimized conditions.

关键词： aluminum matrix composites hybrid reinforcements tensile strength red mud stir casting statistical analysis scanning electron microscopy (SEM)

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Genetic diversity and population structure of Pisum sativum accessions for marker-trait association of lipid content

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The Crop Journal 2015年第3期3卷 238-245页

作者： Sajjad Ahmad Simerjeet Kaur Neil Dylan Lamb-Palmer Mark Lefsrud jaswinder singh Department of Plant Science Mc Gill University Ste Anne de Bellevue Quebec H9X 3V9 Canada Department of Bioresource Engineering Mc Gill University Ste Anne de Bellevue Quebec H9X 3V9 Canada

Field pea(Pisum sativum L.) is an important protein-rich pulse crop produced globally. Increasing the lipid content of Pisum seeds through conventional and contemporary molecular breeding tools may bring added value to the crop. However, knowledge about genetic diversity and lipid content in field pea is limited. An understanding of genetic diversity and population structure in diverse germplasm is important and a prerequisite for genetic dissection of complex characteristics and marker-trait associations. Fifty polymorphic microsatellite markers detecting a total of 207 alleles were used to obtain information on genetic diversity, population structure and marker-trait associations. Cluster analysis was performed using UPGMA to construct a dendrogram from a pairwise similarity matrix. Pea genotypes were divided into five major clusters. A model-based population structure analysis divided the pea accessions into four groups. Percentage lipid content in 35 diverse pea accessions was used to find potential associations with the SSR markers. Markers AD73, D21, and AA5 were significantly associated with lipid content using a mixed linear model(MLM) taking population structure(Q) and relative kinship(K) into account. The results of this preliminary study suggested that the population could be used for marker-trait association mapping studies.

关键词： Diversity Field Pea Lipid content Marker-trait association Mixed linear model SSR

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Desmoid type fibromatosis: A case report with an unusual etiology

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World Journal of Gastrointestinal Oncology 2017年第9期9卷 385-389页

作者： Syed Faisal Jafri Obada Obaisi Gerardo G Vergara Joe Cates jaswinder singh Jennifer Feeback Harathi Yandrapu Gastroenterology Research Medical CenterKansas City School of Medicine University of Missouri in Kansas City Pathology Research Medical CenterKansas City General and Vascular Surgery Research Medical CenterKansas City Hematology/Oncology Research Medical CenterKansas City Clinical Research Research Medical CenterKansas City Internal Medicine Department of Research Medical Center and Research Department of Kansas City Veterans Affairs Medical Center

Desmoid type fibromatosis(DTF) is a rare, locally invasive, non-metastasizing soft tissue tumor. We report an interesting case of DTF involving the pancreatic head of a 54-year-old woman. She presented with intermittent dysphagia and significant weight loss within a 3-mo period. Laboratory findings showed mild elevation of transaminases, significant elevation of alkaline phosphatase and direct hyperbilirubinemia, indicating obstructive jaundice. Computerized tomography of the abdomen revealed a mass in the head of the pancreas, dilated common bile duct, and dilated pancreatic duct. Endoscopic retrograde cholangiopancreatography and endoscopic ultrasound showed a large hypoechoic massin the head of the pancreas causing extrahepatic biliary obstruction and pancreatic ductal dilation. The patient underwent a successful partial pancreatico-duodenectomy and cholecystectomy. She received no additional therapy after surgery, and liver function tests were normalized within nine days after surgery. Currently, surgical resection is the recommended first line treatment. The patient will be followed for any recurrence.

关键词： Desmoid type fibromatosis Desmoid tumor Aggressive fibromatosis Pancreas Painless jaundice

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Analysis of Non-Selective Catalyst Reduction Performance with Dedicated Exhaust Gas Recirculation

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Advances in Chemical Engineering and Science 2022年第2期12卷 114-129页

作者： Chris A. Van Roekel David T. Montgomery jaswinder singh Daniel B. Olsen Energy Institute Colorado State University Fort Collins USA Caterpillar Inc Peoria USA

Rich burn industrial natural gas engines offer best in class post catalyst emissions by using a non-selective catalyst reduction aftertreatment technology. However, they operate with reduced power density when compared to lean burn engines. Dedicated exhaust gas recirculation (EGR) offers a possible pathway for rich burn engines to use non-selective catalyst reduction aftertreatment technology without sacrificing power density. In order to achieve best in class post catalyst emissions, the precious metals and washcoat of a non-selective catalyst must be designed according to the expected exhaust composition of an engine. In this work, a rich burn industrial natural gas engine operating with dedicated EGR was paired with a commercially available non-selective catalyst. At rated brake mean effective pressure (BMEP) the air-fuel ratio was swept between rich and lean conditions to compare the catalyst reduction efficiency and post catalyst emissions of rich burn and dedicated EGR combustion. It was found that due to low oxides of nitrogen (NOx) emissions across the entire air-fuel ratio range, dedicated EGR offers a much larger range of air-fuel ratios where low regulated emissions can be met. Low engine out NOx also points towards a possibility of using an oxidation catalyst rather than a non-selective catalyst for dedicated EGR applications. The location of the NOx-CO tradeoff was shifted to more rich conditions using dedicated EGR.

关键词： Natural Gas Engine Rich Burn Dedicated Exhaust Gas Recirculation Catalyst

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Therapeutic Applications of Naringenin, a Flavanone Enriched in Citrus Fruits, for Disorders beyond Diabetes

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Phyton-International Journal of Experimental Botany 2020年第4期89卷 795-803页

作者： jaswinder Kaur Manish Vyas Joginder singh Ram Prasad Jeena Gupta School of Bioengineering and Biosciences Lovely Professional UniversityPhagwaraPunjab144411India School of Pharmaceutical Sciences Lovely Professional UniversityPhagwaraPunjab144411India Department of Botany Mahatma Gandhi Central UniversityMotihariBihar845801India

In recent years,there has been an increase in epidemiological studies to highlight the health benefits of plant secondary ***(polyphenolic plant secondary metabolites)are recently emerging as an important source for the discovery of new drugs increasing their pharmaceuticals,nutraceutical and medicinal *** is a flavanone,enriched in citrus fruits,tomatoes,bergamot,*** has been evaluated extensively for managing ***,in addition to this,naringenin had been ascribed to various important biological activities like antioxidant,antiviral,anticancer,anti-inflammatory,antiestrogenic,*** article aims at highlighting the therapeutic value of naringenin in managing disorders other than diabetes and its role in regulating gene expression by altering chromatin structure as histone deacetylase *** understanding of these phenomena will increase the overall knowledge of the various health-promoting effects of citrus fruits.

关键词： Naringenin flavanone anti-viral hepatoprotective anti-cancer anti-estrogenic

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