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  1. Article ; Online: Enhance photoluminescence properties of Ca-Eu:Y

    Dwivedi, Arpita / Anuradha / Srivastava, Monika / Srivastava, Amit / Kumar, Rajneesh / Srivastava, Sanjay Kumar

    Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy

    2023  Volume 299, Page(s) 122782

    Abstract: The divalent ( ... ...

    Abstract The divalent (Ca
    Language English
    Publishing date 2023-05-13
    Publishing country England
    Document type Journal Article
    ZDB-ID 210413-1
    ISSN 1873-3557 ; 0370-8322 ; 0584-8539 ; 1386-1425
    ISSN (online) 1873-3557
    ISSN 0370-8322 ; 0584-8539 ; 1386-1425
    DOI 10.1016/j.saa.2023.122782
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Pulmonary Sarcoidosis: An Unusual Presentation with Acute Abdominal Pain.

    Prasad, Durga / Verma, Abhai / Srivastava, Rajneesh Kumar

    The Journal of pediatrics

    2021  Volume 231, Page(s) 290–293

    MeSH term(s) Abdominal Pain/etiology ; Acute Pain/etiology ; Adolescent ; Humans ; Male ; Sarcoidosis, Pulmonary/complications ; Sarcoidosis, Pulmonary/diagnosis
    Language English
    Publishing date 2021-01-01
    Publishing country United States
    Document type Case Reports ; Journal Article
    ZDB-ID 3102-1
    ISSN 1097-6833 ; 0022-3476
    ISSN (online) 1097-6833
    ISSN 0022-3476
    DOI 10.1016/j.jpeds.2020.12.074
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: Echocardiographic and Angiographic Assessment of Right Ventricular Function and Right Coronary Artery Stenosis in Acute Inferior Wall Myocardial Infarction.

    Kumar, Rajneesh / Kumar, Prakash / Srivastava, Prabin K / Kumar, Prashant

    Cureus

    2023  Volume 15, Issue 10, Page(s) e46403

    Abstract: Background: Cardiovascular diseases (CVDs) are a global concern. CVD remains a primary cause of death despite reduced coronary heart disease death rates. Acute coronary syndrome (ACS) involves myocardial infarction (MI) and unstable angina, sharing ... ...

    Abstract Background: Cardiovascular diseases (CVDs) are a global concern. CVD remains a primary cause of death despite reduced coronary heart disease death rates. Acute coronary syndrome (ACS) involves myocardial infarction (MI) and unstable angina, sharing mechanisms such as plaque instability. Our study assesses the right ventricular (RV) function's predictive value in acute inferior wall MI (IWMI) to identify high-risk patients with an elevated likelihood of experiencing severe cardiac complications, hemodynamic instability, or a higher mortality risk following an acute IWMI.
    Methodology: The research was conducted in the Department of Cardiology at the Rajendra Institute of Medical Sciences (RIMS), Ranchi, from July 2021 to June 2022, following the necessary ethical approval. A cohort of 140 patients with IWMI, carefully chosen according to rigorous criteria, clearly understood the study's objectives before providing informed consent. The evaluations were conducted in the following order: clinical assessments, followed by blood testing, then echocardiography, and finally, coronary angiography. Furthermore, the study examined risk factors and utilized statistical methods to elucidate the associations between qualities and results.
    Results: The study included 140 participants, with 61% being male and 39% female. Among the participants, 14% were aged 30-45, 50% were aged 46-60, and 30% were over 60. Age shows significant proportions in different categories. Diabetes, dyslipidemia, hypertension, and smoking/tobacco addiction did not differ among stenosis groups. Proximal right coronary artery (RCA) stenosis patients had elevated jugular venous pressure (JVP). The echocardiograms were performed within 48 hours of post-percutaneous coronary intervention, and significant differences between groups were observed. Participants with proximal stenosis had lower tricuspid annular plane systolic excursion (TAPSE) and right ventricular fractional area change (RVFAC), which showed compromised RV systolic function. Proximal stenosis patients had reduced systolic motion velocity (Sm), indicating impaired myocardial contraction. Echocardiographic parameters such as early diastolic velocity (Em), atrial contraction velocity (Am), Em/Am ratio (a marker of diastolic function), isovolumic relaxation time (IVRT), isovolumic contraction time (IVCT), and ejection time (ET) between groups were different, indicating distinct cardiac functions. Proximal stenosis increased the myocardial performance index (MPI), indicating cardiac impairment. The left ventricular ejection fraction (LVEF) was comparable in the two stenosis groups, indicating similar left ventricular performance.
    Conclusion:  Echocardiography showed significant RV function differences in acute inferior wall ST-segment elevation myocardial infarction (STEMI) patients with proximal and distal RCA lesions. RV dysfunction is linked to right ventricle myocardial infarction (RVMI), and echocardiographic markers can provide valuable insights. Results emphasize that acute inferior wall STEMI is diagnosed by electrocardiogram (ECG) criteria, particularly ST-segment elevation. However, these markers emphasize the importance of RV assessment in RCA involvement assessment. These findings suggest that RV function can help diagnose acute inferior wall STEMI RCA involvement. In acute inferior STEMIs, RV function echocardiography is essential for RCA lesion location.
    Language English
    Publishing date 2023-10-03
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2747273-5
    ISSN 2168-8184
    ISSN 2168-8184
    DOI 10.7759/cureus.46403
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Transcriptome-wide high-throughput mapping of protein-RNA occupancy profiles using POP-seq.

    Srivastava, Mansi / Srivastava, Rajneesh / Janga, Sarath Chandra

    Scientific reports

    2021  Volume 11, Issue 1, Page(s) 1175

    Abstract: Interaction between proteins and RNA is critical for post-transcriptional regulatory processes. Existing high throughput methods based on crosslinking of the protein-RNA complexes and poly-A pull down are reported to contribute to biases and are not ... ...

    Abstract Interaction between proteins and RNA is critical for post-transcriptional regulatory processes. Existing high throughput methods based on crosslinking of the protein-RNA complexes and poly-A pull down are reported to contribute to biases and are not readily amenable for identifying interaction sites on non poly-A RNAs. We present Protein Occupancy Profile-Sequencing (POP-seq), a phase separation based method in three versions, one of which does not require crosslinking, thus providing unbiased protein occupancy profiles on whole cell transcriptome without the requirement of poly-A pulldown. Our study demonstrates that ~ 68% of the total POP-seq peaks exhibited an overlap with publicly available protein-RNA interaction profiles of 97 RNA binding proteins (RBPs) in K562 cells. We show that POP-seq variants consistently capture protein-RNA interaction sites across a broad range of genes including on transcripts encoding for transcription factors (TFs), RNA-Binding Proteins (RBPs) and long non-coding RNAs (lncRNAs). POP-seq identified peaks exhibited a significant enrichment (p value < 2.2e-16) for GWAS SNPs, phenotypic, clinically relevant germline as well as somatic variants reported in cancer genomes, suggesting the prevalence of uncharacterized genomic variation in protein occupied sites on RNA. We demonstrate that the abundance of POP-seq peaks increases with an increase in expression of lncRNAs, suggesting that highly expressed lncRNA are likely to act as sponges for RBPs, contributing to the rewiring of protein-RNA interaction network in cancer cells. Overall, our data supports POP-seq as a robust and cost-effective method that could be applied to primary tissues for mapping global protein occupancies.
    MeSH term(s) Binding Sites/genetics ; Cell Line, Tumor ; Gene Expression Regulation/genetics ; Genome/genetics ; High-Throughput Nucleotide Sequencing/methods ; Humans ; K562 Cells ; Protein Interaction Maps/genetics ; RNA, Long Noncoding/genetics ; RNA-Binding Proteins/genetics ; Sequence Analysis, RNA/methods ; Transcriptome/genetics
    Chemical Substances RNA, Long Noncoding ; RNA-Binding Proteins
    Language English
    Publishing date 2021-01-13
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-020-80846-5
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Transcriptome-wide high-throughput mapping of protein–RNA occupancy profiles using POP-seq

    Mansi Srivastava / Rajneesh Srivastava / Sarath Chandra Janga

    Scientific Reports, Vol 11, Iss 1, Pp 1-

    2021  Volume 15

    Abstract: Abstract Interaction between proteins and RNA is critical for post-transcriptional regulatory processes. Existing high throughput methods based on crosslinking of the protein–RNA complexes and poly-A pull down are reported to contribute to biases and are ...

    Abstract Abstract Interaction between proteins and RNA is critical for post-transcriptional regulatory processes. Existing high throughput methods based on crosslinking of the protein–RNA complexes and poly-A pull down are reported to contribute to biases and are not readily amenable for identifying interaction sites on non poly-A RNAs. We present Protein Occupancy Profile-Sequencing (POP-seq), a phase separation based method in three versions, one of which does not require crosslinking, thus providing unbiased protein occupancy profiles on whole cell transcriptome without the requirement of poly-A pulldown. Our study demonstrates that ~ 68% of the total POP-seq peaks exhibited an overlap with publicly available protein–RNA interaction profiles of 97 RNA binding proteins (RBPs) in K562 cells. We show that POP-seq variants consistently capture protein–RNA interaction sites across a broad range of genes including on transcripts encoding for transcription factors (TFs), RNA-Binding Proteins (RBPs) and long non-coding RNAs (lncRNAs). POP-seq identified peaks exhibited a significant enrichment (p value < 2.2e−16) for GWAS SNPs, phenotypic, clinically relevant germline as well as somatic variants reported in cancer genomes, suggesting the prevalence of uncharacterized genomic variation in protein occupied sites on RNA. We demonstrate that the abundance of POP-seq peaks increases with an increase in expression of lncRNAs, suggesting that highly expressed lncRNA are likely to act as sponges for RBPs, contributing to the rewiring of protein–RNA interaction network in cancer cells. Overall, our data supports POP-seq as a robust and cost-effective method that could be applied to primary tissues for mapping global protein occupancies.
    Keywords Medicine ; R ; Science ; Q
    Subject code 612
    Language English
    Publishing date 2021-01-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: Lantern: an integrative repository of functional annotations for lncRNAs in the human genome.

    Daulatabad, Swapna Vidhur / Srivastava, Rajneesh / Janga, Sarath Chandra

    BMC bioinformatics

    2021  Volume 22, Issue 1, Page(s) 279

    Abstract: Background: With advancements in omics technologies, the range of biological processes where long non-coding RNAs (lncRNAs) are involved, is expanding extensively, thereby generating the need to develop lncRNA annotation resources. Although, there are a ...

    Abstract Background: With advancements in omics technologies, the range of biological processes where long non-coding RNAs (lncRNAs) are involved, is expanding extensively, thereby generating the need to develop lncRNA annotation resources. Although, there are a plethora of resources for annotating genes, despite the extensive corpus of lncRNA literature, the available resources with lncRNA ontology annotations are rare.
    Results: We present a lncRNA annotation extractor and repository (Lantern), developed using PubMed's abstract retrieval engine and NCBO's recommender annotation system. Lantern's annotations were benchmarked against lncRNAdb's manually curated free text. Benchmarking analysis suggested that Lantern has a recall of 0.62 against lncRNAdb for 182 lncRNAs and precision of 0.8. Additionally, we also annotated lncRNAs with multiple omics annotations, including predicted cis-regulatory TFs, interactions with RBPs, tissue-specific expression profiles, protein co-expression networks, coding potential, sub-cellular localization, and SNPs for ~ 11,000 lncRNAs in the human genome, providing a one-stop dynamic visualization platform.
    Conclusions: Lantern integrates a novel, accurate semi-automatic ontology annotation engine derived annotations combined with a variety of multi-omics annotations for lncRNAs, to provide a central web resource for dissecting the functional dynamics of long non-coding RNAs and to facilitate future hypothesis-driven experiments. The annotation pipeline and a web resource with current annotations for human lncRNAs are freely available on sysbio.lab.iupui.edu/lantern.
    MeSH term(s) Genome, Human ; Humans ; Molecular Sequence Annotation ; RNA, Long Noncoding/genetics
    Chemical Substances RNA, Long Noncoding
    Language English
    Publishing date 2021-05-26
    Publishing country England
    Document type Journal Article
    ZDB-ID 2041484-5
    ISSN 1471-2105 ; 1471-2105
    ISSN (online) 1471-2105
    ISSN 1471-2105
    DOI 10.1186/s12859-021-04207-3
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Lantern

    Swapna Vidhur Daulatabad / Rajneesh Srivastava / Sarath Chandra Janga

    BMC Bioinformatics, Vol 22, Iss 1, Pp 1-

    an integrative repository of functional annotations for lncRNAs in the human genome

    2021  Volume 19

    Abstract: Abstract Background With advancements in omics technologies, the range of biological processes where long non-coding RNAs (lncRNAs) are involved, is expanding extensively, thereby generating the need to develop lncRNA annotation resources. Although, ... ...

    Abstract Abstract Background With advancements in omics technologies, the range of biological processes where long non-coding RNAs (lncRNAs) are involved, is expanding extensively, thereby generating the need to develop lncRNA annotation resources. Although, there are a plethora of resources for annotating genes, despite the extensive corpus of lncRNA literature, the available resources with lncRNA ontology annotations are rare. Results We present a lncRNA annotation extractor and repository (Lantern), developed using PubMed’s abstract retrieval engine and NCBO’s recommender annotation system. Lantern’s annotations were benchmarked against lncRNAdb’s manually curated free text. Benchmarking analysis suggested that Lantern has a recall of 0.62 against lncRNAdb for 182 lncRNAs and precision of 0.8. Additionally, we also annotated lncRNAs with multiple omics annotations, including predicted cis-regulatory TFs, interactions with RBPs, tissue-specific expression profiles, protein co-expression networks, coding potential, sub-cellular localization, and SNPs for ~ 11,000 lncRNAs in the human genome, providing a one-stop dynamic visualization platform. Conclusions Lantern integrates a novel, accurate semi-automatic ontology annotation engine derived annotations combined with a variety of multi-omics annotations for lncRNAs, to provide a central web resource for dissecting the functional dynamics of long non-coding RNAs and to facilitate future hypothesis-driven experiments. The annotation pipeline and a web resource with current annotations for human lncRNAs are freely available on sysbio.lab.iupui.edu/lantern.
    Keywords LncRNA ; Ontology ; Expression ; Interaction ; eCLIP ; Coding potential ; Computer applications to medicine. Medical informatics ; R858-859.7 ; Biology (General) ; QH301-705.5
    Language English
    Publishing date 2021-05-01T00:00:00Z
    Publisher BMC
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article ; Online: CASowary: CRISPR-Cas13 guide RNA predictor for transcript depletion.

    Krohannon, Alexander / Srivastava, Mansi / Rauch, Simone / Srivastava, Rajneesh / Dickinson, Bryan C / Janga, Sarath Chandra

    BMC genomics

    2022  Volume 23, Issue 1, Page(s) 172

    Abstract: Background: Recent discovery of the gene editing system - CRISPR (Clustered Regularly Interspersed Short Palindromic Repeats) associated proteins (Cas), has resulted in its widespread use for improved understanding of a variety of biological systems. ... ...

    Abstract Background: Recent discovery of the gene editing system - CRISPR (Clustered Regularly Interspersed Short Palindromic Repeats) associated proteins (Cas), has resulted in its widespread use for improved understanding of a variety of biological systems. Cas13, a lesser studied Cas protein, has been repurposed to allow for efficient and precise editing of RNA molecules. The Cas13 system utilizes base complementarity between a crRNA/sgRNA (crispr RNA or single guide RNA) and a target RNA transcript, to preferentially bind to only the target transcript. Unlike targeting the upstream regulatory regions of protein coding genes on the genome, the transcriptome is significantly more redundant, leading to many transcripts having wide stretches of identical nucleotide sequences. Transcripts also exhibit complex three-dimensional structures and interact with an array of RBPs (RNA Binding Proteins), both of which may impact the effectiveness of transcript depletion of target sequences. However, our understanding of the features and corresponding methods which can predict whether a specific sgRNA will effectively knockdown a transcript is very limited.
    Results: Here we present a novel machine learning and computational tool, CASowary, to predict the efficacy of a sgRNA. We used publicly available RNA knockdown data from Cas13 characterization experiments for 555 sgRNAs targeting the transcriptome in HEK293 cells, in conjunction with transcriptome-wide protein occupancy information. Our model utilizes a Decision Tree architecture with a set of 112 sequence and target availability features, to classify sgRNA efficacy into one of four classes, based upon expected level of target transcript knockdown. After accounting for noise in the training data set, the noise-normalized accuracy exceeds 70%. Additionally, highly effective sgRNA predictions have been experimentally validated using an independent RNA targeting Cas system - CIRTS, confirming the robustness and reproducibility of our model's sgRNA predictions. Utilizing transcriptome wide protein occupancy map generated using POP-seq in HeLa cells against publicly available protein-RNA interaction map in Hek293 cells, we show that CASowary can predict high quality guides for numerous transcripts in a cell line specific manner.
    Conclusions: Application of CASowary to whole transcriptomes should enable rapid deployment of CRISPR/Cas13 systems, facilitating the development of therapeutic interventions linked with aberrations in RNA regulatory processes.
    MeSH term(s) CRISPR-Cas Systems ; Gene Editing/methods ; HEK293 Cells ; HeLa Cells ; Humans ; RNA, Guide, CRISPR-Cas Systems/genetics ; Reproducibility of Results
    Chemical Substances RNA, Guide, CRISPR-Cas Systems
    Language English
    Publishing date 2022-03-02
    Publishing country England
    Document type Journal Article
    ZDB-ID 2041499-7
    ISSN 1471-2164 ; 1471-2164
    ISSN (online) 1471-2164
    ISSN 1471-2164
    DOI 10.1186/s12864-022-08366-2
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article: A systematic approach towards optimization of brackish groundwater treatment using nanofiltration (NF) and reverse osmosis (RO) hybrid membrane filtration system

    Srivastava, Alka / Singh, Rajneesh / Rajput, Vishnu D. / Minkina, Tatiana / Agarwal, Smriti / Garg, Manoj Chandra

    Chemosphere. 2022 Sept., v. 303

    2022  

    Abstract: This research compares the performance efficiencies of Nanofiltration (NF), Reverse osmosis (RO), and Nanofiltration-Reverse Osmosis (NF-RO) hybrid membrane filtration systems, for treatment of brackish groundwater in Delhi-NCR region. Central composite ... ...

    Abstract This research compares the performance efficiencies of Nanofiltration (NF), Reverse osmosis (RO), and Nanofiltration-Reverse Osmosis (NF-RO) hybrid membrane filtration systems, for treatment of brackish groundwater in Delhi-NCR region. Central composite design (CCD) of response surface methodology (RSM) were applied to formulate predictive models for the optimization and simulation of various responses, viz. Water flux, salt rejection, permeate recovery and specific energy consumption (SEC). Three different input factors (feed concentration, pH and pressure) were evaluated. Significance of RSM model was tested and validated with use of an analysis of variance (ANOVA). The models were also compared graphically for their prediction ability. The optimum conditions were determined by numerical optimization of the NF and RO membrane pilot plants. Finally, hybrid configurations of NF and RO were investigated utilising the optimum conditions to identify the technology suitable for the remediation of brackish groundwater. Despite, RO membrane eliminating over 99% of TDS from groundwater, the lower recovery rate renders it environmentally unfavourable. Result indicates that recovery of the hybrid system (40.35%) was greater than that of RO alone (18.796%) and SEC also decreases (5.090–3.8 kW H/m³). Hence, combining a hybrid membrane arrangement with NF-RO to treat brackish groundwater for improved recovery and lower SEC is a viable alternative.
    Keywords analysis of variance ; groundwater ; groundwater treatment ; microfiltration ; models ; nanofiltration ; pH ; prediction ; remediation ; response surface methodology ; reverse osmosis ; specific energy
    Language English
    Dates of publication 2022-09
    Publishing place Elsevier Ltd
    Document type Article
    ZDB-ID 120089-6
    ISSN 1879-1298 ; 0045-6535 ; 0366-7111
    ISSN (online) 1879-1298
    ISSN 0045-6535 ; 0366-7111
    DOI 10.1016/j.chemosphere.2022.135230
    Database NAL-Catalogue (AGRICOLA)

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  10. Article: Current Utility of Transgastric Percutaneous Drainage for the Management of Pancreatitis-Related Retrogastric Walled-Off Necrotic Collections: A Prospective Observational Study.

    Agrawal, Sarthak / Arya, Asmita / Gautam, Avinash D / Yadav, Rajanikant R / Singh, Ashish / Boruah, Deb / Mohindra, Samir / Gupta, Archana / Srivastava, Anshu / Gurjar, Mohan / Singh, Rajneesh K / Rahul, Rahul

    Cureus

    2024  Volume 16, Issue 3, Page(s) e56443

    Abstract: Introduction Pancreatic fluid collection (PFC) is one of the most frequent complications associated with acute pancreatitis. The route of drainage is guided by the size and site of collection. The present study aims to assess the clinical and technical ... ...

    Abstract Introduction Pancreatic fluid collection (PFC) is one of the most frequent complications associated with acute pancreatitis. The route of drainage is guided by the size and site of collection. The present study aims to assess the clinical and technical success of transgastric percutaneous drainage (PCD) for managing retrogastric walled-off pancreatic necrosis (WOPN). Materials and methods A total of 44 patients with acute pancreatitis diagnosed with WOPN who underwent transgastric PCD with ultrasound or CT guidance as part of standard clinical management were included in the study. Patients were observed for improvement in clinical parameters, and treatment outcomes were noted in terms of technical success, clinical success, adverse events, need for additional procedures, hospital stay, and duration of placement of all drains. Data for the internalization of transgastric PCD was also observed in the study. Results Technical success during the drain placement was observed in 93% (n=41) of patients.Internalization of the transgastric drain was attempted in 12 patients and successful in 11 (91%). The median duration of hospital stay from the time of placement of the first PCD until discharge and the median duration of all PCDs placed were higher in patients where the transgastric drain was not internalized as compared to patients where the transgastric drain was internalized. Conclusion In WOPN, transgastric drain placement and successful internalization in any form help in the early resolution of peripancreatic and abdominal collections. It also reduces the time to percutaneous catheter removal, which in turn reduces the morbidity and decreases the need for additional interventions or surgery.
    Language English
    Publishing date 2024-03-19
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2747273-5
    ISSN 2168-8184
    ISSN 2168-8184
    DOI 10.7759/cureus.56443
    Database MEDical Literature Analysis and Retrieval System OnLINE

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