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101. Optimization of Delay Sequencing in Multi-Row Blast using Single Hole Blast Concepts

Author: Hemant Agrawal, B. S. Choudhary, M. L. Sharma, and Hemant Kumar
Subjects: 0209 industrial biotechnology, business.industry, Mechanical Engineering, Metals and Alloys, 02 engineering and technology, Structural engineering, Geotechnical Engineering and Engineering Geology, Vibration, 020303 mechanical engineering & transports, 020901 industrial engineering & automation, 0203 mechanical engineering, Face (geometry), Single hole, Materials Chemistry, Superimposition, Reduction (mathematics), business, Row, Intensity (heat transfer), Mathematics, Rock blasting
Abstract: The control of blast-induced ground vibration and generation of back break are main concerns of mine management. Because it damages structures near to the blasting face and makes highwall instable. It was observed during prediction of blast-induced ground vibration through scaled distance technique that it does not consider the superimposition effect of waves. Therefore, the predicted values of ground vibration differ from actual value. This study was conducted to see the superimposition effect using single hole blast concept and optimizing the blast design parameters. By this method, it is possible to nullify the chances of superimposition of waves and their influence on generation of blast-induced ground vibration and backbreak. From the study, it was found that at 92 ms delay between rows generate less backbreak compared to 42 ms and 67 ms delay. It has been found that a significant reduction in vibration can be achieved using 92 ms delay between rows, i.e., reduction up to 31% to 61% compare to 42 ms delay between row and 7% to 42% compare to 67 ms delay between rows, when blast intensity generated by single hole was 10 mm/sec.
Published: 2021

102. Tocilizumab plus standard care versus standard care in patients in India with moderate to severe COVID-19-associated cytokine release syndrome (COVINTOC): an open-label, multicentre, randomised, controlled, phase 3 trial

Author: Arvinder S. Soin, Vipul Mishra, Suneetha Narreddy, Ashish Gupta, Dhruva Chaudhry, Narendra S. Choudhary, Rahul A Pandit, Shashikala A Sangle, Vikas Agarwal, Pawan Kumar Singh, Vikas Deswal, Sushila Kataria, Yatin Mehta, Deepak Govil, Suresh Kumar, Pooja Sharma, Rajesh Chawla, Athimalaipet V Ramanan, Kuldeep Kumar, and Manoj Goel
Subjects: Male, Pulmonary and Respiratory Medicine, medicine.medical_specialty, Critical Care, Population, India, Antibodies, Monoclonal, Humanized, Severity of Illness Index, law.invention, chemistry.chemical_compound, Tocilizumab, Randomized controlled trial, law, Internal medicine, Intensive care, Severity of illness, Clinical endpoint, Humans, Immunologic Factors, Medicine, Mortality, Adverse effect, education, Respiratory Distress Syndrome, education.field_of_study, SARS-CoV-2, business.industry, COVID-19, Articles, Middle Aged, Receptors, Interleukin-6, Respiration, Artificial, Clinical trial, Treatment Outcome, chemistry, Female, Drug Monitoring, Cytokine Release Syndrome, business
Abstract: BACKGROUND: Global randomised controlled trials of the anti-IL-6 receptor antibody tocilizumab in patients admitted to hospital with COVID-19 have shown conflicting results but potential decreases in time to discharge and burden on intensive care. Tocilizumab reduced progression to mechanical ventilation and death in a trial population enriched for racial and ethnic minorities. We aimed to investigate whether tocilizumab treatment could prevent COVID-19 progression in the first multicentre randomised controlled trial of tocilizumab done entirely in a lower-middle-income country. METHODS: COVINTOC is an open-label, multicentre, randomised, controlled, phase 3 trial done at 12 public and private hospitals across India. Adults (aged ≥18 years) admitted to hospital with moderate to severe COVID-19 (Indian Ministry of Health grading) confirmed by positive SARS-CoV-2 PCR result were randomly assigned (1:1 block randomisation) to receive tocilizumab 6 mg/kg plus standard care (the tocilizumab group) or standard care alone (the standard care group). The primary endpoint was progression of COVID-19 (from moderate to severe or from severe to death) up to day 14 in the modified intention-to-treat population of all participants who had at least one post-baseline assessment for the primary endpoint. Safety was assessed in all randomly assigned patients. The trial is completed and registered with the Clinical Trials Registry India (CTRI/2020/05/025369). FINDINGS: 180 patients were recruited between May 30, 2020, and Aug 31, 2020, and randomly assigned to the tocilizumab group (n=90) or the standard care group (n=90). One patient randomly assigned to the standard care group inadvertently received tocilizumab at baseline and was included in the tocilizumab group for all analyses. One patient randomly assigned to the standard care group withdrew consent after the baseline visit and did not receive any study medication and was not included in the modified intention-to-treat population but was still included in safety analyses. 75 (82%) of 91 in the tocilizumab group and 68 (76%) of 89 in the standard care group completed 28 days of follow-up. Progression of COVID-19 up to day 14 occurred in eight (9%) of 91 patients in the tocilizumab group and 11 (13%) of 88 in the standard care group (difference -3·71 [95% CI -18·23 to 11·19]; p=0·42). 33 (36%) of 91 patients in the tocilizumab group and 22 (25%) of 89 patients in the standard care group had adverse events; 18 (20%) and 15 (17%) had serious adverse events. The most common adverse event was acute respiratory distress syndrome, reported in seven (8%) patients in each group. Grade 3 adverse events were reported in two (2%) patients in the tocilizumab group and five (6%) patients in the standard care group. There were no grade 4 adverse events. Serious adverse events were reported in 18 (20%) patients in the tocilizumab group and 15 (17%) in the standard care group; 13 (14%) and 15 (17%) patients died during the study. INTERPRETATION: Routine use of tocilizumab in patients admitted to hospital with moderate to severe COVID-19 is not supported. However, post-hoc evidence from this study suggests tocilizumab might still be effective in patients with severe COVID-19 and so should be investigated further in future studies. FUNDING: Medanta Institute of Education and Research, Roche India, Cipla India, and Action COVID-19 India.
Published: 2021

103. A systematic CRISPR screen defines mutational mechanisms underpinning signatures caused by replication errors and endogenous DNA damage

Author: Tauanne Dias Amarante, Gene Ching Chiek Koh, Glen Brice, Chukwuma A. Agu, Arjun Scott Nanda, Katie Urgo, Jyoti S. Choudhary, Sophie Momen, Theodoros I. Roumeliotis, Lucy Side, Rebecca Harris, Vanesa Perez-Alonso, Daniel Rueda, Andrea Degasperi, Serena Nik-Zainal, Wendy Bushell, Josef Jiricny, Cherif Badja, Celine Gomez, Jamie Young, William C Skarne, and Xueqing Zou
Subjects: Genomic instability, Genome instability, Cancer Research, DNA damage, Induced Pluripotent Stem Cells, Biology, medicine.disease_cause, Article, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, Neoplastic Syndromes, Hereditary, medicine, Humans, cancer, CRISPR, Clustered Regularly Interspaced Short Palindromic Repeats, Gene, Polymerase, 030304 developmental biology, Genetics, cancer genomics, 0303 health sciences, Brain Neoplasms, Oncology, chemistry, 030220 oncology & carcinogenesis, Mutation, biology.protein, CRISPR-Cas9 systems, DNA mismatch repair, Colorectal Neoplasms, Carcinogenesis, DNA, DNA Damage
Abstract: Mutational signatures are imprints of pathophysiological processes arising through tumorigenesis. We generated isogenic CRISPR-Cas9 knockouts (Δ) of 43 genes in human induced pluripotent stem cells, cultured them in the absence of added DNA damage, and performed whole-genome sequencing of 173 subclones. ΔOGG1, ΔUNG, ΔEXO1, ΔRNF168, ΔMLH1, ΔMSH2, ΔMSH6, ΔPMS1, and ΔPMS2 produced marked mutational signatures indicative of being critical mitigators of endogenous DNA modifications. Detailed analyses revealed mutational mechanistic insights, including how 8-oxo-dG elimination is sequence-context-specific while uracil clearance is sequence-context-independent. Mismatch repair (MMR) deficiency signatures are engendered by oxidative damage (C>A transversions), differential misincorporation by replicative polymerases (T>C and C>T transitions), and we propose a ‘reverse template slippage’ model for T>A transversions. ΔMLH1, ΔMSH6, and ΔMSH2 signatures were similar to each other but distinct from ΔPMS2. Finally, we developed a classifier, MMRDetect, where application to 7,695 WGS cancers showed enhanced detection of MMR-deficient tumors, with implications for responsiveness to immunotherapies.
Published: 2021

104. A perspective on corrosion of multi-principal element alloys

Author: John R. Scully, S. Choudhary, Mitra L. Taheri, and Nick Birbilis
Subjects: 010302 applied physics, Materials science, Materials Science (miscellaneous), Metallurgy, 02 engineering and technology, 021001 nanoscience & nanotechnology, 01 natural sciences, Corrosion, Metallic alloy, Chemistry (miscellaneous), 0103 physical sciences, Corrosion resistant, Materials Chemistry, Ceramics and Composites, TA401-492, Principal element, 0210 nano-technology, Materials of engineering and construction. Mechanics of materials
Abstract: Metallic alloys are critical to essentially all advanced technologies and engineered systems. The well-documented impact of corrosion (and oxidation) of alloys, remains a significant industrial and economic challenge, year on year. Recent activity in the field of metallurgy has revealed a class of metallic alloys, termed multi principal element alloys (MPEAs) that present unique physical properties. Such MPEAs have in many instances also demonstrated a high resistance to corrosion – which may permit the broader use of MPEAs as corrosion resistant alloys (CRAs) in harsh environments. Herein, the progress in MPEA research to date, along with prospects and challenges, are concisely reviewed—with potential future lines of research elaborated.
Published: 2021

105. Incorporating Tumor Biology to Predict Hepatocellular Carcinoma Recurrence in Patients Undergoing Living Donor Liver Transplantation Using Expanded Selection Criteria

Author: Neeraj Saraf, Dheeraj Gautam, Prashant Bhangui, Rohan Jagat Chaudhary, Amit Rastogi, A.S. Soin, Sanjay Kumar Yadav, Samiran Nundy, Narendra S. Choudhary, Sanjiv Saigal, Tarun Piplani, and S. Thiagarajan
Subjects: medicine.medical_specialty, Carcinoma, Hepatocellular, Cirrhosis, medicine.medical_treatment, Disease, 030230 surgery, Liver transplantation, Gastroenterology, 03 medical and health sciences, 0302 clinical medicine, Internal medicine, Living Donors, medicine, Humans, Avidity, Risk factor, Biology, Retrospective Studies, Transplantation, Hepatology, business.industry, Patient Selection, Liver Neoplasms, medicine.disease, Liver Transplantation, Hepatocellular carcinoma, San Francisco, 030211 gastroenterology & hepatology, Surgery, alpha-Fetoproteins, Neoplasm Recurrence, Local, Alpha-fetoprotein, business, Living donor liver transplantation
Abstract: Conventional selection criteria for liver transplantation in patients with hepatocellular carcinoma (HCC) based on tumour size and number alone, do not consider vital surrogates of tumor biology like alpha-fetoprotein (AFP) and tumour FDG-18 PET avidity. We follow an expanded selection criteria for living donor liver transplantation (LDLT) in patients with cirrhosis and HCC (HCC-cirr): no extrahepatic disease, no major vascular invasion, irrespective of tumour size and number. We analyzed survival outcomes in 405 HCC-cirr patients (51% beyond Milan, 43% beyond UCSF criteria), and predictors of HCC recurrence. The 5-yr overall (OS) and recurrence-free (RFS) were 64% and 70%, respectively. Recurrence rate in 300 patients (excluding postoperative deaths, and those with deficient preoperative data) was 17.6%, with 3 preoperatively available factors predicting worse RFS; pre-LT AFP ≥100 ng/ml (p=0.005, HR:2.190), tumour burden beyond UCSF criteria (p=0.001, HR:2.640), and FDG-18 PET avidity (p=0.004, HR:2.442). Tumour FDG-18 PET avidity and AFP ≥100 mg/ml predicted OS. A prognostic model based on the number of, and combination of the above pre operative risk factors for recurrence, was developed using a competing-risk RFS model, and helped stratify patients into 3 risk groups: low risk (none or a single risk factor present, 9.3% recurrence), moderate risk (AFP≥100 ng/ml and FDG-18 PET avidity, or beyond UCSF tumour and FDG-18 PET avidity, 25% recurrence), and high risk (AFP≥100 ng/ml and beyond UCSF, or presence of all 3 risk factors, 46% recurrence). Conclusion: Acceptable post-LDLT long term outcomes were achieved using our expanded selection criteria. Our prognostic model to predict recurrence based on pre operative biological and morphological factors could guide pre-transplant management (downstaging vs. upfront LDLT), with the aim of reducing post-LDLT recurrence.
Published: 2021

106. Prediction of back break in blasting using random decision trees

Author: Shankar Kumar, B. S. Choudhary, and A. K. Mishra
Subjects: geography, geography.geographical_feature_category, Mean squared error, Explosive material, General Engineering, Decision tree, Process (computing), Computer Science Applications, Random forest, Rockfall, Modeling and Simulation, Linear regression, Geotechnical engineering, Rock mass classification, Software, Geology
Abstract: Back break is an unsolicited phenomenon caused due to rock condition, blast geometry, explosive and initiation system in mines. It does not help in creating a smooth high wall and free face for next blasting due to cracks, overhang and under-hang. It can cause rockfall during drilling due to the cracks present in the in situ rock mass at the perimeter. Due to improper free face created from the previous blast and the presence of loose strata in the face increases the overall cost of production. Therefore, predicting and subsequently optimising back break shall reduce their problems to some extent. In this paper, an attempt is made to predict back break using the random forest method. The variables used for the study was such as burden to spacing ratio, stemming to hole-depth ratio, p-wave velocity and the density of explosive. For the random forest model, R2 0.9791 and RMSE 0.87899 and for linear regression was R2 was 0.824 and root mean square error (RMSE) 0.72, respectively. From the field trials, it was evident that the use of low-density emulsion can help in reducing the back break and optimise the overall cost of the blasting process. The same results were validated using Random forest method wherein the model R2 was 0.9791 and RMSE was 0.8799.
Published: 2021

107. High Taxonomic and Functional Diversity of Bacterial Communities Associated with Melon Fly, Zeugodacus cucurbitae (Diptera: Tephritidae)

Author: Arun Kumar Singh, Jaipal S. Choudhary, Chandra S. Prabhakar, B. P. Bhatt, Naiyar Naaz, and Bikash Das
Subjects: Melon fly, 0303 health sciences, Tenericutes, biology, 030306 microbiology, Firmicutes, fungi, food and beverages, Zoology, General Medicine, Ribosomal RNA, biology.organism_classification, Applied Microbiology and Biotechnology, Microbiology, 03 medical and health sciences, Metagenomics, Tephritidae, Proteobacteria, Bacterial phyla, 030304 developmental biology
Abstract: The next generation sequencing (NGS) approach has facilitated the investigations of gut microbiota with high throughput and resolution. The present study was focused on the taxonomic and functional characterization of bacterial community associated with different developmental stages of melon fly, Zeugodacus cucurbitae using 16S ribosomal RNA (rRNA) gene amplicons metagenomics. Z. cucurbitae is considered an invasive and most staid polyphagous pest of cucurbitaceous and other related crops. The taxonomic analysis of highly variable V3–V4 region of bacterial 16S rRNA gene sequencing indicated that the bacterial community associated with Z. cucurbitae consists of a total of 23 bacterial phyla (including unclassified and unassigned bacteria), comprising 32 classes, 69 orders, 99 families and 130 genera. Proteobacteria, Firmicutes, Actinobacteria and Tenericutes were dominant phyla of which family, Enterobacteriaceae was the most abundant in the larval and adult female stages, whereas Mycoplasmataceae was the dominant in the pupal stage. In larval stages of Z. cucurbitae, genus Providencia and Comamonas were the most abundant. However, genus Candidatus-Bacilloplasma and Klebsiella were the most dominant in pupae and adult females of Z. cucurbitae, respectively. PICRUSt analysis conducted for prediction of metabolic activities revealed that associated microbiota were involved in membrane transport, carbohydrate metabolism, amino acid metabolism, energy metabolism, replication and repair processes as well as cellular processes and signalling. The higher number of OTUs was annotated for phosphoglycerate mutase and transketolase in adult females followed by larval stages, which may support the digestive function of the microbiota in larvae and adult females. Our findings provide insights about the high variation in microbiota across developmental stages and basis for microbiota-based management strategies of fruit flies.
Published: 2021

108. Successful Outcome of Bariatric Surgery in Living Donor Liver Transplant Recipients With Multidisciplinary Approach: A Preliminary Experience

Author: Narendra S. Choudhary, Swapnil Dhampalwar, Adarsh Chaudhary, Sanjiv Saigal, Vikas Singhal, Neeraj Saraf, and Arvinder S. Soin
Subjects: medicine.medical_specialty, Hepatology, medicine.diagnostic_test, business.industry, medicine.medical_treatment, Case Report, Immunosuppression, Liver transplantation, medicine.disease, Organ transplantation, Surgery, Endoscopy, 03 medical and health sciences, 0302 clinical medicine, 030220 oncology & carcinogenesis, Diabetes mellitus, medicine, 030211 gastroenterology & hepatology, Steatohepatitis, Metabolic syndrome, Complication, business
Abstract: Introduction Liver transplant recipients may develop weight gain, metabolic syndrome, and subsequent nonalcoholic steatohepatitis of the transplanted liver which impairs graft function. Bariatric surgery is an effective modality for management of morbid obesity and metabolic syndrome. Our aim is to review the role of bariatric surgery in such high-risk posttransplant patients not responding to medical management and highlight the important considerations. Methodology We review the management of two cases with posttransplant metabolic syndrome not responding to medical management and discuss the literature available on bariatric surgery in organ transplant patients. Results The first patient was a 51-year-old man who underwent living donor liver transplantation 3 years prior, and follow-up ultrasound and fibroscan was suggestive of steatohepatitis of the graft. After liver transplantation, he had gained 30 Kg weight and was on oral hypoglycemic agents with HbA1c of 8%. The second patient was a 65-year-old man, who gained 30 Kg weight with risk of graft impairment 4 years after of combined liver and kidney transplant. Both patients were evaluated thoroughly preoperatively for risk stratification including an upper gastro-intestinal (GI) endoscopy. The immunosuppression was reduced and monitored closely perioperatively. Both patients underwent laparoscopic sleeve gastrectomy (LSG) and were discharged on postoperative day 3. The first patient was evaluated a year after surgery with body mass index (BMI) reduction from 42 to 34 and second at 2 months with BMI reduction from 38 to 33; both patients were free of diabetes and had stable graft functions. Conclusion Bariatric surgery in liver transplant recipients has significant challenges with higher complication rates as patients are on immunosuppression which often impairs wound healing. LSG is safe and effective in such patients which often requires good coordination between the bariatric team and liver transplant team.
Published: 2021

109. RIPPER PRODUCTION PREDICTION FOR LATERITE EXCAVATION IN IRON ORE MINES

Author: B. S. Choudhary and Akhil Avchar
Subjects: Iron ore, Mining engineering, Production cost, Laterite, engineering, Production (economics), Geology, Multiple linear regression analysis, Excavation, engineering.material, Geotechnical Engineering and Engineering Geology, Rock mass classification
Abstract: The mining of iron ore, an essential raw material for iron and steel industry, is of prime importance among all mining activities undertaken by any country. Therefore it is important that the iron ore mining should be environment-friendly and sustainable. Ripper Dozer combination is one of the most commonly used excavation methods in Iron ore mines of Goa because of the presence of soft and friable rock mass and also it can bring the mining project more productivity, accuracy, safety and the additional option of selective mining. Improper selection of ripper dozer and unscientific deployment can lead to high production cost. So, performance prediction is an important issue for successful ripper application which deals with exposed rock mass properties and ripper machine parameters. Ripper production prediction using multiple linear regression analysis (MLR) and artificial neural network (ANN) is performed to estimate ripper production in the lateritic rock formation.
Published: 2021

110. Geological Reserve Estimation of Limestone Deposit: A Comparative Study Between ISDW and OK

Author: Gnananandh Budi, Manas Kumar Mallick, and B. S. Choudhary
Subjects: Estimation, Modeling and Simulation, Geochemistry, General Chemistry, Geology, Computer Science Applications, General Environmental Science
Abstract: Geostatistics plays an important role for reserve estimation in mining industry. Geostatistical tools became popular because of its high degree of accuracy and time saving process for estimation. The uncertainty of geological deposit can be populated by geo-statistical tools. The limestone ore deposit was studied in this paper. The assay value of individual constituents of limestone ore i.e CaO, SiO2, Al2O3 and Fe2O3 were determined for a block by using Inverse Square Distance Weighting (ISDW) method. The average assay value of those individual constituents were 45.85, 15.94, 1.56 and 0.82 percentage respectively. The assay value of CaO was also estimated by two linear method of estimation i.e ISDW and Ordinary Kriging (OK). The assay value of CaO were determined 45.85 and 44.67 percentage respectively. The assay values were properly validated and concluded accordingly. The application of ISDW and OK were implemented to build the resource model together in order to assess the uncertainty of the deposit. Grade estimation by using different geo-statistical techniques are done by SURPAC mine planning software.
Published: 2020

111. GENCODE 2021

Author: Fabio C. P. Navarro, Jonathan M. Mudge, S. Mohanan, Adam Frankish, Joel Armstrong, Tiago Grego, Irwin Jungreis, Roderic Guigó, Jinrui Xu, Benedict Paten, Cristina Sisu, Daniel R. Zerbino, Julien Lagarde, Mark Diekhans, José M. González, Michael L. Tress, E. Stapleton, Osagie G. Izuogu, Mark Gerstein, Ian T. Fiddes, Toby Hunt, Sarah Donaldson, Marie Marthe Suner, Fernando Pozo, Andrew D. Yates, S. Carbonell Sala, T. Di Domenico, Matthew Hardy, Barbara Uszczynska-Ratajczak, Fiona Cunningham, Andrew Berry, Anne Parker, Laura Martinez, Alexandra Bignell, Bianca M. Schmitt, Yan Zhang, Jane E. Loveland, Baikang Pei, Jyoti S. Choudhary, F. C. Riera, Paul R. Muir, C. Garcia Giron, Tim Hubbard, Fergal J. Martin, Rory Johnson, Magali Ruffier, If Barnes, James C. Wright, I. Sycheva, Manolis Kellis, Carles Boix, Thibaut Hourlier, Paul Flicek, Maxim Y Wolf, Y. T. Yang, and Kerstin Howe
Subjects: Transcription, Genetic, AcademicSubjects/SCI00010, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), 610 Medicine & health, Computational biology, Genome browser, Biology, Genome, Mice, 03 medical and health sciences, Annotation, 0302 clinical medicine, Databases, Genetic, Genetics, Database Issue, Animals, Humans, Ensembl, Epidemics, GeneralLiterature_REFERENCE(e.g.,dictionaries,encyclopedias,glossaries), 030304 developmental biology, Internet, 0303 health sciences, SARS-CoV-2, GENCODE, COVID-19, Computational Biology, Molecular Sequence Annotation, Genomics, ComputingMethodologies_PATTERNRECOGNITION, Genome Biology, RNA, Long Noncoding, Pseudogenes, 030217 neurology & neurosurgery, Reference genome
Abstract: © The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research. The GENCODE project annotates human and mouse genes and transcripts supported by experimental data with high accuracy, providing a foundational resource that supports genome biology and clinical genomics. GENCODE annotation processes make use of primary data and bioinformatic tools and analysis generated both within the consortium and externally to support the creation of transcript structures and the determination of their function. Here, we present improvements to our annotation infrastructure, bioinformatics tools, and analysis, and the advances they support in the annotation of the human and mouse genomes including: the completion of first pass manual annotation for the mouse reference genome; targeted improvements to the annotation of genes associated with SARS-CoV-2 infection; collaborative projects to achieve convergence across reference annotation databases for the annotation of human and mouse protein-coding genes; and the first GENCODE manually supervised automated annotation of lncRNAs. Our annotation is accessible via Ensembl, the UCSC Genome Browser and https://www.gencodegenes.org. National Human Genome Research Institute of the National Institutes of Health [U41HG007234]; the content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health; Wellcome Trust [WT108749/Z/15/Z, WT200990/Z/16/Z]; European Molecular Biology Laboratory; Swiss National Science Foundation through the National Center of Competence in Research ‘RNA & Disease’ (to R.J.); Medical Faculty of the University of Bern (to R.J). Funding for open access charge: National Institutes of Health.
Published: 2020

112. Pyrimethamine, a STAT3 Inhibitor, Synergizes with Venetoclax and Shows Efficacy in Hypomethylating Agent Resistant MDS and AML

Author: Bianca L Rivera, Samarpana Chakraborty, Yang Shi, Hui Zhang, Gaurav S Choudhary, Shanisha Gordon, Kith Pradhan, Bowen Fu, Isidora Tosic, Rongbao Zhao, Mendel Goldfinger, Ioannis Mantzaris, Milagros Carbajal, Nandini Ramachandra, Marina Konopleva, David Frank, Yogenthiran Saunthararajah, Amit Verma, and Aditi Shastri
Subjects: Immunology, Cell Biology, Hematology, Biochemistry
Published: 2022

113. Unfolding the mitochondrial genome structure of green semilooper (Chrysodeixis acuta Walker): An emerging pest of onion (Allium cepa L.)

Author: Soumia P. S., Dhananjay V. Shirsat, Ram Krishna, Guru Pirasanna Pandi G., Jaipal S. Choudhary, Naiyar Naaz, Karuppaiah V., Pranjali A. Gedam, Anandhan S., and Major Singh
Subjects: Multidisciplinary, Base Sequence, RNA, Transfer, Genome, Mitochondrial, Onions, Codon, Terminator, Animals, DNA, Intergenic, Sequence Analysis, DNA, Moths, Ecosystem, Phylogeny
Abstract: Onion is the most important crop challenged by a diverse group of insect pests in the agricultural ecosystem. The green semilooper (Chrysodeixis acuta Walker), a widespread tomato and soybean pest, has lately been described as an emergent onion crop pest in India. C. acuta whole mitochondrial genome was sequenced in this work. The circular genome of C. acuta measured 15,743 base pairs (bp) in length. Thirteen protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and one control region were found in the 37 sequence elements. With an average 395 bp gene length, the maximum and minimum gene length observed was 1749 bp and 63 bp of nad5 and trnR, respectively. Nine of the thirteen PCGs have (ATN) as a stop codon, while the other four have a single (T) as a stop codon. Except for trnS1, all of the tRNAs were capable of producing a conventional clover leaf structure. Conserved ATAGA motif sequences and poly-T stretch were identified at the start of the control region. Six overlapping areas and 18 intergenic spacer regions were found, with sizes ranged from 1 to 20 bp and 1 to 111 bp correspondingly. Phylogenetically, C. acuta belongs to the Plusiinae subfamily of the Noctuidae superfamily, and is closely linked to Trichoplusia ni species from the same subfamily. In the present study, the emerging onion pest C. acuta has its complete mitochondrial genome sequenced for the first time.
Published: 2022

114. Lung Function Test Changes in Symptomatic Patients Using E-cigarette and Vaping Products

Author: S. Choudhary, M.B. Pirzada, S. Ocal, A. Lin, S. Safi, and M. Akerman
Published: 2022

115. Variation in Lung Function in Pediatric and Adolescent Population Post SARS-COV-2 Infection: Pediatric Pulmonary Practice Experience

Author: M. Rashed, S. Choudhary, A. Mock, M. Akerman, and M. Pirzada
Published: 2022

116. Aneuploidy tolerance caused by BRG1 loss allows chromosome gains and recovery of fitness

Author: Federica Schiavoni, Pedro Zuazua-Villar, Theodoros I. Roumeliotis, Graeme Benstead-Hume, Mercedes Pardo, Frances M. G. Pearl, Jyoti S. Choudhary, and Jessica A. Downs
Subjects: Multidisciplinary, General Physics and Astronomy, General Chemistry, General Biochemistry, Genetics and Molecular Biology
Abstract: Aneuploidy results in decreased cellular fitness in many species and model systems. However, aneuploidy is commonly found in cancer cells and often correlates with aggressive growth, suggesting that the impact of aneuploidy on cellular fitness is context dependent. The BRG1 (SMARCA4) subunit of the SWI/SNF chromatin remodelling complex is frequently lost in cancer. Here, we use a chromosomally stable cell line to test the effect of BRG1 loss on the evolution of aneuploidy. BRG1 deletion leads to an initial loss of fitness in this cell line that improves over time. Notably, we find increased tolerance to aneuploidy immediately upon loss of BRG1, and the fitness recovery over time correlates with chromosome gain. These data show that BRG1 loss creates an environment where karyotype changes can be explored without a fitness penalty. At least in some genetic backgrounds, therefore, BRG1 loss can affect the progression of tumourigenesis through tolerance of aneuploidy.
Published: 2022

117. Multifactorial remodeling of the cancer immunopeptidome by interferon gamma

Author: Alice Newey, Lu Yu, Louise J Barber, Jyoti S. Choudhary, Michal Bassani-Sternberg, and Marco Gerlinger
Abstract: IFNγ alters the immunopeptidome presented on HLA class I (HLA-I), and its activity on cancer cells is known to be important for effective immunotherapy responses. We performed proteomic analyses of untreated and IFNγ-treated colorectal cancer patient-derived organoids (PDOs) and combined this with transcriptomic and HLA-I immunopeptidomics data to dissect mechanisms that lead to remodeling of the immunopeptidome through IFNγ. IFNγ-induced changes in the abundance of source proteins, switching from the constitutive- to the immunoproteasome, and differential upregulation of different HLA alleles explained some, but not all, observed peptide abundance changes. By selecting for peptides which increased or decreased the most in abundance, but originated from proteins with limited abundance changes, we discovered that the amino acid composition of presented peptides also influences whether a peptide is up- or downregulated on HLA-I through IFNγ. The presence of proline within the peptide core was most strongly associated with peptide downregulation. This was validated in an independent dataset. Proline substitution in relevant core positions did not influence the predicted HLA-I binding affinity or stability, indicating that proline effects on peptide processing may be most relevant. Understanding the multiple factors that influence the abundance of peptides presented on HLA-I in the absence or presence of IFNγ is important to identify the best targets for antigen-specific cancer immunotherapies such as vaccines or T-cell receptor engineered therapeutics.
Published: 2022

118. Post-trabeculectomy early bleb localization mimicking a 'ring of steel'

Author: S Kaushik, S Choudhary, M Kaur, and SS Pandav
Subjects: Blister, Cysts, Steel, Humans, Trabeculectomy, General Medicine, Middle Aged, Intraocular Pressure, Retrospective Studies
Abstract: A 54-year-old-man underwent trabeculectomy with mitomycin-C (0.02%). At 4-week follow-up, there was an elevated, well-circumscribed bleb with raised intra-ocular pressure (IOP) of 32-mmHg, with a classic "ring of steel" appearance, typically seen in a tenon's cyst. A sub-tenon needle revision re-established aqueous flow. Two weeks later, the IOP was 8-mmHg without any anti-glaucoma medications. A diffuse well formed bleb was noted. Careful ocular examination helps to identify early post-operative localized bleb that may appear like a "ring of steel" but can be managed by needling, unlike a tenon's cyst, which would require more extensive intervention.
Published: 2022

119. Activation of targetable inflammatory immune signaling is seen in Myelodysplastic Syndromes with SF3B1 mutations

Author: Gaurav S Choudhary, Andrea Pellagatti, Bogos Agianian, Molly A Smith, Tushar D Bhagat, Shanisha Gordon-Mitchell, Sanjay Pandey, Nishi Shah, Srinivas Aluri, Leya Schwartz, Violetta Steeples, Robert N Booher, Murali Ramachandra, Maria Elena Samson, Milagros Carbajal, Kith Pradhan, Teresa V. Bowman, Manoj M Pillai, Britta Will, Amittha Wickrema, Aditi Shastri, Robert Bradley, Robert Martell, Ulrich G. Steidl, Evripidis Gavathiotis, Jacqueline Boultwood, Daniel T. Starczynowski, and Amit Verma
Abstract: BackgroundMutations in the SF3B1 splicing factor are commonly seen in Myelodysplastic syndromes (MDS) and Acute Myeloid Leukemia (AML), yet the specific oncogenic pathways activated by missplicing have not been fully elucidated. Inflammatory immune pathways have been shown to play roles in pathogenesis of MDS, though the exact mechanisms of their activation in splicing mutant cases are not well understood.MethodsRNA-seq data from SF3B1 mutant samples was analyzed and functional roles of IRAK4 isoforms were determined. Efficacy of IRAK4 inhibition was evaluated in pre-clinical models of MDS/AMLResultsRNA-seq splicing analysis of innate immune mediators in SF3B1 mutant MDS samples revealed retention of full-length exon 6 of interleukin-1 receptor-associated kinase 4 (IRAK4), a critical downstream mediator that links the Myddosome to inflammatory NF-kB activation. Exon 6 retention leads to a longer isoform, encoding a protein (IRAK4-Long) that contains the entire death domain and kinase domain, leading to maximal activation of NF-kB. Cells with wild-type SF3B1 contain smaller IRAK4 isoforms that are targeted for proteosomal degradation. Expression of IRAK4-Long in SF3B1 mutant cells induces TRAF6 activation leading to K63-linked ubiquitination of CDK2, associated with a block in hematopoietic differentiation. Inhibition of IRAK4 with CA-4948, leads to reduction in NF-kB activation, inflammatory cytokine production, enhanced myeloid differentiation in vitro and reduced leukemic growth in xenograft models.ConclusionsSF3B1 mutation leads to expression of a therapeutically targetable, longer, oncogenic IRAK4 isoform in AML/MDS models.
Published: 2022

120. Model-based Cross-correlation Search for Gravitational Waves from the Low-mass X-Ray Binary Scorpius X-1 in LIGO O3 Data

Author: Abbott, R, Abe, H, Acernese, F, Ackley, K, Adhicary, S, Adhikari, N, Adhikari, R, Adkins, V, Adya, V, Affeldt, C, Agarwal, D, Agathos, M, Aguiar, O, Aiello, L, Ain, A, Ajith, P, Akutsu, T, Albanesi, S, Alfaidi, R, Alléné, C, Allocca, A, Altin, P, Amato, A, Anand, S, Ananyeva, A, Anderson, S, Anderson, W, Ando, M, Andrade, T, Andres, N, Andrés-Carcasona, M, Andrić, T, Ansoldi, S, Antelis, J, Antier, S, Apostolatos, T, Appavuravther, E, Appert, S, Apple, S, Arai, K, Araya, A, Araya, M, Areeda, J, Arène, M, Aritomi, N, Arnaud, N, Arogeti, M, Aronson, S, Asada, H, Ashton, G, Aso, Y, Assiduo, M, Assis de Souza Melo, S, Aston, S, Astone, P, Aubin, F, Aultoneal, K, Babak, S, Badaracco, F, Badger, C, Bae, S, Bae, Y, Bagnasco, S, Bai, Y, Baier, J, Baird, J, Bajpai, R, Baka, T, Ball, M, Ballardin, G, Ballmer, S, Baltus, G, Banagiri, S, Banerjee, B, Bankar, D, Barayoga, J, Barish, B, Barker, D, Barneo, P, Barone, F, Barr, B, Barsotti, L, Barsuglia, M, Barta, D, Bartlett, J, Barton, M, Bartos, I, Basak, S, Bassiri, R, Basti, A, Bawaj, M, Bayley, J, Bazzan, M, Bécsy, B, Bedakihale, V, Beirnaert, F, Bejger, M, Belahcene, I, Bell, A, Benedetto, V, Beniwal, D, Benoit, W, Bentley, J, Benyaala, M, Bera, S, Berbel, M, Bergamin, F, Berger, B, Bernuzzi, S, Beroiz, M, Bersanetti, D, Bertolini, A, Betzwieser, J, Beveridge, D, Bhandare, R, Bhandari, A, Bhardwaj, U, Bhatt, R, Bhattacharjee, D, Bhaumik, S, Bianchi, A, Bilenko, I, Bilicki, M, Billingsley, G, Bini, S, Birnholtz, O, Biscans, S, Bischi, M, Biscoveanu, S, Bisht, A, Biswas, B, Bitossi, M, Bizouard, M, Blackburn, J, Blair, C, Blair, D, Blair, R, Bobba, F, Bode, N, Boër, M, Bogaert, G, Boldrini, M, Bolingbroke, G, Bonavena, L, Bondarescu, R, Bondu, F, Bonilla, E, Bonnand, R, Booker, P, Bork, R, Boschi, V, Bose, N, Bose, S, Bossilkov, V, Boudart, V, Bouffanais, Y, Bozzi, A, Bradaschia, C, Brady, P, Bramley, A, Branch, A, Branchesi, M, Brau, J, Breschi, M, Briant, T, Briggs, J, Brillet, A, Brinkmann, M, Brockill, P, Brooks, A, Brooks, J, Brown, D, Brunett, S, Bruno, G, Bruntz, R, Bryant, J, Bucci, F, Buchanan, J, Bulik, T, Bulten, H, Buonanno, A, Burtnyk, K, Buscicchio, R, Buskulic, D, Buy, C, Byer, R, Cabourn Davies, G, Cabras, G, Cabrita, R, Cadonati, L, Cagnoli, G, Cahillane, C, Calderón Bustillo, J, Callaghan, J, Callister, T, Calloni, E, Camp, J, Canepa, M, Caneva, G, Cannavacciuolo, M, Cannon, K, Cao, H, Cao, Z, Capistran, L, Capocasa, E, Capote, E, Carapella, G, Carbognani, F, Carlassara, M, Carlin, J, Carpinelli, M, Carrillo, G, Carter, J, Carullo, G, Casanueva Diaz, J, Casentini, C, Castaldi, G, Caudill, S, Cavaglià, M, Cavalier, F, Cavalieri, R, Cella, G, Cerdá-Durán, P, Cesarini, E, Chaibi, W, Chakalis, W, Chalathadka Subrahmanya, S, Champion, E, Chan, C, Chan, K, Chan, M, Chandra, K, Chang, I, Chang, W, Chanial, P, Chao, S, Chapman-Bird, C, Charlton, P, Chassande-Mottin, E, Chatterjee, C, Chatterjee, D, Chaturvedi, M, Chaty, S, Chen, C, Chen, D, Chen, H, Chen, J, Chen, K, Chen, X, 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Jain, T, James, A, Jan, A, Jani, K, Janquart, J, Janssens, K, Janthalur, N, Jaranowski, P, Jariwala, D, Jarov, S, Jaume, R, Jenkins, A, Jenner, K, Jeon, C, Jia, W, Jiang, J, Jin, H, Johns, G, Johnston, R, Johny, N, Jones, A, Jones, D, Jones, P, Jones, R, Joshi, P, Ju, L, Jung, K, Jung, P, Junker, J, Juste, V, Kaihotsu, K, Kajita, T, Kakizaki, M, Kalaghatgi, C, Kalogera, V, Kamai, B, Kamiizumi, M, Kanda, N, Kandhasamy, S, Kang, G, Kanner, J, Kao, Y, Kapadia, S, Kapasi, D, Karat, S, Karathanasis, C, Karki, S, Kashyap, R, Kasprzack, M, Kastaun, W, Kato, T, Katsanevas, S, Katsavounidis, E, Katzman, W, Kaur, T, Kawabe, K, Kawaguchi, K, Kéfélian, F, Keitel, D, Key, J, Khadka, S, Khalili, F, Khan, S, Khanam, T, Khazanov, E, Khetan, N, Khursheed, M, Kijbunchoo, N, Kim, C, Kim, J, Kim, K, Kim, P, Kim, W, Kim, Y, Kimball, C, Kimura, N, King, B, Kinley-Hanlon, M, Kirchhoff, R, Kissel, J, Klimenko, S, Klinger, T, Knee, A, Knust, N, Kobayashi, Y, Koch, P, Koehlenbeck, S, Koekoek, G, Kohri, K, 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Pierro, G. Pillant, M. Pillas, F. Pilo, L. Pinard, C. Pineda-Bosque, I. M. Pinto, M. Pinto, B. J. Piotrzkowski, K. Piotrzkowski, M. Pirello, M. D. Pitkin, A. Placidi, E. Placidi, M. L. Planas, W. Plastino, R. Poggiani, E. Polini, D. Y. T. Pong, S. Ponrathnam, E. K. Porter, C. Posnansky, R. Poulton, J. Powell, M. Pracchia, T. Pradier, A. K. Prajapati, K. Prasai, R. Prasanna, G. Pratten, M. Principe, G. A. Prodi, L. Prokhorov, P. Prosposito, L. Prudenzi, A. Puecher, M. Punturo, F. Puosi, P. Puppo, M. Pürrer, H. Qi, N. Quartey, V. Quetschke, P. J. Quinonez, R. Quitzow-James, F. J. Raab, G. Raaijmakers, H. Radkins, N. Radulesco, P. Raffai, S. X. Rail, S. Raja, C. Rajan, K. E. Ramirez, T. D. Ramirez, A. Ramos-Buades, D. Rana, J. Rana, P. R. Rangnekar, P. Rapagnani, A. Ray, V. Raymond, N. Raza, M. Razzano, J. Read, T. Regimbau, L. Rei, S. Reid, S. W. Reid, M. Reinhard, D. H. Reitze, P. Relton, A. Renzini, P. Rettegno, B. Revenu, J. Reyes, A. Reza, M. Rezac, A. S. Rezaei, F. Ricci, D. 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Xiao, N. Yadav, T. Yamada, H. Yamamoto, K. Yamamoto, T. Yamamoto, K. Yamashita, R. Yamazaki, F. W. Yang, K. Z. Yang, L. Yang, Y. -C. Yang, Y. Yang, Yang Yang, M. J. Yap, D. W. Yeeles, S. -W. Yeh, A. B. Yelikar, J. Yokoyama, T. Yokozawa, J. Yoo, T. Yoshioka, Hang Yu, Haocun Yu, H. Yuzurihara, A. Zadrożny, M. Zanolin, S. Zeidler, T. Zelenova, J. -P. Zendri, M. Zevin, M. Zhan, H. Zhang, J. Zhang, L. Zhang, R. Zhang, T. Zhang, Y. Zhang, C. Zhao, G. Zhao, Y. Zhao, Yue Zhao, Y. Zheng, R. Zhou, X. J. Zhu, Z. -H. Zhu, A. B. Zimmerman, M. E. Zucker, and J. Zweizig
Abstract: We present the results of a model-based search for continuous gravitational waves from the low-mass X-ray binary Scorpius X-1 using LIGO detector data from the third observing run of Advanced LIGO and Advanced Virgo. This is a semicoherent search that uses details of the signal model to coherently combine data separated by less than a specified coherence time, which can be adjusted to balance sensitivity with computing cost. The search covered a range of gravitational-wave frequencies from 25 to 1600 Hz, as well as ranges in orbital speed, frequency, and phase determined from observational constraints. No significant detection candidates were found, and upper limits were set as a function of frequency. The most stringent limits, between 100 and 200 Hz, correspond to an amplitude h(0) of about 10(-25) when marginalized isotropically over the unknown inclination angle of the neutron star's rotation axis, or less than 4 x 10(-26) assuming the optimal orientation. The sensitivity of this search is now probing amplitudes predicted by models of torque balance equilibrium. For the usual conservative model assuming accretion at the surface of the neutron star, our isotropically marginalized upper limits are close to the predicted amplitude from about 70 to 100 Hz; the limits assuming that the neutron star spin is aligned with the most likely orbital angular momentum are below the conservative torque balance predictions from 40 to 200 Hz. Assuming a broader range of accretion models, our direct limits on gravitational-wave amplitude delve into the relevant parameter space over a wide range of frequencies, to 500 Hz or more.
Published: 2022

121. Search for Gravitational Waves Associated with Gamma-Ray Bursts Detected by Fermi and Swift during the LIGO-Virgo Run O3b

Author: Abbott, R, Abbott, T, Acernese, F, Ackley, K, Adams, C, Adhikari, N, Adhikari, R, Adya, V, Affeldt, C, Agarwal, D, Agathos, M, Agatsuma, K, Aggarwal, N, Aguiar, O, Aiello, L, Ain, A, Ajith, P, Akutsu, T, Albanesi, S, Allocca, A, Altin, P, Amato, A, Anand, C, Anand, S, Ananyeva, A, Anderson, S, Anderson, W, Ando, M, Andrade, T, Andres, N, Andri??, T, Angelova, S, Ansoldi, S, Antelis, J, Antier, S, Appert, S, Arai, K, Arai, Y, Araki, S, Araya, A, Araya, M, Areeda, J, Ar??ne, M, Aritomi, N, Arnaud, N, Aronson, S, Arun, K, Asada, H, Asali, Y, Ashton, G, Aso, Y, Assiduo, M, Aston, S, Astone, P, Aubin, F, Austin, C, Babak, S, Badaracco, F, Bader, M, Badger, C, Bae, S, Bae, Y, Baer, A, Bagnasco, S, Bai, Y, Baiotti, L, Baird, J, Bajpai, R, Ball, M, Ballardin, G, Ballmer, S, Balsamo, A, Baltus, G, Banagiri, S, Bankar, D, Barayoga, J, Barbieri, C, Barish, B, Barker, D, Barneo, P, Barone, F, Barr, B, Barsotti, L, Barsuglia, M, Barta, D, Bartlett, J, Barton, M, Bartos, I, Bassiri, R, Basti, A, Bawaj, M, Bayley, J, Baylor, A, Bazzan, M, B??csy, B, Bedakihale, V, Bejger, M, Belahcene, I, Benedetto, V, Beniwal, D, Bennett, T, Bentley, J, Benyaala, M, Bergamin, F, Berger, B, Bernuzzi, S, Berry, C, Bersanetti, D, Bertolini, A, Betzwieser, J, Beveridge, D, Bhandare, R, Bhardwaj, U, Bhattacharjee, D, Bhaumik, S, Bilenko, I, Billingsley, G, Bini, S, Birney, R, Birnholtz, O, Biscans, S, Bischi, M, Biscoveanu, S, Bisht, A, Biswas, B, Bitossi, M, Bizouard, M, Blackburn, J, Blair, C, Blair, D, Blair, R, Bobba, F, Bode, N, Boer, M, Bogaert, G, Boldrini, M, Bonavena, L, Bondu, F, Bonilla, E, Bonnand, R, Booker, P, Boom, B, Bork, R, Boschi, V, Bose, N, Bose, S, Bossilkov, V, Boudart, V, Bouffanais, Y, Bozzi, A, Bradaschia, C, Brady, P, Bramley, A, Branch, A, Branchesi, M, Brau, J, Breschi, M, Briant, T, Briggs, J, Brillet, A, Brinkmann, M, Brockill, P, Brooks, A, Brooks, J, Brown, D, Brunett, S, Bruno, G, Bruntz, R, Bryant, J, Bulik, T, Bulten, H, Buonanno, A, Buscicchio, R, 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Laghi, E. Lalande, T. L. Lam, A. Lamberts, M. Landry, B. B. Lane, R. N. Lang, J. Lange, B. Lantz, I. La Rosa, A. Lartaux-Vollard, P. D. Lasky, M. Laxen, A. Lazzarini, C. Lazzaro, P. Leaci, S. Leavey, Y. K. Lecoeuche, H. K. Lee, H. M. Lee, H. W. Lee, J. Lee, K. Lee, R. Lee, J. Lehmann, A. Lema??tre, M. Leonardi, N. Leroy, N. Letendre, C. Levesque, Y. Levin, J. N. Leviton, K. Leyde, A. K. Y. Li, B. Li, J. Li, K. L. Li, T. G. F. Li, X. Li, C-Y. Lin, F-K. Lin, F-L. Lin, H. L. Lin, L. C. -C. Lin, F. Linde, S. D. Linker, J. N. Linley, T. B. Littenberg, G. C. Liu, J. Liu, K. Liu, X. Liu, F. Llamas, M. Llorens-Monteagudo, R. K. L. Lo, A. Lockwood, L. T. London, A. Longo, D. Lopez, M. Lopez Portilla, M. Lorenzini, V. Loriette, M. Lormand, G. Losurdo, T. P. Lott, J. D. Lough, C. O. Lousto, G. Lovelace, J. F. Lucaccioni, H. L??ck, D. Lumaca, A. P. Lundgren, L. -W. Luo, J. E. Lynam, R. Macas, M. MacInnis, D. M. Macleod, I. A. O. MacMillan, A. Macquet, I. Maga??a Hernandez, C. Magazz??, R. M. 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Merritt, M. Merzougui, S. Meshkov, C. Messenger, C. Messick, P. M. Meyers, F. Meylahn, A. Mhaske, A. Miani, H. Miao, I. Michaloliakos, C. Michel, Y. Michimura, H. Middleton, L. Milano, A. L. Miller, A. Miller, B. Miller, M. Millhouse, J. C. Mills, E. Milotti, O. Minazzoli, Y. Minenkov, N. Mio, Ll. M. Mir, M. Miravet-Ten??s, C. Mishra, T. Mishra, T. Mistry, S. Mitra, V. P. Mitrofanov, G. Mitselmakher, R. Mittleman, O. Miyakawa, A. Miyamoto, Y. Miyazaki, K. Miyo, S. Miyoki, Geoffrey Mo, E. Moguel, K. Mogushi, S. R. P. Mohapatra, S. R. Mohite, I. Molina, M. Molina-Ruiz, M. Mondin, M. Montani, C. J. Moore, D. Moraru, F. Morawski, A. More, C. Moreno, G. Moreno, Y. Mori, S. Morisaki, Y. Moriwaki, B. Mours, C. M. Mow-Lowry, S. Mozzon, F. Muciaccia, Arunava Mukherjee, D. Mukherjee, Soma Mukherjee, Subroto Mukherjee, Suvodip Mukherjee, N. Mukund, A. Mullavey, J. Munch, E. A. Mu??iz, P. G. Murray, R. Musenich, S. Muusse, S. L. Nadji, K. Nagano, S. Nagano, A. Nagar, K. Nakamura, H. Nakano, M. Nakano, R. Nakashima, Y. Nakayama, V. Napolano, I. Nardecchia, T. Narikawa, L. Naticchioni, B. Nayak, R. K. Nayak, R. Negishi, B. F. Neil, J. Neilson, G. Nelemans, T. J. N. Nelson, M. Nery, P. Neubauer, A. Neunzert, K. Y. Ng, S. W. S. Ng, C. Nguyen, P. Nguyen, T. Nguyen, L. Nguyen Quynh, W. -T. Ni, S. A. Nichols, A. Nishizawa, S. Nissanke, E. Nitoglia, F. Nocera, M. Norman, C. North, S. Nozaki, L. K. Nuttall, J. Oberling, B. D. O???Brien, Y. Obuchi, J. O???Dell, E. Oelker, W. Ogaki, G. Oganesyan, J. J. Oh, K. Oh, S. H. Oh, M. Ohashi, N. Ohishi, M. Ohkawa, F. Ohme, H. Ohta, M. A. Okada, Y. Okutani, K. Okutomi, C. Olivetto, K. Oohara, C. Ooi, R. Oram, B. O???Reilly, R. G. Ormiston, N. D. Ormsby, L. F. Ortega, R. O???Shaughnessy, E. O???Shea, S. Oshino, S. Ossokine, C. Osthelder, S. Otabe, D. J. Ottaway, H. Overmier, A. E. Pace, G. Pagano, M. A. Page, G. Pagliaroli, A. Pai, S. A. Pai, J. R. Palamos, O. Palashov, C. Palomba, H. Pan, K. Pan, P. K. Panda, H. Pang, P. T. H. Pang, C. Pankow, F. Pannarale, B. C. Pant, F. H. Panther, F. Paoletti, A. Paoli, A. Paolone, A. Parisi, H. Park, J. Park, W. Parker, D. Pascucci, A. Pasqualetti, R. Passaquieti, D. Passuello, M. Patel, M. Pathak, B. Patricelli, A. S. Patron, S. Patrone, S. Paul, E. Payne, M. Pedraza, M. Pegoraro, A. Pele, F. E. Pe??a Arellano, S. Penn, A. Perego, A. Pereira, T. Pereira, C. J. Perez, C. P??rigois, C. C. Perkins, A. Perreca, S. Perri??s, J. Petermann, D. Petterson, H. P. Pfeiffer, K. A. Pham, K. S. Phukon, O. J. Piccinni, M. Pichot, M. Piendibene, F. Piergiovanni, L. Pierini, V. Pierro, G. Pillant, M. Pillas, F. Pilo, L. Pinard, I. M. Pinto, M. Pinto, K. Piotrzkowski, M. Pirello, M. D. Pitkin, E. Placidi, L. Planas, W. Plastino, C. Pluchar, R. Poggiani, E. Polini, D. Y. T. Pong, S. Ponrathnam, P. Popolizio, E. K. Porter, R. Poulton, J. Powell, M. Pracchia, T. Pradier, A. K. Prajapati, K. Prasai, R. Prasanna, G. Pratten, M. Principe, G. A. Prodi, L. Prokhorov, P. Prosposito, L. Prudenzi, A. Puecher, M. Punturo, F. Puosi, P. Puppo, M. P??rrer, H. Qi, V. Quetschke, R. Quitzow-James, F. J. Raab, G. Raaijmakers, H. Radkins, N. Radulesco, P. Raffai, S. X. Rail, S. Raja, C. Rajan, K. E. Ramirez, T. D. Ramirez, A. Ramos-Buades, J. Rana, P. Rapagnani, U. D. Rapol, A. Ray, V. Raymond, N. Raza, M. Razzano, J. Read, L. A. Rees, T. Regimbau, L. Rei, S. Reid, S. W. Reid, D. H. Reitze, P. Relton, A. Renzini, P. Rettegno, M. Rezac, F. Ricci, D. Richards, J. W. Richardson, L. Richardson, G. Riemenschneider, K. Riles, S. Rinaldi, K. Rink, M. Rizzo, N. A. Robertson, R. Robie, F. Robinet, A. Rocchi, S. Rodriguez, L. Rolland, J. G. Rollins, M. Romanelli, R. Romano, C. L. Romel, A. Romero-Rodr??guez, I. M. Romero-Shaw, J. H. Romie, S. Ronchini, L. Rosa, C. A. Rose, D. Rosi??ska, M. P. Ross, S. Rowan, S. J. Rowlinson, S. Roy, Santosh Roy, Soumen Roy, D. Rozza, P. Ruggi, K. Ryan, S. Sachdev, T. Sadecki, J. Sadiq, N. Sago, S. Saito, Y. Saito, K. Sakai, Y. Sakai, M. Sakellariadou, Y. Sakuno, O. S. Salafia, L. Salconi, M. Saleem, F. Salemi, A. Samajdar, E. J. Sanchez, J. H. Sanchez, L. E. Sanchez, N. Sanchis-Gual, J. R. Sanders, A. Sanuy, T. R. Saravanan, N. Sarin, B. Sassolas, H. Satari, B. S. Sathyaprakash, S. Sato, T. Sato, O. Sauter, R. L. Savage, T. Sawada, D. Sawant, H. L. Sawant, S. Sayah, D. Schaetzl, M. Scheel, J. Scheuer, M. Schiworski, P. Schmidt, S. Schmidt, R. Schnabel, M. Schneewind, R. M. S. Schofield, A. Sch??nbeck, B. W. Schulte, B. F. Schutz, E. Schwartz, J. Scott, S. M. Scott, M. Seglar-Arroyo, T. Sekiguchi, Y. Sekiguchi, D. Sellers, A. S. Sengupta, D. Sentenac, E. G. Seo, V. Sequino, A. Sergeev, Y. Setyawati, T. Shaffer, M. S. Shahriar, B. Shams, L. Shao, A. Sharma, P. Sharma, S. Sharma-Chaudhary, P. Shawhan, N. S. Shcheblanov, S. Shibagaki, M. Shikauchi, R. Shimizu, T. Shimoda, K. Shimode, H. Shinkai, T. Shishido, A. Shoda, D. H. Shoemaker, D. M. Shoemaker, S. ShyamSundar, M. Sieniawska, D. Sigg, L. P. Singer, D. Singh, N. Singh, A. Singha, A. M. Sintes, V. Sipala, V. Skliris, B. J. J. Slagmolen, T. J. Slaven-Blair, J. Smetana, J. R. Smith, R. J. E. Smith, J. Soldateschi, S. N. Somala, K. Somiya, E. J. Son, K. Soni, S. Soni, V. Sordini, F. Sorrentino, N. Sorrentino, H. Sotani, R. Soulard, T. Souradeep, E. Sowell, V. Spagnuolo, A. P. Spencer, M. Spera, R. Srinivasan, A. K. Srivastava, V. Srivastava, K. Staats, C. Stachie, D. A. Steer, J. Steinlechner, S. Steinlechner, D. J. Stops, M. Stover, K. A. Strain, L. C. Strang, G. Stratta, A. Strunk, R. Sturani, A. L. Stuver, S. Sudhagar, V. Sudhir, R. Sugimoto, H. G. Suh, T. Z. Summerscales, H. Sun, L. Sun, S. Sunil, A. Sur, J. Suresh, P. J. Sutton, Takamasa Suzuki, Toshikazu Suzuki, B. L. Swinkels, M. J. Szczepa??czyk, P. Szewczyk, M. Tacca, H. Tagoshi, S. C. Tait, H. Takahashi, R. Takahashi, A. Takamori, S. Takano, H. Takeda, M. Takeda, C. J. Talbot, C. Talbot, H. Tanaka, Kazuyuki Tanaka, Kenta Tanaka, Taiki Tanaka, Takahiro Tanaka, A. J. Tanasijczuk, S. Tanioka, D. B. Tanner, D. Tao, L. Tao, E. N. Tapia San Martin, E. N. Tapia San Mart??n, C. Taranto, J. D. Tasson, S. Telada, R. Tenorio, J. E. Terhune, L. Terkowski, M. P. Thirugnanasambandam, M. Thomas, P. Thomas, E. E. Thompson, J. E. Thompson, S. R. Thondapu, K. A. Thorne, E. Thrane, Shubhanshu Tiwari, Srishti Tiwari, V. Tiwari, A. M. Toivonen, K. Toland, A. E. Tolley, T. Tomaru, Y. Tomigami, T. Tomura, M. Tonelli, A. Torres-Forn??, C. I. Torrie, I. Tosta e Melo, D. T??yr??, A. Trapananti, F. Travasso, G. Traylor, M. Trevor, M. C. Tringali, A. Tripathee, L. Troiano, A. Trovato, L. Trozzo, R. J. Trudeau, D. S. Tsai, D. Tsai, K. W. Tsang, T. Tsang, J-S. Tsao, M. Tse, R. Tso, K. Tsubono, S. Tsuchida, L. Tsukada, D. Tsuna, T. Tsutsui, T. Tsuzuki, K. Turbang, M. Turconi, D. Tuyenbayev, A. S. Ubhi, N. Uchikata, T. Uchiyama, R. P. Udall, A. Ueda, T. Uehara, K. Ueno, G. Ueshima, C. S. Unnikrishnan, F. Uraguchi, A. L. Urban, T. Ushiba, A. Utina, H. Vahlbruch, G. Vajente, A. Vajpeyi, G. Valdes, M. Valentini, V. Valsan, N. van Bakel, M. van Beuzekom, J. F. J. van den Brand, C. Van Den Broeck, D. C. Vander-Hyde, L. van der Schaaf, J. V. van Heijningen, J. Vanosky, M. H. P. M. van Putten, N. van Remortel, M. Vardaro, A. F. Vargas, V. Varma, M. Vas??th, A. Vecchio, G. Vedovato, J. Veitch, P. J. Veitch, J. Venneberg, G. Venugopalan, D. Verkindt, P. Verma, Y. Verma, D. Veske, F. Vetrano, A. Vicer??, S. Vidyant, A. D. Viets, A. Vijaykumar, V. Villa-Ortega, J. -Y. Vinet, A. Virtuoso, S. Vitale, T. Vo, H. Vocca, E. R. G. von Reis, J. S. A. von Wrangel, C. Vorvick, S. P. Vyatchanin, L. E. Wade, M. Wade, K. J. Wagner, R. C. Walet, M. Walker, G. S. Wallace, L. Wallace, S. Walsh, J. Wang, J. Z. Wang, W. H. Wang, R. L. Ward, J. Warner, M. Was, T. Washimi, N. Y. Washington, J. Watchi, B. Weaver, S. A. Webster, M. Weinert, A. J. Weinstein, R. Weiss, C. M. Weller, F. Wellmann, L. Wen, P. We??els, K. Wette, J. T. Whelan, D. D. White, B. F. Whiting, C. Whittle, D. Wilken, D. Williams, M. J. Williams, A. R. Williamson, J. L. Willis, B. Willke, D. J. Wilson, W. Winkler, C. C. Wipf, T. Wlodarczyk, G. Woan, J. Woehler, J. K. Wofford, I. C. F. Wong, C. Wu, D. S. Wu, H. Wu, S. Wu, D. M. Wysocki, L. Xiao, W-R. Xu, T. Yamada, H. Yamamoto, Kazuhiro Yamamoto, Kohei Yamamoto, T. Yamamoto, K. Yamashita, R. Yamazaki, F. W. Yang, L. Yang, Y. Yang, Yang Yang, Z. Yang, M. J. Yap, D. W. Yeeles, A. B. Yelikar, M. Ying, K. Yokogawa, J. Yokoyama, T. Yokozawa, J. Yoo, T. Yoshioka, Hang Yu, Haocun Yu, H. Yuzurihara, A. Zadro??ny, M. Zanolin, S. Zeidler, T. Zelenova, J. -P. Zendri, M. Zevin, M. Zhan, H. Zhang, J. Zhang, L. Zhang, T. Zhang, Y. Zhang, C. Zhao, G. Zhao, Y. Zhao, Yue Zhao, Y. Zheng, R. Zhou, Z. Zhou, X. J. Zhu, Z. -H. Zhu, A. B. Zimmerman, M. E. Zucker, and J. Zweizig
Abstract: We search for gravitational-wave signals associated with gamma-ray bursts (GRBs) detected by the Fermi and Swift satellites during the second half of the third observing run of Advanced LIGO and Advanced Virgo (2019 November 1 15:00 UTC-2020 March 27 17:00 UTC). We conduct two independent searches: A generic gravitational-wave transients search to analyze 86 GRBs and an analysis to target binary mergers with at least one neutron star as short GRB progenitors for 17 events. We find no significant evidence for gravitational-wave signals associated with any of these GRBs. A weighted binomial test of the combined results finds no evidence for subthreshold gravitational-wave signals associated with this GRB ensemble either. We use several source types and signal morphologies during the searches, resulting in lower bounds on the estimated distance to each GRB. Finally, we constrain the population of low-luminosity short GRBs using results from the first to the third observing runs of Advanced LIGO and Advanced Virgo. The resulting population is in accordance with the local binary neutron star merger rate.
Published: 2022

122. Outcome of hepatitis C–related liver transplantation in direct-acting antiviral era

Author: Srinivas Thiagrajan, Prashant Bhangui, Sanjiv Saigal, Amit Rastogi, Arvinder S. Soin, Neeraj Saraf, and Narendra S. Choudhary
Subjects: Hepatitis, medicine.medical_specialty, Cirrhosis, business.industry, medicine.medical_treatment, Gastroenterology, Hepatitis C, Liver transplantation, Hepatitis B, Chronic liver disease, medicine.disease, digestive system diseases, Transplantation, Liver disease, Internal medicine, medicine, business
Abstract: Hepatitis C virus (HCV) has become an easily treatable disease after the introduction of sofosbuvir-based direct-acting antiviral (DAA) regimens. This is a large single center experience of changing severity and outcome profile of HCV-related liver disease after availability of DAAs. A retrospective analysis of prospectively collected liver transplantation (LT) database of adults (age > 18 years at the time of LT) was performed from June 2010 to July 2018. A total of 410 patients (including 26 co-infection with hepatitis B) underwent LT for hepatitis C–related decompensated cirrhosis and/or hepatocellular carcinoma (HCC) out of 1754 adult transplantation in the defined period. The study group comprised of 296 males and 114 females aged 52.1 ± 7.9 years. HCV-related decompensated cirrhosis and/or HCC as indication of LT was present in 289/1016 (28.4%) during 2010–2014, which was reduced to 121/738 (16.3%) during 2015–2018 (p = 0.000). The LT recipients for HCV-related cirrhosis had significantly lower Child’s and model for end-stage liver disease (MELD) score during 2015–2018 as compared to that during 2010–2014; Child’s score was 7.9 ± 2.2 vs. 8.6 ± 2.1, p = 0.003; MELD score was 13.9 ± 5.3 vs. 17.1 ± 5.8, p = 0.000, respectively. There was a trend towards better survival in HCV patients during 2015–2018 as compared to that during 2010–2014. Significantly more patients had HCV RNA negative status before LT during 2015–2018 (38.8% vs. 13%, p = 0.000); moreover, the proportion of LT for decompensated cirrhosis (without HCC) decreased significantly in the latter period, 64.0% vs. 42.1% (p = 0.000). In the DAA era, HCV as an indication for LT has decreased and patients have less severe disease at transplantation. There is a trend towards better patient survival.
Published: 2020

123. Gene Silencing in Horticultural Transgenic Plants: Mechanisms, Technologies and Applications in Horticultural Crops

Author: M. Sewda, R. S. R. Krishnan, M. R. Hindala, S. Choudhary, R. Sharma, and S. K. Barolia
Subjects: business.industry, Horticultural crops, Gene silencing, Genetically modified crops, Biology, business, Biotechnology
Published: 2020

124. Nonalcoholic fatty liver disease should be considered for treatment allocation in standard management algorithms for type 2 diabetes

Author: Sunil Kumar Mishra, Anoop Misra, Mohammad Shafi Kuchay, and Narendra S. Choudhary
Subjects: Cirrhosis, endocrine system diseases, Endocrinology, Diabetes and Metabolism, Population, MEDLINE, India, Disease, Type 2 diabetes, digestive system, 03 medical and health sciences, 0302 clinical medicine, Non-alcoholic Fatty Liver Disease, Diabetes mellitus, Nonalcoholic fatty liver disease, Internal Medicine, medicine, Humans, 030212 general & internal medicine, education, education.field_of_study, business.industry, Fatty liver, Disease Management, nutritional and metabolic diseases, General Medicine, medicine.disease, digestive system diseases, Diabetes Mellitus, Type 2, 030211 gastroenterology & hepatology, business, Algorithm, Algorithms
Abstract: Background and aims Type 2 diabetes (T2D) and nonalcoholic fatty liver disease (NAFLD) often exist together. This is a high-risk population, as presence of T2D promotes the progression of NAFLD to more severe liver pathologies. There are several international guidelines for managing T2D, however guidance for management of NAFLD in individuals with T2D is scarce. In India, there is hardly any screening programme for identification of high-risk NAFLD individuals. Methods A literature search was performed with Medline (PubMed), Scopus and Google Scholar electronic databases till October 2020, using relevant keywords (nonalcoholic fatty liver disease; NAFLD; nonalcoholic steatohepatitis; NASH screening and management; metabolic associated fatty liver disease) to extract relevant studies describing screening and management strategies of NAFLD/NASH, especially in patients with T2D. Results An estimated 12.4 million Indian people are living with coexisting T2D and NAFLD-related advanced liver fibrosis, which is a major determinant of liver-related mortality in these individuals. Several studies have reported screening tools for identification of high risk NAFLD patients with coexisting T2D. The emphasis has been laid on the identification of advanced liver fibrosis and cirrhosis, using noninvasive tests at the primary level. For management, lifestyle measures and appropriate glucose-lowering medication have been proposed that help patients with coexisting T2D and NAFLD. Timely referral to specialists is also critical for preventing complications of cirrhosis. Conclusions While current management algorithms for T2D include atherosclerotic cardiovascular disease, kidney dysfunction and obesity as co-morbidities to direct appropriate therapies, NAFLD should be considered as additional pathway to select appropriate treatment.
Published: 2020

125. Morphological and Biochemical Characterization of Bacteria Associated with the Developmental Stage of the Peach Fruit Fly, Bactrocera zonata (Diptera: Tephritidae)

Author: Naiyar Naaz, Jaipal S. Choudhary, Abhijit Dutta, and Ashok Kumar Choudhary
Subjects: Developmental stage, Horticulture, biology, Tephritidae, biology.organism_classification, Bacteria, Bactrocera zonata, Peach fruit fly
Published: 2020

126. Pit Optimization for Improved NPV and Life of Mine in Heterogeneous Iron Ore Deposit

Author: S. K. Sinha and B. S. Choudhary
Subjects: 0209 industrial biotechnology, business.industry, Mechanical Engineering, Commodity, Final product, Metals and Alloys, Open-pit mining, 02 engineering and technology, engineering.material, Geotechnical Engineering and Engineering Geology, Economic parameters, Highly sensitive, Product mix, 020303 mechanical engineering & transports, 020901 industrial engineering & automation, 0203 mechanical engineering, Mining engineering, Iron ore, Materials Chemistry, engineering, Production (economics), Environmental science, business
Abstract: Operations planning and management of a large open pit mine is an enormous and complex task, particularly for mines having long life. The long-term planning of open pit mine is a dynamic process and should be reviewed periodically for enhancing the NPV and life of mine. Pit optimization through soft computing can be gainfully applied to resolve a number of important problems that arise in developing suitable planning strategies and management of a mine. Pit optimization starts with the assumption of initial production capacities and the estimates for the related costs and commodity prices. Once the economic parameters are known, the analysis of the ultimate pit limits of the mine is undertaken to determine the portion of the deposit that can be mined economically and safely from geotechnical stability view point. In this research, pit optimization for a heterogeneous iron ore deposit (Deposit-A) has been carried out successfully using Whittle Software. The key aspect investigated was the optimal pit shell across a range of selling prices, as it enables understanding the characteristics of the deposit and potential development strategies considering the areas of greater value. The methodology can be very well utilized when fluctuations in the selling price occur, for predicting the future selling price of the commodity and also strategizing mining plan. For the deposit investigated, it was found that the mine is likely to generate final product of 66.55 MT of Lump Ore (+ 10 mm − 150 mm) and Fines Ore 156.45 MT (− 10 mm) during the life of the mine. The NPV is found to be highly sensitive to the price of Fine ore as quantity of fines in total ore body is around 70%. Except waste, all ore types, no matter how inferior the grade is having (around 10 MT of low grade coming in between Fe @ 45% and Fe @ 25% can be also utilized), are mineable and can be suitably blended to give a product mix of Fe @ 61.68% and more.
Published: 2020

127. De Novo Malignancy After Living Donor Liver Transplantation: A Large Volume Experience

Author: Thiagrajan Srinivasan, Sujeet Saha, Neeraj Saraf, Arvinder S. Soin, Narendra S. Choudhary, A. K. Tiwari, Samiran Nundy, Prashant Bhangui, Sanjiv Saigal, Amit Rastogi, Dheeraj Gautam, and Sanjay Kumar Yadav
Subjects: medicine.medical_specialty, Hepatology, business.industry, medicine.medical_treatment, Incidence (epidemiology), Immunosuppression, Liver transplantation, medicine.disease, Malignancy, Gastroenterology, Organ transplantation, Transplantation, 03 medical and health sciences, 0302 clinical medicine, Interquartile range, 030220 oncology & carcinogenesis, Internal medicine, Carcinoma, medicine, Original Article, 030211 gastroenterology & hepatology, business
Abstract: Background and aims Liver transplantation (LT) recipients such as all organ transplant recipients, have a risk of developing de novo malignancies owing to prolonged immunosuppression. However, there is limited data on this after living donor liver transplantation (LDLT), wherein immunosuppression levels are less than in deceased donor transplantation. We aim to describe experience of de novo malignancies from a predominantly LDLT center. Materials and methods A total of 2100 adults (age >18 years) who underwent LT between January 2006 and December 2017 were retrospectively analyzed from a prospectively collected database. The data were analyzed up to June 2019. Data are shown as number, percentage, mean ± standard deviation, and median (interquartile range). Results Of 2100 patients who underwent LDLT, 21 (1%) patients developed de novo malignancy after transplantation. The de novo malignancy cohort comprised 20 males and 1 female, aged 50 ± 8.8 years. The distribution of de novo malignancies was as follows: 7 oropharyngeal (carcinoma of buccal and oral mucosa), 4 lung, 2 squamous cell carcinoma of skin, 2 lymphoma, 1 each of brain, colonic, gastric; ovary, pancreatic, and prostate. These malignancies were diagnosed at a median follow-up of 42 months (32–73) after LT. Over a median follow-up of 38 months (10–56) after the diagnosis of de novo malignancy, 6 patients (28.5%) died. Patients with de novo malignancy had a higher follow-up after LDLT, 94.3 ± 32.9 versus 62.5 ± 41.8 months, P = 0.000. Patients with alcohol as etiology for LT had higher trend of de novo malignancies (33.3% versus 26.4%), P = 0.46. Conclusion The incidence of de novo malignancy was 1% at a median follow-up of 42 (32–73) months. De novo malignancies following LDLT, although uncommon, are associated with significant mortality. A careful screening protocol should be followed after transplantation for early detection of de novo malignancies.
Published: 2020

128. Effect of dulaglutide on liver fat in patients with type 2 diabetes and NAFLD: randomised controlled trial (D-LIFT trial)

Author: Ambrish Mithal, Sunil Kumar Mishra, Tarannum Bano, Mohammad Shafi Kuchay, Manish K. Singh, Khalid Jamal Farooqui, Jasjeet Singh Wasir, Parjeet Kaur, Sonal Krishan, Narendra S. Choudhary, and Harmandeep Kaur Gill
Subjects: 0301 basic medicine, medicine.medical_specialty, Recombinant Fusion Proteins, Endocrinology, Diabetes and Metabolism, Glucagon-Like Peptides, 030209 endocrinology & metabolism, Type 2 diabetes, Gastroenterology, law.invention, 03 medical and health sciences, 0302 clinical medicine, Liver Function Tests, Randomized controlled trial, Non-alcoholic Fatty Liver Disease, law, Diabetes mellitus, Internal medicine, Internal Medicine, medicine, Humans, Hypoglycemic Agents, Aspartate Aminotransferases, business.industry, Liraglutide, Standard treatment, Fatty liver, Alanine Transaminase, medicine.disease, Immunoglobulin Fc Fragments, 030104 developmental biology, Diabetes Mellitus, Type 2, Liver, Dulaglutide, Transient elastography, business, medicine.drug
Abstract: Liraglutide, a daily injectable glucagon-like peptide-1 receptor (GLP-1r) agonist, has been shown to reduce liver fat content (LFC) in humans. Data regarding the effect of dulaglutide, a once-weekly GLP-1r agonist, on human LFC are scarce. This study examined the effect of dulaglutide on LFC in individuals with type 2 diabetes and non-alcoholic fatty liver disease (NAFLD).Effect of dulaglutide on liver fat (D-LIFT) was a 24 week, open-label, parallel-group, randomised controlled trial to determine the effect of dulaglutide on liver fat at a tertiary care centre in India. Adults (n = 64), who had type 2 diabetes and MRI-derived proton density fat fraction-assessed LFC of ≥6.0% at baseline, were randomly assigned to receive dulaglutide weekly for 24 weeks (add-on to usual care) or usual care, based on a predefined computer-generated number with a 1:1 allocation that was concealed using serially numbered, opaque, sealed envelopes. The primary endpoint was the difference of the change in LFC from 0 (baseline) to 24 weeks between groups. The secondary outcome measures included the difference of the change in pancreatic fat content (PFC), change in liver stiffness measurement (LSM in kPa) measured by vibration-controlled transient elastography, and change in liver enzymes.Eighty-eight patients were screened; 32 were randomly assigned to the dulaglutide group and 32 to the control group. Overall, 52 participants were included for per-protocol analysis: those who had MRI-PDFF data at baseline and week 24. Dulaglutide treatment resulted in a control-corrected absolute change in LFC of -3.5% (95% CI -6.6, -0.4; p = 0.025) and relative change of -26.4% (-44.2, -8.6; p = 0.004), corresponding to a 2.6-fold greater reduction. Dulaglutide-treated participants also showed a significant reduction in γ-glutamyl transpeptidase (GGT) levels (mean between-group difference -13.1 U/l [95% CI -24.4, -1.8]; p = 0.025) and non-significant reductions in aspartate aminotransferase (AST) (-9.3 U/l [-19.5, 1.0]; p = 0.075) and alanine aminotransferase (ALT) levels (-13.1 U/l [-24.4, 2.5]; p = 0.10). Absolute changes in PFC (-1.4% [-3.2, 0.3]; p = 0.106) and LSM (-1.31 kPa [-2.99, 0.37]; p = 0.123) were not significant when comparing the two groups. There were no serious drug-related adverse events.When included in the standard treatment for type 2 diabetes, dulaglutide significantly reduces LFC and improves GGT levels in participants with NAFLD. There were non-significant reductions in PFC, liver stiffness, serum AST and serum ALT levels. Dulaglutide could be considered for the early treatment of NAFLD in patients with type 2 diabetes.ClinicalTrials.gov NCT03590626 FUNDING: The current study was supported by an investigator-initiated study grant from Medanta-The Medicity's departmental research fund and a grant from the Endocrine and Diabetes Foundation (EDF), India. Graphical abstract.
Published: 2020

129. Host plant-mediated effects of elevated CO2 and temperature on growth and developmental parameters of Zygogramma bicolorata (Coleoptera: Chrysomelidae)

Author: Bhumesh Kumar, Sushilkumar, Jaipal S. Choudhary, and Lavkush Kumar
Subjects: 0106 biological sciences, biology, Hatching, Biological pest control, Parthenium hysterophorus, 04 agricultural and veterinary sciences, General Medicine, Diapause, biology.organism_classification, 01 natural sciences, Parthenium, Pupa, 010602 entomology, Horticulture, Zygogramma bicolorata, Insect Science, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Population dynamics, Agronomy and Crop Science
Abstract: Mexican beetle, Zygogramma bicolorata Pallister (Coleptera: Chrysomelidae) is a potential weed control biocontrol agent in Australia, India and other countries. Its grubs and adults feed on the leaves of parthenium weed, Parthenium hysterophorus and check the further growth of the plant. Experiments were conducted to understand host plant-mediated effects of elevated temperature and elevated CO2 on biocontrol agent Z. bicolorata. Food consumption, utilization, ecological efficiency and life-table parameters of Z. bicolorata were studied in grubs and adults stage up to diapause. Reduction of leaf nitrogen in parthenium weed foliage with a significant increase in carbon and C:N ratio was recorded at elevated CO2. Elevated CO2 and temperature had no effect on adult longevity before diapausing. Duration of egg's hatching, specific stages of grub and pupa of Z. bicolorata were significantly longer when beetles fed on leaves grown under elevated CO2 but these parameters decreased significantly on leaves grown under elevated temperature. Significantly high consumption rates with low growth and digestion conversions were observed under elevated CO2 and/or in coupled with elevated temperature. Elevated CO2 and temperature-grown parthenium weed foliage also had a significant effect on Z. bicolorata intrinsic rate of increase (R), finite rate of increase (λ), mean generation time (T), and gross reproductive rate. Changed quality of parthenium weed leaves in elevated CO2 and temperature levels resulted in the increase of consumption, slower food conversion rates, increase in developmental period with reduced reproduction efficiency of Z. bicolorata. Our results indicate that the reproduction efficiency of Z. bicolorata is likely to be reduced as the climate changes, despite increased feeding rates exhibited by grubs and adult beetles on parthenium weed foliage.
Published: 2020

130. Study of ionospheric scintillation during geomagnetic storms at equatorial anomaly region Bhopal

Author: Gupta C. Rashmi, S. Choudhary, and A. K. Gwal
Subjects: 010302 applied physics, Geomagnetic storm, Scintillation, General Physics and Astronomy, Geophysics, Space weather, GPS signals, 01 natural sciences, Physics::Geophysics, Latitude, Earth's magnetic field, Interplanetary scintillation, Physics::Space Physics, 0103 physical sciences, Environmental science, Ionosphere, Physics::Atmospheric and Oceanic Physics
Abstract: GPS L-band signals get affected by ionospheric scintillation; as a result, satellite navigation too gets affected. The most extreme scintillation activity is expected to occur near the equatorial region during geomagnetic storms. The behavior and morphology of low-latitude ionosphere are different from the other latitudes. The space weather conditions in low latitude show different nature because of the geomagnetic field. Due to penetration of soft, high energetic particles, the plasma density increases, which is the main source of generation of ionospheric irregularities scintillation. GPS scintillation at low latitudes is primarily associated with equatorial spread F. Equatorial spread F is caused by ionospheric irregularities with a spatial spectrum extending from 100 km to less than 1 m. When GPS signals encounter the ionospheric irregularities of various sizes produced during high geomagnetic and solar activity, they undergo drastic changes in their phase and amplitude scintillation indices. The accuracy and reliability of GPS system get affected by scintillation. Also the atmosphere air molecule’s content and deviation of electrons, protons, neutrons according to flow rate are observed. In the present paper, we have studied the scintillation activity at low-latitude station Bhopal.
Published: 2020

131. Normal Values And Variation Of Thyroid Stimulating Hormone (Tsh) In Cord Blood Of Babies Bornover A Period Of 1 Year

Author: Suresh S Choudhary, Langade R A, and Kshirsagar V Y
Subjects: medicine.medical_specialty, Obstetrics, business.industry, Vaginal delivery, Incidence (epidemiology), medicine.disease, Congenital hypothyroidism, Gestational diabetes, Thyroid-stimulating hormone, Cord blood, medicine, Apgar score, General Pharmacology, Toxicology and Pharmaceutics, business, Prospective cohort study
Abstract: A hospital-based prospective study was conducted with 1200 neonates to evaluate the normal values of cord blood TSH and its variations among term babies and identify maternal factors affecting the cord blood TSH. ResultsMajority of the mothers (53.8%) were in the age group of 26-35 years.44.6% mothers were primigravida, None of the mothers had a history of anti-thyroid drug intake or a history of maternal goitre. Majority of the mothers (97.1%) were from a rural area, 70 (55.11%) and 22 (17.32%) mothers developed hypertension and hypothyroidism respectively while 20 (15.74%) and 15 (11.81%) patients developed Gestational diabetes mellitus and HTN+GDM respectively of 127 mothers with antenatal complications: 708 (59%) and 48 (4%) newborns delivered through Normal Vaginal Delivery. Maximum neonates (98.9%) were Appropriate for Gestational Age (AGA) while 0.8%. The incidence of male and female neonates was 640 (53.3%) and 560 (46.7%) respectively. 655 (54.6%) and 531 (44.3%) neonates weighed in the range of 2.501 – 3.000 kgs and 3.001– 3.500 kgs respectively. 1125 (93.7%) neonates had an APGAR score of 5-7. Eighty-two neonates had CBTSH level of >20mIU/L. Eighty-two neonates with CBTSH level of >20mIU/L were followed up on 7thday and 21stday of life. On 7th day, 12 neonates had raised TSH and low T4.On the 21st day out of these 12 neonates, only two neonates had significant raised TSH and low values of T4. Treatment was started for these two neonates. The CBTSH levels were found to increase with increasing maternal age. There was a significant association of CBTSH levels and maternal age, mode of delivery, antenatal complications. There is an urgent need for adopting universal screening of all neonates for congenital hypothyroidism. Babies with CBTSH levels of >20mIU/L should be evaluated on 7th and 21st day of life for TSH and T4 levels for earlier interpretation of congenital hypothyroidism.
Published: 2020

132. Crop rotation and tillage management options for sustainable intensification of rice-fallow agro-ecosystem in eastern India

Author: K. K. Rao, Rakesh Kumar, Hansraj Hans, J. S. Mishra, Surajit Mondal, Jaipal S. Choudhary, Kali Krishna Hazra, and B. P. Bhatt
Subjects: Irrigation, Multidisciplinary, Conventional tillage, Moisture, lcsh:R, lcsh:Medicine, 04 agricultural and veterinary sciences, 010501 environmental sciences, Crop rotation, 01 natural sciences, Article, Environmental sciences, Crop, Tillage, Agronomy, 040103 agronomy & agriculture, 0401 agriculture, forestry, and fisheries, Environmental science, lcsh:Q, lcsh:Science, Water content, Cropping, Climate sciences, 0105 earth and related environmental sciences
Abstract: Presently, rice-fallows are targeted for cropping intensification in South Asia. Rice-fallows a rainfed mono-cropping system remain fallow after rice due to lack of irrigation facilities and poor socio-economic condition of the farmers. Nevertheless, there is the scope of including ecologically adaptable winter crops in water-limited rice-fallow conditions with effective moisture conservation practices. The study aimed to identify the winter-crops that are adaptable and productive in rice-fallow conditions and to evaluate the different tillage-based crop establishment practices for soil moisture conservation, grain yield, economics, and sustainability parameters. Six different crop establishment and residue management (CERM) practices viz., zero-tillage direct seeded rice (ZTDSR), zero-tillage transplanted rice (ZTTPR), puddled transplanted rice (PTR), ZTDSR with rice residue retention (ZTDSRR+), ZTTPR with rice residue retention (ZTTPRR+), PTR with rice residue retention (PTRR+) as main-plot treatment and five winter crops (chickpea, lentil, safflower, linseed, and mustard) as sub-plot treatment were evaluated in a split-plot design. The productivity of grain legumes (chickpea and lentil) was higher over oilseed crops in rice-fallow conditions with an order of chickpea > lentil > safflower > mustard > linseed. Among the CERM practices, ZTDSRR+ and ZTDSR treatments increased the grain yield of all the winter crops over PTR treatment, which was primarily attributed to higher soil moisture retention for an extended period. Grain yield increment with conservation tillage practices was highly prominent in safflower (190%) followed by lentil (93%) and chickpea (70%). Rice grain yield was higher (7–35%) under PTR treatment followed by ZTDSR treatment. Conservation tillage practices (ZTDSR, ZTTPR) reduced energy use (11–20%) and increased the energy ratio over conventional tillage practice (PTR), higher in rice-safflower, rice-lentil and rice-chickpea rotations. Higher net return was attained in rice-safflower and rice-chickpea rotations with ZTDSRR+ treatment. Predicted emission of greenhouse gases was markedly reduced in ZTDSR treatment (30%) compared to ZTTPR and PTR treatments. Hence, the study suggests that cropping intensification of rice-fallows with the inclusion of winter crops like chickpea, lentil, and safflower following conservation tillage practices (ZTDSRR+ in particular) could be the strategic options for achieving the higher system productivity, economic returns, and energy use efficiency with the reduced emission of greenhouse gases.
Published: 2020

133. Mutations in FAM50A suggest that Armfield XLID syndrome is a spliceosomopathy

Author: Charles E. Schwartz, Emil Alexov, Jyoti S. Choudhary, Sujata Srikanth, Joy Norris, Keri Ramsey, Lu Yu, David J. Adams, Yu-Ri Lee, Karen W. Gripp, Ed Spence, Cheol-Hee Kim, Aida Telegrafi, Roger E. Stevenson, Chelsea Roadhouse, Trevor Moreland, Tae Ik Choi, Soo Jeong Kwon, Hee Moon Park, Erica E. Davis, Ingrid M. Wentzensen, Won Do Heo, Kim Armfield-Uhas, Cindy Skinner, Nicholas Katsanis, Yunhui Peng, Kamal Khan, Mercedes Pardo, Kirsty McWalter, Shahid Mahmood Baig, Marie R. Mooney, Nicola A. Thompson, Michael J. Lyons, Chumei Li, Daseuli Yu, and Kirk Aleck
Subjects: 0301 basic medicine, Male, Molecular biology, General Physics and Astronomy, 030105 genetics & heredity, medicine.disease_cause, Transcriptome, Mice, RNA, Small Nuclear, Missense mutation, lcsh:Science, Child, Zebrafish, Genetics, Mutation, Multidisciplinary, Gene Expression Regulation, Developmental, RNA-Binding Proteins, Syndrome, Phenotype, Pedigree, DNA-Binding Proteins, Protein Transport, Child, Preschool, Female, Adult, Spliceosome, congenital, hereditary, and neonatal diseases and abnormalities, RNA Splicing, Science, Mutation, Missense, Biology, General Biochemistry, Genetics and Molecular Biology, Article, 03 medical and health sciences, Intellectual Disability, Developmental biology, medicine, Animals, Humans, Family, RNA, Messenger, Cell Nucleus, Alternative splicing, General Chemistry, Zebrafish Proteins, biology.organism_classification, Xq28, nervous system diseases, 030104 developmental biology, Mental Retardation, X-Linked, NIH 3T3 Cells, Spliceosomes, lcsh:Q, Neuroscience
Abstract: Intellectual disability (ID) is a heterogeneous clinical entity and includes an excess of males who harbor variants on the X-chromosome (XLID). We report rare FAM50A missense variants in the original Armfield XLID syndrome family localized in Xq28 and four additional unrelated males with overlapping features. Our fam50a knockout (KO) zebrafish model exhibits abnormal neurogenesis and craniofacial patterning, and in vivo complementation assays indicate that the patient-derived variants are hypomorphic. RNA sequencing analysis from fam50a KO zebrafish show dysregulation of the transcriptome, with augmented spliceosome mRNAs and depletion of transcripts involved in neurodevelopment. Zebrafish RNA-seq datasets show a preponderance of 3′ alternative splicing events in fam50a KO, suggesting a role in the spliceosome C complex. These data are supported with transcriptomic signatures from cell lines derived from affected individuals and FAM50A protein-protein interaction data. In sum, Armfield XLID syndrome is a spliceosomopathy associated with aberrant mRNA processing during development., Armfield X-linked disability (XLID) disorder has previously been linked to a locus in Xq28. Here, the authors report rare missense variants in FAM50A at Xq28, show that FAM50A interacts with the spliceosome, and that mis-splicing is enriched in knockout zebrafish suggesting it is a spliceosomopathy.
Published: 2020

134. Comparison of Nutrient Content, Uptake and Protein Content in Varieties of Different types of Maize Growing under Organic Farming

Author: Gajanand Jat, Ravindra Kumar Jain, Shanti Kumar Sharma, Roshan Choudhary, S K Yadav, and R. S. Choudhary
Subjects: Protein content, Agronomy, Organic farming, Biology, Nutrient content
Published: 2020

135. Single-cell transcriptomics identifies an effectorness gradient shaping the response of CD4+ T cells to cytokines

Author: Nikolina Nakic, Jyoti S. Choudhary, Paola G. Bronson, Eddie Cano-Gamez, Marta Baldrighi, Blagoje Soskic, Christopher G. C. Larminie, Gosia Trynka, David R. Willé, Ernest C. So, David F. Tough, Theodoros I. Roumeliotis, Deborah J. Smyth, Wendy C. Rowan, and Jorge Esparza-Gordillo
Subjects: 0301 basic medicine, CD4-Positive T-Lymphocytes, Male, Chemokine, Proteome, medicine.medical_treatment, General Physics and Astronomy, Lymphocyte Activation, 0302 clinical medicine, Single-cell analysis, Gene expression, lcsh:Science, CD4-positive T cells, 0303 health sciences, Principal Component Analysis, Multidisciplinary, biology, Effector, Cell Polarity, Middle Aged, Acquired immune system, Phenotype, Cell biology, Cytokine, medicine.anatomical_structure, Cytokines, medicine.symptom, Single-Cell Analysis, Cell type, T cell, Science, Adaptive immunity, Receptors, Antigen, T-Cell, Systems analysis, Inflammation, General Biochemistry, Genetics and Molecular Biology, Article, 03 medical and health sciences, Immune system, Antigen, CD28 Antigens, medicine, Humans, 030304 developmental biology, General Chemistry, Gene regulation in immune cells, 030104 developmental biology, Gene Expression Regulation, biology.protein, lcsh:Q, Transcriptome, 030217 neurology & neurosurgery
Abstract: Naïve CD4+ T cells coordinate the immune response by acquiring an effector phenotype in response to cytokines. However, the cytokine responses in memory T cells remain largely understudied. Here we use quantitative proteomics, bulk RNA-seq, and single-cell RNA-seq of over 40,000 human naïve and memory CD4+ T cells to show that responses to cytokines differ substantially between these cell types. Memory T cells are unable to differentiate into the Th2 phenotype, and acquire a Th17-like phenotype in response to iTreg polarization. Single-cell analyses show that T cells constitute a transcriptional continuum that progresses from naïve to central and effector memory T cells, forming an effectorness gradient accompanied by an increase in the expression of chemokines and cytokines. Finally, we show that T cell activation and cytokine responses are influenced by the effectorness gradient. Our results illustrate the heterogeneity of T cell responses, furthering our understanding of inflammation., Cytokines critically control the differentiation and functions of activated naïve and memory T cells. Here the authors show, using multi-omics and single-cell analyses, that naïve and memory T cells exhibit distinct cytokine responses, in which an ‘effectorness gradient’ is depicted by a transcriptional continuum, which shapes the downstream genetic programs.
Published: 2020

136. Impact of Different Dates of Inoculation and Evaluation of Sugarcane Varieties against Red Rot Disease of Sugarcane

Author: C. S. Choudhary, Saurabh Dubey, Md. Minnatullah, Shivam Maurya, and Abhay Ranjan
Subjects: Horticulture, Inoculation, Biology
Published: 2020

137. Liver Transplantation for Acute Liver Failure in Presence of Acute Kidney Injury

Author: Neeraj Saraf, Narendra S. Choudhary, Sanjiv Saigal, and Arvinder S. Soin
Subjects: medicine.medical_specialty, Poor prognosis, Catastrophic illness, medicine.medical_treatment, Review Article, Liver transplantation, urologic and male genital diseases, Gastroenterology, 03 medical and health sciences, 0302 clinical medicine, Internal medicine, medicine, In patient, Renal replacement therapy, Hepatology, urogenital system, business.industry, digestive, oral, and skin physiology, High mortality, Acute kidney injury, Liver failure, medicine.disease, female genital diseases and pregnancy complications, 030220 oncology & carcinogenesis, 030211 gastroenterology & hepatology, business
Abstract: Acute liver failure (ALF) is a catastrophic illness, which is associated with high mortality in absence of liver transplantation. ALF is associated with multisystem involvement including acute kidney injury (AKI). AKI worsens the already poor prognosis of ALF. There is limited literature on impact of AKI on outcomes of liver transplantation (LT). The use of continuous renal replacement therapy (CRRT) may have a role in transplant-free survival or bridging to LT. Although results suggest a somewhat lower survival in patients with ALF and AKI, LT is a life-saving option and should not be deferred in absence of other contraindications. In the current review, we discuss impact of AKI on transplant-free survival, possible role of CRRT, and role of LT in patients with ALF associated with AKI.
Published: 2020

138. Metastatic leiomyosarcoma to the pancreas diagnosed on endoscopic ultrasound‐guided fine needle aspiration – A report of two cases with review of spindle cell lesions of pancreas

Author: Haimanti Sarin, Abha Thakur, and Narendra S. Choudhary
Subjects: Endoscopic ultrasound, medicine.medical_specialty, Histology, medicine.diagnostic_test, business.industry, Cell, General Medicine, Pathology and Forensic Medicine, Fine-needle aspiration, medicine.anatomical_structure, Metastatic leiomyosarcoma, medicine, Radiology, business, Pancreas
Published: 2020

139. Prediction of Ground Vibration Induced Due to Single Hole Blast Using Explicit Dynamics

Author: A. K. Mishra, Hemant Agrawal, R. K. Sinha, Desh Deepak, Shankar Kumar, and B. S. Choudhary
Subjects: Explosive material, Field (physics), business.industry, Mechanical Engineering, Numerical analysis, Dynamics (mechanics), 0211 other engineering and technologies, Metals and Alloys, Detonation, 02 engineering and technology, General Chemistry, Structural engineering, Geotechnical Engineering and Engineering Geology, Vibration, Control and Systems Engineering, hemic and lymphatic diseases, Materials Chemistry, Range (statistics), Ground vibrations, business, 021102 mining & metallurgy
Abstract: There are several methods (empirical, statistical, and machine learning tools) to calculate blast-induced ground vibration. Still, due to complications in the blasting procedure, under varying blasting loads and strata conditions, it is not easy to predict and simulate blast vibration precisely. Therefore, a study was conducted to simulate the field blast data in Ansys software using explicit dynamics. For this study, monitoring of ground vibration for 20 single hole blasts was carried out. The density of emulsion explosives was in the range of 0.9 to 1.15 g/cc. In the laboratory, rock properties were determined from the rock sample collected from the mine site before blasting. The in-hole velocity of detonation (VoD) and the density of the emulsion explosive were also determined. These parameters were used for numerical analysis to know the ground vibrations at specified points. The results of ground vibration predicted by the model are validated using field data.
Published: 2020

140. Branched Ligand Ethyl 2‐Mercaptopropionate as a Stabilizer for CdTe Quantum Dots and its use as a Cu 2+ Ions Probe in Aqueous Medium

Author: Yogesh S. Choudhary and N. Gomathi
Subjects: Materials science, Aqueous medium, chemistry, Ligand, Quantum dot, Cu2 ions, chemistry.chemical_element, General Chemistry, Photochemistry, Copper, Cadmium telluride photovoltaics, Stabilizer (chemistry)
Published: 2020

141. Poor Performance Status Predicts Mortality After Living Donor Liver Transplantation

Author: Arvinder S. Soin, Prashant Bhangui, Sanjay Kumar Yadav, Amit Rastogi, Narendra S. Choudhary, Amey Sonavane, Sanjiv Saigal, Srinivasan Thiagrajan, Sujeet Saha, and Neeraj Saraf
Subjects: medicine.medical_specialty, Hepatology, Performance status, business.industry, Hazard ratio, Hepatitis C, Hepatitis B, medicine.disease, 03 medical and health sciences, Liver disease, 0302 clinical medicine, Interquartile range, 030220 oncology & carcinogenesis, Internal medicine, Hepatocellular carcinoma, Cohort, medicine, Original Article, 030211 gastroenterology & hepatology, business
Abstract: Background/Aims Performance status may adversely affect living donor liver transplantation (LDLT) outcomes. We present our data regarding performance status and posttransplantation survival in a large LDLT cohort. Methods Patients with ABO incompatibility, of pediatric age, with acute liver failure, with hepatocellular carcinoma, and/or who had incomplete data were excluded. Two hundred sixty adults who had decompensated cirrhosis and underwent LDLT from January 2016 to March 2018 were included. Performance status was assessed by Karnofsky Performance Score (KPS). The data are depicted as number, mean (SD), or median (25–75 interquartile range [IQR]). Results The cohort included 232 males and 28 females, aged 48.3 ± 9.8 years. Etiology of liver disease was hepatitis B in 33, hepatitis C in 19, alcohol related in 120, nonalcoholic steatohepatitis/cryptogenic in 68, and other etiologies in 20 patients. The mean Child's score was 9.6 ± 1.7, Model for End-Stage Liver Disease (MELD) score was 18.0 ± 5.8, and donor age was 33.4 ± 9.9 years. Forty-one recipients died at median follow-up of 11 months. The KPS was 100 in 6 (no deaths), 90 in 53 (2 deaths), 80 in 93 (12 deaths), 70 in 69 (14 deaths), 60 in 26 (8 deaths), and 50 in 13 (5 deaths) (p = 0.003). The area under the receiver operating characteristic curve of KPS to predict mortality was 0.698 (p = 0.000, 95% confidence interval [CI] = 0.616–0.780), and the best sensitivity (63%) and specificity (67%) were achieved at KPS ≤70. The survivors and nonsurvivors had a significant difference with respect to KPS (77.6 ± 10.9 versus 69.5 ± 10.9, p 0.000), age of the patient (47.8 ± 9.4 versus 51.1 ± 11.7; p = 0.047), postoperative infections (53.8% versus 85.3%, p = 0.001), and need of packed red cells transfusion. Multivariate analysis (Cox proportional-hazard) showed KPS (hazard ratio [HR] = 0.96, 95% CI = 0.93–0.99, p = 0.007), postoperative infections (HR = 2.3, 95% CI = 1.04–5.1, p = 0.038), and recipient age (HR = 1.03, 95% CI = 1.002–1.07, p = 0.039) as predictors of mortality. Conclusion Pretransplant performance status is one of the predictors of mortality after LDLT.
Published: 2020

142. Study of structural and magnetic properties of Zinc-Substituted Cadmium ferrite nanocrystals

Author: A. K. Nandanwar, D.L. Chaodhary, S. N. Kamde, K. G. Rewatkar, and D. S. Choudhary
Subjects: 010302 applied physics, Materials science, Spinel, Analytical chemistry, chemistry.chemical_element, 02 engineering and technology, Zinc, engineering.material, Coercivity, 021001 nanoscience & nanotechnology, 01 natural sciences, law.invention, Magnetization, chemistry, law, 0103 physical sciences, engineering, Ferrite (magnet), Calcination, Crystallite, 0210 nano-technology, Superparamagnetism
Abstract: Polycrystalline CdxZn1-xFe2O4 ferrites with (x = 0.2 and 0.8) have been prepared by conventional microwave induce sol–gel method. The Calcination of samples was performed at 800 OC for 4 h. The prepared powder samples were structural and compositional characterized by XRD and FE-SEM. Rietveld refined XRD patterns exposed the cubic spinel phase. The magnetic property of prepared samples was investigated using VSM. Magnetization measurements have shown that the particles have superparamagnetic behavior at room temperature. The hysteresis curves of the sample exhibited the reduction of saturation magnetization and coercivity by Zn2+ ions substitution.
Published: 2020

143. Influence of Cr3+ on structural and dielectric properties of Ni0.25Cu0.2Zn0.55Fe2O4 nanoparticles

Author: A. M. Shahare, D. S. Choudhary, Y.S. Bopche, and A.V. Bagde
Subjects: 010302 applied physics, Diffraction, Materials science, Scanning electron microscope, Doping, Analytical chemistry, Nanoparticle, 02 engineering and technology, Dielectric, 021001 nanoscience & nanotechnology, 01 natural sciences, Lattice constant, 0103 physical sciences, Ferrite (magnet), Dielectric loss, 0210 nano-technology
Abstract: The Cr3+ doped ferrite Ni0.25Cu0.2Zn0.55Fe2-xCrxO4 (x = 0.0, 0.05, 0.01, 0.15, 0.2, 0.25) were synthesized by sol–gel auto combustion method. The samples has been investigated by X-ray diffraction (XRD), scanning electron microscopy (SEM) and impedance analyzer. The XRD patterns reveal single phase cubic structure. The crystalline size and the lattice parameter of samples are found to be reduced with increase in Cr concentration. The SEM images show various conical shape particles for all the samples. The dielectric loss of Cr doped samples is found greater than the un-doped sample. The increase in concentration of Cr3+ ions results decrease in dielectric constant (e′) whereas increase in AC Conductivity.
Published: 2020

144. Structure of a nucleosome-bound MuvB transcription factor complex reveals DNA remodelling

Author: Marios G. Koliopoulos, Reyhan Muhammad, Theodoros I. Roumeliotis, Fabienne Beuron, Jyoti S. Choudhary, and Claudio Alfieri
Subjects: Multidisciplinary, Gene Expression Regulation, Cell Cycle, Cryoelectron Microscopy, General Physics and Astronomy, General Chemistry, DNA, General Biochemistry, Genetics and Molecular Biology, Nucleosomes, Transcription Factors
Abstract: Genes encoding the core cell cycle machinery are transcriptionally regulated by the MuvB family of protein complexes in a cell cycle-specific manner. Complexes of MuvB with the transcription factors B-MYB and FOXM1 activate mitotic genes during cell proliferation. The mechanisms of transcriptional regulation by these complexes are still poorly characterised. Here, we combine biochemical analysis and in vitro reconstitution, with structural analysis by cryo-electron microscopy and cross-linking mass spectrometry, to functionally examine these complexes. We find that the MuvB:B-MYB complex binds and remodels nucleosomes, thereby exposing nucleosomal DNA. This remodelling activity is supported by B-MYB which directly binds the remodelled DNA. Given the remodelling activity on the nucleosome, we propose that the MuvB:B-MYB complex functions as a pioneer transcription factor complex. In this work, we rationalise prior biochemical and cellular studies and provide a molecular framework of interactions on a protein complex that is key for cell cycle regulation.
Published: 2022

145. Exploring antecedents of electronic word-of-mouth in tourism: a case of Tripadvisor

Author: Farah S. Choudhary and Alka Sharma
Published: 2022

146. Numerical Analysis of Innovative Sacrificial Protection System under Blast Loading

Author: Sandeep Panchal, N. S. Choudhary, and Manmohan Dass Goel
Subjects: Nonlinear system, Materials science, Arts and Humanities (miscellaneous), Blast load, business.industry, Numerical analysis, Building and Construction, Structural engineering, Protection system, business, Civil and Structural Engineering
Abstract: In the present study, an innovative sacrificial system, comprising hollow tubes, for resisting blast load, is analyzed on a RC panel using the three-dimensional (3D) nonlinear finite-elemen...
Published: 2022

147. Citrobacter rodentium Infection Induces Persistent Molecular Changes and Interferon Gamma-Dependent Major Histocompatibility Complex Class II Expression in the Colonic Epithelium

Author: Caroline Mullineaux-Sanders, Zuzanna Kozik, Julia Sanchez-Garrido, Eve G. D. Hopkins, Jyoti S. Choudhary, Gad Frankel, Wellcome Trust, and Medical Research Council (MRC)
Subjects: antigen presentation, Science & Technology, HOST-DEFENSE, Virology, VIRULENCE, Citrobacter rodentium, enteric infection, PATHOGEN, Life Sciences & Biomedicine, STEM-CELLS, Microbiology, 0605 Microbiology, Research Article
Abstract: Most studies of infections at mucosal surfaces have focused on the acute phase of the disease. Consequently, little is known about the molecular processes that underpin tissue recovery and the long-term consequences postinfection. Here, we conducted temporal deep quantitative proteomic analysis of colonic intestinal epithelial cells (cIECs) from mice infected with the natural mouse pathogen Citrobacter rodentium over time points corresponding to the late steady-state phase (10 days postinfection [DPI]), the clearance phase (13 to 20 DPI), and 4 weeks after the pathogen has been cleared (48 DPI). C. rodentium, which relies on a type III secretion system to infect, is used to model infections with enteropathogenic and enterohemorrhagic Escherichia coli. We observe a strong upregulation of inflammatory signaling and nutritional immunity responses during the clearance phase of the infection. Despite morphological tissue recovery, chromogranin B (ChgB)-positive endocrine cells remained significantly below baseline levels at 48 DPI. In contrast, we observed an increased abundance of proteins involved in antigen processing and presentation 4 weeks after pathogen clearance. In particular, long-term changes were characterized by a persistent interferon gamma (IFN-γ) response and the expression of major histocompatibility complex class II (MHCII) molecules in 60% of the EpCAM+ cIECs, which were not seen in Ifnγ−/− mice. Nonetheless, both wild-type and Ifnγ−/− mice mounted similar systemic and colonic IgG responses to C. rodentium and were equally protected from rechallenge, suggesting that cIEC MHCII is not necessary for protective immunity against C. rodentium.
Published: 2022

148. Integration of Genomics Approaches in Abiotic Stress Tolerance in Groundnut (Arachis hypogaea L.): An Overview

Author: B. Aravind, Spurthi N. Nayak, Rakeshkumar S. Choudhary, Spoorti S. Gandhadmath, P. V. V. Prasad, Manish K. Pandey, Ramesh S. Bhat, Naveen Puppala, Putta Latha, Palagiri Sudhakar, and Rajeev K. Varshney
Published: 2022

149. GENCODE: reference annotation for the human and mouse genomes in 2023

Author: Adam Frankish, Sílvia Carbonell-Sala, Mark Diekhans, Irwin Jungreis, Jane E Loveland, Jonathan M Mudge, Cristina Sisu, James C Wright, Carme Arnan, If Barnes, Abhimanyu Banerjee, Ruth Bennett, Andrew Berry, Alexandra Bignell, Carles Boix, Ferriol Calvet, Daniel Cerdán-Vélez, Fiona Cunningham, Claire Davidson, Sarah Donaldson, Cagatay Dursun, Reham Fatima, Stefano Giorgetti, Carlos Garcıa Giron, Jose Manuel Gonzalez, Matthew Hardy, Peter W Harrison, Thibaut Hourlier, Zoe Hollis, Toby Hunt, Benjamin James, Yunzhe Jiang, Rory Johnson, Mike Kay, Julien Lagarde, Fergal J Martin, Laura Martínez Gómez, Surag Nair, Pengyu Ni, Fernando Pozo, Vivek Ramalingam, Magali Ruffier, Bianca M Schmitt, Jacob M Schreiber, Emily Steed, Marie-Marthe Suner, Dulika Sumathipala, Irina Sycheva, Barbara Uszczynska-Ratajczak, Elizabeth Wass, Yucheng T Yang, Andrew Yates, Zahoor Zafrulla, Jyoti S Choudhary, Mark Gerstein, Roderic Guigo, Tim J P Hubbard, Manolis Kellis, Anshul Kundaje, Benedict Paten, Michael L Tress, and Paul Flicek
Subjects: Genetics, 610 Medicine & health
Abstract: Data availability: No new data were generated or analysed in support of this research. Copyright © The Author(s) 2022. GENCODE produces high quality gene and transcript annotation for the human and mouse genomes. All GENCODE annotation is supported by experimental data and serves as a reference for genome biology and clinical genomics. The GENCODE consortium generates targeted experimental data, develops bioinformatic tools and carries out analyses that, along with externally produced data and methods, support the identification and annotation of transcript structures and the determination of their function. Here, we present an update on the annotation of human and mouse genes, including developments in the tools, data, analyses and major collaborations which underpin this progress. For example, we report the creation of a set of non-canonical ORFs identified in GENCODE transcripts, the LRGASP collaboration to assess the use of long transcriptomic data to build transcript models, the progress in collaborations with RefSeq and UniProt to increase convergence in the annotation of human and mouse protein-coding genes, the propagation of GENCODE across the human pan-genome and the development of new tools to support annotation of regulatory features by GENCODE. Our annotation is accessible via Ensembl, the UCSC Genome Browser and https://www.gencodegenes.org. National Human Genome Research Institute of the National Institutes of Health [U41HG007234, R01HG004037]; Wellcome Trust [WT222155/Z/20/Z]; European Molecular Biology Laboratory. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. Funding for open access charge: National Institutes of Health.
Published: 2022
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150. Endoscopic Ultrasound for Gastrointestinal Tuberculosis

Author: Rinkesh Kumar Bansal, Gursimran Kaur, Narendra S. Choudhary, and Rajesh Puri
Published: 2022

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