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Twitter User Classification using Ambient Metadata [article]

Chirag Nagpal, Khushboo Singhal
2014 arXiv   pre-print
Microblogging websites, especially Twitter have become an important means of communication, in today's time. Often these services have been found to be faster than conventional news services. With millions of users, a need was felt to classify users based on ambient metadata associated with their user accounts. We particularly look at the effectiveness of the profile description field in order to carry out the task of user classification. Our results show that such metadata can be an effective feature for any classification task.
arXiv:1407.8499v1 fatcat:jq5dv7s67jefrj7ebv5deadvhi

Mapping Hindi-English Text Re-use Document Pairs [chapter]

Parth Gupta, Khushboo Singhal
2013 Lecture Notes in Computer Science  
Singhal 2 1 NLE Lab, UPV, Spain, 2 IR-Lab, DA-IICT, India Mapping Hindi-English Text Re-use Document Pairs θ = 15.0 P. Gupta 1 ,K.  ...  Singhal 2 1 NLE Lab, UPV, Spain, 2 IR-Lab, DA-IICT, IndiaMapping Hindi-English Text Re-use Document Pairs http://www.clt.iitb.ac.in/hdict/webinterface_user/index.php http://www.clt.iitb.ac.in  ... 
doi:10.1007/978-3-642-40087-2_8 fatcat:64fwtud35jewjhso4imcgqbfu4

The information technology knowledge infrastructure and research in South Asia

VivekKumar Singh, Khushboo Singhal, SumitKumar Banshal, Ashraf Uddin
2014 Journal of Scientometric Research  
The South Asian region habitat about 17% of the world population and it is very important that we ensure development and prosperity of the citizens in the region for a developed and prosperous world. Information technology (IT) is considered as the technology of the modern world, one which has virtually become necessary for economic and scientific development of a nation. IT sector now plays a very important role in all spheres of life and has a measurable impact on the development trajectory
more » ... a country. The South Asian countries, despite lagging behind in Science and Technology sector development during the second half of the 20 th century, made noticeable progress in the IT sector in the recent past. IT has gradually become one of the largest services sector contributors to economies of the region and one of the major employment providers. However, at the same time, it is also true that the region lacs the effort toward the development of original hardware and software products and services. Most of the products (both hardware and software) are being designed, conceptualized, and manufactured elsewhere, and the South Asian region is merely contributing to the operational part by virtue of utilizing abundant manpower. It is in this context that we have tried to measure the level of preparedness of the core strength of the IT knowledge sector and the level of research efforts in this sector towards creating original algorithms, products, and services. The paper explores and measures the IT knowledge infrastructure and the research competence of South Asian countries and provides a detailed analysis of the scenario.
doi:10.4103/2320-0057.153578 fatcat:knfxitsx4fedtnqs6pff3kxee4

Probable benefits of green tea with genetic implications

Khushboo Gupta, Kavita Singhal, Neerja Raj, Saurabh Singh
2017 Journal of Oral and Maxillofacial Pathology  
doi:10.4103/0973-029x.203758 pmid:28479696 pmcid:PMC5406788 fatcat:wegxzc2lznfslbg2ejdirgenjm

Rapid, field-deployable nucleobase detection and identification using FnCas9 [article]

Mohd Azhar, Rhythm Phutela, Asgar Hussain Ansari, Dipanjali Sinha, Namrata Sharma, Manoj Kumar, Meghali Aich, Saumya Sharma, Khushboo Singhal, Harsha Lad, Pradeep K. Patra, Govind Makharia (+3 others)
2020 bioRxiv   pre-print
Detection of pathogenic sequences or variants in DNA and RNA through a point-of-care diagnostic approach is valuable for rapid clinical prognosis. In recent times, CRISPR based detection of nucleic acids have provided an economical and quicker alternative to sequencing-based platforms which are often difficult to implement in the field. Here, we present FnCas9 Editor Linked Uniform Detection Assay (FELUDA) that employs a highly accurate enzymatic readout for detecting nucleotide sequences,
more » ... ifying nucleobase identity and inferring zygosity with precision. We demonstrate that FELUDA output can be adapted to multiple signal detection platforms and can be quickly designed and deployed for versatile applications including rapid diagnosis during infectious disease outbreaks like COVID-19.
doi:10.1101/2020.04.07.028167 fatcat:2g272r7tpzhbzf654r626fukhe

A Study of Adverse Cutaneous Drug Reactions Due to Nsaids at a Rural Based Tertiary Care Centre, Gujarat

Rita Vora, Singhal Rochit R, Patel Trusha M, Modasia Khushboo H
2018 International Journal of Pharmacovigilance  
January 29, 2018; Published: May 25, 2018 *Corresponding author: Rita Vora, Department of Dermatology & Venereology, Pramukhswami Medical College, Karamsad, Gujarat 388325, India, Tel: Citation: Rita V, Singhal  ... 
doi:10.15226/2476-2431/3/1/00123 fatcat:uuuda6le7zbztmbf7tvppdhzvu

Erratum to: Designing a Composite Index for research performance evaluation at the national or regional level: ranking Central Universities in India

Aparna Basu, Sumit Kumar Banshal, Khushboo Singhal, Vivek Kumar Singh
2016 Scientometrics  
doi:10.1007/s11192-016-2009-z fatcat:k6gfmdmgtbcmpkhdgaonljnwqu

Origin of a novel CYP20A1 lncRNA through 23 Alu exaptations in the human lineage creates a potential multi-miRNA sponge [article]

Aniket Bhattacharya, Vineet Jha, Khushboo Singhal, Mahar Fatima, Dayanidhi Singh, Gaura Chaturvedi, Dhwani Dholakia, Rintu Kutum, Trygve E. Bakken, Pankaj Seth, Beena Pillai, Mitali Mukerji
2019 bioRxiv   pre-print
Alu repeats contribute to lineage specific novelties in conserved transcriptional regulatory networks. We report for the first time the origin of a multi-miRNA human specific sponge through exaptation of 23 Alu repeats that forms a novel principal isoform of CYP20A1 gene with a 9kb 3 prime UTR. This 3 prime UTR, confirmed by RACE, is an outlier in terms of its length, with expression in multiple cell lines including brain as evidenced from single nucleus RNA-seq data of ~16000 human cortical
more » ... rons. It has diverged from its parent gene through exon skipping into a novel lncRNA. Its uniqueness in humans was validated by its presence in rosehip neurons and absence in closely related primate species through RNA-seq datasets. Strikingly, prediction by miRanda revealed ~4700 MREs for ~1000 different miRNAs, majorly in Alu repeats, in this 3 prime UTR. Permutations on 1000 random sets suggest their creation is non-random and post Alu exaptation. We hypothesise this lncRNA is an miRNA sponge as it has cytosolic localization and harbors greater than or equal to 10 MREs for 140 miRNAs (threshold > -25kcal/mol). Under experimental conditions where CYP20A1 displays differential expression, we probed the expression of the miRNAs that map to this 3 prime UTR and their cognate targets through small RNA and mRNA-seq, respectively. We observed correlated expression of our lncRNA and a set of 380 genes with downregulation in heat shock and upregulation in HIV1-Tat treatment in primary neurons. GO analyses suggest the involvement of this sponge lncRNA in modulation of processes linked to neuronal development and hemostasis pathways.
doi:10.1101/618645 fatcat:nwdhbrwzvjfdditbqqepxscufy

Neutrophil Lymphocyte Ratio (NLR) as a Bio Inflammatory Marker in Pre-eclampsia

Khushboo Singhal, Arvind Kumar Pal, Sunita Tiwari, Renu Singh, Rashmi Kushwaha
2019 International Journal of Contemporary Medical Research [IJCMR]  
Pre-eclampsia, a systemic disease unique to pregnancy, affects 3-14% of pregnant women. The aim of the present study was to evaluate Neutrophil Lymphocyte Ratio (NLR) as a bio inflammatory marker of pre-eclampsia (PE), a hypertensive disorder of pregnancy characterized by hypertension and proteinuria after 20 weeks of gestation. Material and Methods: This case control study was carried out over a period of 10 months after informed consent and ethical clearance. The study population included 70
more » ... regnant women (35 pre-eclampsia cases and 35 normotensive pregnant subjects as controls). 3 ml venous blood samples were obtained from both the cases and controls. Complete blood count was done using semi-automated three part haematology analyser which gives the reading of cell counts, NLR was calculated manually. Results: The case group (subjects with pre-eclampsia) were found to have higher neutrophil to lymphocyte ratio (NLR) than that of the control group. This difference was statistically significant (p<0.001). The receiver operating curve (ROC) analysis showed significant diagnostic accuracy of NLR to discriminate cases and controls (area under the curve [AUC] = 0.73, P < 0.001) at cutoff value of >= 4.86, 68.6% sensitivity and 80% specificity. Conclusion: Unlike many other inflammatory markers, NLR proves to be an inexpensive and readily available biomarkers, obtained from routinely done complete blood counts that may be useful for prediction and diagnosis of pre-eclampsia.
doi:10.21276/ijcmr.2019.6.4.17 fatcat:4oxcirdawjdsbkkcosofuitd3m

Rapid, accurate, nucleobase detection using FnCas9 [article]

Mohd. Azhar, Rhythm Phutela, Manoj Kumar, Asgar Hussain Ansari, Riya Rauthan, Sneha Gulati, Namrata Sharma, Dipanjali Sinha, Saumya Sharma, Sunaina Singh, Sundaram Acharya, Deepanjan Paul (+14 others)
2020 medRxiv   pre-print
Rapid detection of pathogenic sequences or variants in DNA and RNA through a point-of-care diagnostic approach is valuable for accelerated clinical prognosis as has been witnessed during the recent COVID-19 outbreak. Traditional methods relying on qPCR or sequencing are difficult to implement in settings with limited resources necessitating the development of accurate alternative testing strategies that perform robustly. Here, we present FnCas9 Editor Linked Uniform Detection Assay (FELUDA)
more » ... employs a direct Cas9 based enzymatic readout for detecting nucleotide sequences and identifying nucleobase identity without the requirement of trans-cleavage activity of reporter molecules. We demonstrate that FELUDA is 100% accurate in detecting single nucleotide variants (SNVs) including heterozygous carriers of a mutation and present a simple design strategy in the form of a web-tool, JATAYU, for its implementation. FELUDA is semi quantitative, can be adapted to multiple signal detection platforms and can be quickly designed and deployed for versatile applications such as infectious disease outbreaks like COVID-19. Using a lateral flow readout within 1h, FELUDA shows 100% sensitivity and 97% specificity across all range of viral loads in clinical samples. In combination with RT-RPA and a smartphone application True Outcome Predicted via Strip Evaluation (TOPSE), we present a prototype for FELUDA for CoV-2 detection at home.
doi:10.1101/2020.09.13.20193581 fatcat:j6ufz2hnwzc4de46mvz53jjpkm

Multiple Alu exonization in 3'UTR of a primate specific isoform of CYP20A1 creates a potential miRNA sponge

Aniket Bhattacharya, Vineet Jha, Khushboo Singhal, Mahar Fatima, Dayanidhi Singh, Gaura Chaturvedi, Dhwani Dholakia, Rintu Kutum, Rajesh Pandey, Trygve E Bakken, Pankaj Seth, Beena Pillai (+2 others)
2020 Genome Biology and Evolution  
Alu repeats contribute to phylogenetic novelties in conserved regulatory networks in primates. Our study highlights how exonized Alus could nucleate large-scale mRNA-miRNA interactions. Using a functional genomics approach, we characterize a transcript isoform of an orphan gene, CYP20A1 (CYP20A1_Alu-LT) that has exonization of 23 Alus in its 3'UTR. CYP20A1_Alu-LT, confirmed by 3'RACE, is an outlier in length (9 kb 3'UTR) and widely expressed. Using publically available datasets, we demonstrate
more » ... ts expression in higher primates and presence in single nucleus RNA-seq of 15928 human cortical neurons. miRanda predicts ∼4700 miRNA recognition elements (MREs) for ∼1000 miRNAs, primarily originated within these 3'UTR-Alus. CYP20A1_Alu-LT could be a potential multi-miRNA sponge as it harbors ≥10 MREs for 140 miRNAs and has cytosolic localization. We further tested whether expression of CYP20A1_Alu-LT correlates with mRNAs harboring similar MRE targets. RNA-seq with conjoint miRNA-seq analysis was done in primary human neurons where we observed CYP20A1_Alu-LT to be downregulated during heat shock response and upregulated in HIV1-Tat treatment. 380 genes were positively correlated with its expression (significantly downregulated in heat shock and upregulated in Tat) and they harbored MREs for nine expressed miRNAs which were also enriched in CYP20A1_Alu-LT. MREs were significantly enriched in these 380 genes compared to random sets of differentially expressed genes (p = 8.134e-12). Gene ontology suggested involvement of these genes in neuronal development and hemostasis pathways thus proposing a novel component of Alu-miRNA mediated transcriptional modulation that could govern specific physiological outcomes in higher primates.
doi:10.1093/gbe/evaa233 pmid:33434274 pmcid:PMC7802813 fatcat:o4ylmehb3raejg5ygoplaqa26e

Traditional use of Cissampelos pareira L. for hormone disorder and fever provides molecular links of ESR1 modulation to viral inhibition [article]

Madiha Haider, Dhwani Dholakia, Aleksha Panwar, Parth Garg, Vivek Anand, Atish Gheware, Khushboo Singhal, Dayanidhi Singh, Shaunak A Burse, M. Ghalib Enayathullah, Yash Parekh, Sushma Ram (+8 others)
2021 bioRxiv   pre-print
AbstractIn traditional systems, a single herbal formulation is often used in the treatment of diverse diseases, including some that are newly emergent and prevalent today. We provide here a multi-omics framework to probe the molecular basis of a multicomponent example herb, Cissampelos pareira L. (Cipa) used in the treatment of hormonal disorders and fever in Ayurveda. Cipa treated MCF7 cells exhibit downregulation of signatures of estrogen response. 38 constituent molecules in Cipa potentially
more » ... bind (∆G< -7.5) with ERα at the same site as estrogen. Cipa transcriptome signatures in the connectivity map exhibit positive scores with protein translation inhibitors and knockdown signatures of genes linked to the antiviral response. This includes the knockdown signature of RPL7, a coactivator of ESRI with a connectivity score > 99.92. This axis was found to be upregulated in the COVID-19 patient transcriptome. The antiviral activity through ESR1 modulation was validated in the DENV-2 infection model. We further observed 98% inhibition of SARs-COV-2 replication in infected Vero cell cultures with the whole extract. A few of its prominent pure constituents e.g pareirarine, cissamine, magnoflorine exhibited 40-80% inhibition. This study provides a novel framework for querying the molecular links of multicomponent Ayurveda formulations and explains their use in the treatment of disparate diseases. The novel biological targets identified here can become potential that could be applicable to more than one viral infection, such as the use of Cipa in dengue and COVID-19.
doi:10.1101/2021.02.17.431579 fatcat:mpinhckrmvb6bg2qhj2j6bn3gq

Rapid and accurate nucleobase detection using FnCas9 and its application in COVID-19 diagnosis

Mohd Azhar, Rhythm Phutela, Manoj Kumar, Asgar Hussain Ansari, Riya Rauthan, Sneha Gulati, Namrata Sharma, Dipanjali Sinha, Saumya Sharma, Sunaina Singh, Sundaram Acharya, Sajal Sarkar (+14 others)
2021 Biosensors & bioelectronics  
Khushboo Singhal: Resources. Harsha Lad: Resources, Validation. Pradeep Kumar Patra: Resources, Validation. Govind Makharia: Investigation, Resources. Giriraj Ratan Chandak: Investigation, Resources.  ... 
doi:10.1016/j.bios.2021.113207 pmid:33866136 fatcat:6g7z3zrya5g5znxwpn6j7mlfwe

High throughput detection and genetic epidemiology of SARS-CoV-2 using COVIDSeq next generation sequencing [article]

Rahul C. Bhoyar, Abhinav Jain, Paras Sehgal, Mohit Kumar Divakar, Disha Sharma, Mohamed Imran, Bani Jolly, Gyan Ranjan, Mercy Rophina, Sumit Sharma, Sanjay Siwach, Kavita Pandhare (+45 others)
2020 bioRxiv   pre-print
The rapid emergence of coronavirus disease 2019 (COVID-19) as a global pandemic affecting millions of individuals globally has necessitated sensitive and high-throughput approaches for the diagnosis, surveillance and for determining the genetic epidemiology of SARS-CoV-2. In the present study, we used the COVIDSeq protocol, which involves multiplex-PCR, barcoding and sequencing of samples for high-throughput detection and deciphering the genetic epidemiology of SARS-CoV-2. We used the approach
more » ... n 752 clinical samples in duplicates, amounting to a total of 1536 samples which could be sequenced on a single S4 sequencing flow cell on NovaSeq 6000. Our analysis suggests a high concordance between technical duplicates and a high concordance of detection of SARS-CoV-2 between the COVIDSeq as well as RT-PCR approaches. An in-depth analysis revealed a total of six samples in which COVIDSeq detected SARS-CoV-2 in high confidence which were negative in RT-PCR. Additionally, the assay could detect SARS-CoV-2 in 21 samples and 16 samples which were classified inconclusive and pan-sarbeco positive respectively suggesting that COVIDSeq could be used as a confirmatory test. The sequencing approach also enabled insights into the evolution and genetic epidemiology of the SARS-CoV-2 samples. The samples were classified into a total of 3 clades. This study reports two lineages B.1.112 and B.1.99 for the first time in India. This study also revealed 1,143 unique single nucleotide variants and added a total of 73 novel variants identified for the first time. To the best of our knowledge, this is the first report of the COVIDSeq approach for detection and genetic epidemiology of SARS-CoV-2. Our analysis suggests that COVIDSeq could be a potential high sensitivity assay for the detection of SARS-CoV-2, with an additional advantage of enabling genetic epidemiology of SARS-CoV-2.
doi:10.1101/2020.08.10.242677 fatcat:6k6neffh4nafvelf6lnnubrkoi

High throughput detection and genetic epidemiology of SARS-CoV-2 using COVIDSeq next-generation sequencing

Rahul C Bhoyar, Abhinav Jain, Paras Sehgal, Mohit Kumar Divakar, Disha Sharma, Mohamed Imran, Bani Jolly, Gyan Ranjan, Mercy Rophina, Sumit Sharma, Sanjay Siwach, Kavita Pandhare (+45 others)
2021 PLoS ONE  
The rapid emergence of coronavirus disease 2019 (COVID-19) as a global pandemic affecting millions of individuals globally has necessitated sensitive and high-throughput approaches for the diagnosis, surveillance, and determining the genetic epidemiology of SARS-CoV-2. In the present study, we used the COVIDSeq protocol, which involves multiplex-PCR, barcoding, and sequencing of samples for high-throughput detection and deciphering the genetic epidemiology of SARS-CoV-2. We used the approach on
more » ... 752 clinical samples in duplicates, amounting to a total of 1536 samples which could be sequenced on a single S4 sequencing flow cell on NovaSeq 6000. Our analysis suggests a high concordance between technical duplicates and a high concordance of detection of SARS-CoV-2 between the COVIDSeq as well as RT-PCR approaches. An in-depth analysis revealed a total of six samples in which COVIDSeq detected SARS-CoV-2 in high confidence which were negative in RT-PCR. Additionally, the assay could detect SARS-CoV-2 in 21 samples and 16 samples which were classified inconclusive and pan-sarbeco positive respectively suggesting that COVIDSeq could be used as a confirmatory test. The sequencing approach also enabled insights into the evolution and genetic epidemiology of the SARS-CoV-2 samples. The samples were classified into a total of 3 clades. This study reports two lineages B.1.112 and B.1.99 for the first time in India. This study also revealed 1,143 unique single nucleotide variants and added a total of 73 novel variants identified for the first time. To the best of our knowledge, this is the first report of the COVIDSeq approach for detection and genetic epidemiology of SARS-CoV-2. Our analysis suggests that COVIDSeq could be a potential high sensitivity assay for the detection of SARS-CoV-2, with an additional advantage of enabling the genetic epidemiology of SARS-CoV-2.
doi:10.1371/journal.pone.0247115 pmid:33596239 pmcid:PMC7888613 fatcat:lf7boixozzdt3k2gsqom3jxhz4
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