Ankita Roy - Academia.edu (original) (raw)
Papers by Ankita Roy
Arthritis Care & Research, 2014
ObjectiveGout flares are not well documented by diagnosis codes, making it difficult to conduct a... more ObjectiveGout flares are not well documented by diagnosis codes, making it difficult to conduct accurate database studies. We implemented a computer‐based method to automatically identify gout flares using natural language processing (NLP) and machine learning (ML) from electronic clinical notes.MethodsOf 16,519 patients, 1,264 and 1,192 clinical notes from 2 separate sets of 100 patients were selected as the training and evaluation data sets, respectively, which were reviewed by rheumatologists. We created separate NLP searches to capture different aspects of gout flares. For each note, the NLP search outputs became the ML system inputs, which provided the final classification decisions. The note‐level classifications were grouped into patient‐level gout flares. Our NLP+ML results were validated using a gold standard data set and compared with the claims‐based method used by prior literatures.ResultsFor 16,519 patients with a diagnosis of gout and a prescription for a urate‐lowerin...
The Pharma Innovation Journal, 2021
Publication View. 29298223. Development of a novel approach and a new expression system for the p... more Publication View. 29298223. Development of a novel approach and a new expression system for the production and crystallization of human G protein-coupled receptors (2007). Roy, Ankita. Publication details. Download, http://edoc.mpg.de/346476. ...
Table S2. Positive CUIS. A dictionary of CUISs and the corresponding CUI preferred name that were... more Table S2. Positive CUIS. A dictionary of CUISs and the corresponding CUI preferred name that were retained after filtering. (XLS 23 kb)
Current Opinion in Plant Biology, 2021
Trichomes show 47 morphological phenotypes, while literature reports only two root hair phenotype... more Trichomes show 47 morphological phenotypes, while literature reports only two root hair phenotypes in all plants. However, could hair-like structures exist below-ground in a similar wide range of morphologies like trichomes? Genetic mutants and root hair stress phenotypes point to the possibility of uncharacterized morphological variation existing belowground. For example, such root hairs in Arabidopsis (Arabidopsis thaliana) can be wavy, curled, or branched. We found hints in the literature about hair-like structures that emerge before root hairs belowground. As such, these early emerging hair structures can be potential exceptions to the contrasting morphological variation between trichomes and root hairs. Here, we show a previously unreported 'hooked' hair structure growing below-ground in common bean. The unique 'hooking' shape distinguishes the 'hooked hair' morphologically from root hairs. Currently, we cannot fully characterize the phenotype of our observation due to the lack of automated methods for phenotyping root hairs. This phenotyping bottleneck also handicaps the discovery of more morphology types that might exist below-ground as manual screening across species is slower than computer-assisted high-throughput screening.
Engineering Failure Analysis, 2020
This is a PDF file of an article that has undergone enhancements after acceptance, such as the ad... more This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. This version will undergo additional copyediting, typesetting and review before it is published in its final form, but we are providing this version to give early visibility of the article. Please note that, during the production process, errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.
Journal of Molecular Structure, 2019
We report here the synthesis, characterization and pH sensing properties of a Schiff-base molecul... more We report here the synthesis, characterization and pH sensing properties of a Schiff-base molecule, 2hydroxy-5-methyl-3-((quinolin-2-ylimino)methyl)benzaldehyde (HL-2-qui) to compare the results observed for its isomers having different position of imino linkage on the quinoline unit. Fluorescence intensity of HL-2-qui at 530 nm enhanced gradually with the increase in pH of the media whereas its isomers showed ratiometric pH sensing behavior under similar conditions. HL-2-qui was colorless in acidic condition and yellow in alkaline medium under visible light while under UV light, the colors of the probe changed to indigo and fluorescent green, respectively. The chemosensor was applied in the detection of different pH regions using lemon juice and river water as the real sample.
Journal of Healthcare Informatics Research, 2019
Accurately identifying distant recurrences in breast cancer from the electronic health records (E... more Accurately identifying distant recurrences in breast cancer from the electronic health records (EHR) is important for both clinical care and secondary analysis. Although multiple applications have been developed for computational phenotyping in breast cancer, distant recurrence identification still relies heavily on manual chart review. In this study, we aim to develop a model that identifies distant recurrences in breast cancer using clinical narratives and structured data from EHR. We applied MetaMap to extract features from clinical narratives and also retrieved structured clinical data from EHR. Using these features, we trained a support vector machine model to identify distant recurrences in breast cancer patients. We trained the model using 1396 doubleannotated subjects and validated the model using 599 double-annotated subjects. In addition, we validated the model on a set of 4904 single-annotated subjects as a generalization test. In the held-out test and generalization test, we obtained F-measure scores of 0.78 and 0.74, area under curve (AUC) scores of 0.95 and 0.93, respectively. To explore the representation learning utility of deep neural networks, we designed multiple convolutional neural networks and multilayer neural networks to identify distant recurrences. Using the same test set and generalizability test set, we obtained F-measure scores of 0.79 ± 0.02 and 0.74 ± 0.004, AUC scores of 0.95 ± 0.002 and 0.95 ± 0.01, respectively. Our model can accurately and efficiently identify distant recurrences in breast cancer by combining features extracted from unstructured clinical narratives and structured clinical data.
Journal of Luminescence, 2017
We have synthesized and characterized three Schiff-base molecules, namely, 1-(((2hydroxybenzylide... more We have synthesized and characterized three Schiff-base molecules, namely, 1-(((2hydroxybenzylidene)hydrazono)methyl)naphthalen-2-ol (H 2 L), (1-(((2-hydroxy-5nitrobenzylidene)hydrazono)methyl)naphthalen-2-ol (H 2 L-NO 2) and 1-(((2-hydroxy-5methylbenzylidene)hydrazono)methyl)naphthalen-2-ol) (H 2 L-Me). Out of these three compounds, H 2 L-NO 2 has been found to be a selective fluorescent chemosensor for Al 3+. Fluorescence intensity of H 2 L-NO 2 at 517 nm (λ ex = 390 nm) is increased significantly in the presence of Al 3+. Other relevant metal ions cannot induce considerable enhancement in its emission intensity. The enhancement has been explained using PET and CHEF mechanism. Quantum yield and lifetime of H 2 L-NO 2 have increased in the presence of one equivalent of Al 3+. H 2 L-NO 2 forms 1:1 complex with the metal ion which is confirmed from Job's plot and ESI mass spectral analysis. Its sensitivity has been determined by 3σ method and found to be moderate. Emission intensity of H 2 L and H 2 L-Me does not increase appreciably in the presence of Al 3+. Presence of electron withdrawing group in H 2 L-NO 2 may be responsible for its aluminum sensing properties.
Sensors and Actuators B: Chemical, 2016
Abstract 1-((quinolin-3-ylimino)methyl)naphthalen-2-ol (HL) has been synthesized by one step Schi... more Abstract 1-((quinolin-3-ylimino)methyl)naphthalen-2-ol (HL) has been synthesized by one step Schiff-base condensation reaction between 2-hydroxy-naphthaldehyde and 3-aminoquinoline in 1:1 ratio in acetonitrile and characterized by elemental analysis and different spectroscopic techniques. Emission spectrum of HL shows peak at 412 nm with high intensity in methanol when it is excited at 350 nm. In the presence of Al3+ ion, emission intensity of the Schiff-base at 412 nm decreases and a new peak at 464 nm emerges indicating HL as a ratiometric chemosensor for the Al3+ ion. Other metal ions are not able to change the fluorescence intensity or peak position significantly. Job’s plot analysis indicates 1:1 binding with the formation of complex (complex 1) which is supported by mass spectral measurement. Emission intensity of complex 1 at 464 nm (excitation at 350 nm) decreases with the gradual addition of F− ion with the concomitant development of a peak at 412 nm with fast increasing intensity. Small LOD value of HL suggests it is sensitive towards Al3+. Based on change in fluorescence intensity of HL in the presence of Al3+ and F− ions at 412 and 464 nm, INHIBIT and IMPLICATION molecular logic gates have been constructed and interpreted.
This research using Hyperspectral imaging involves recognizing targets through spatial and spectr... more This research using Hyperspectral imaging involves recognizing targets through spatial and spectral matching and spectral un-mixing of data ranging from remote sensing to medical imaging kernels for clinical studies based on Hyperspectral data-sets generated using the VFTHSI ...
Journal of the Textile Institute Transactions, 1954
It has been shown that the lignin contents of partially delignified jute, determined with 72 per ... more It has been shown that the lignin contents of partially delignified jute, determined with 72 per cent sulphuric acid either at 2°C or at 22°C, are almost the same as the calculated values obtained by applying the necessary correction factors described in a previous communication.
The FASEB Journal, 2012
ABSTRACT Aldosterone stimulates NaCl reabsorption in the distal nephron in part by increasing thi... more ABSTRACT Aldosterone stimulates NaCl reabsorption in the distal nephron in part by increasing thiazide-sensitive cotransporter (NCC) phosphorylation. Through undefined upstream mechanisms, WNK1 kinase participates in this process by activating SPAK and OSR1, which phosphorylate NCC directly. In the kidney, WNK1 is expressed as kinase active (L-WNK1) and defective (KS-WNK1) isoforms; exons 11 and 12 are differentially spliced into both gene products, but the role of these events in WNK1 function is unclear. Here, we explore how exons 11 and 12 link WNK1 to aldosterone action. Both exons harbor PY motifs ([L/P]PXY); these conserved sequences are absent from the rest of WNK1 and are binding sites for Nedd4-2, an E3 ligase which is inhibited by the aldo-induced kinase SGK1. In mammalian cells, Nedd 4-2 associated with WNK1, accelerating its degradation by the ubiquitin proteasome pathway in a PY motif dependent manner. In mpkCCD cells, 100nM aldosterone increased L-WNK and KS-WNK1 protein abundance within 2h, and both isoforms formed an endogenous complex with Nedd 4-2 and SGK1. Antisera specific to exon 12 confirmed the enrichment of Nedd4-2 sensitive WNK1 isoforms in the distal nephron. These results suggest that exons 11 and 12 function as modular "PY cassettes" that alter WNK1 abundance in response to aldosterone via Nedd4-2, revealing a mechanism that directly connects aldosterone signaling to NCC phosphorylation.
Arthritis Care & Research, 2014
ObjectiveGout flares are not well documented by diagnosis codes, making it difficult to conduct a... more ObjectiveGout flares are not well documented by diagnosis codes, making it difficult to conduct accurate database studies. We implemented a computer‐based method to automatically identify gout flares using natural language processing (NLP) and machine learning (ML) from electronic clinical notes.MethodsOf 16,519 patients, 1,264 and 1,192 clinical notes from 2 separate sets of 100 patients were selected as the training and evaluation data sets, respectively, which were reviewed by rheumatologists. We created separate NLP searches to capture different aspects of gout flares. For each note, the NLP search outputs became the ML system inputs, which provided the final classification decisions. The note‐level classifications were grouped into patient‐level gout flares. Our NLP+ML results were validated using a gold standard data set and compared with the claims‐based method used by prior literatures.ResultsFor 16,519 patients with a diagnosis of gout and a prescription for a urate‐lowerin...
The Pharma Innovation Journal, 2021
Publication View. 29298223. Development of a novel approach and a new expression system for the p... more Publication View. 29298223. Development of a novel approach and a new expression system for the production and crystallization of human G protein-coupled receptors (2007). Roy, Ankita. Publication details. Download, http://edoc.mpg.de/346476. ...
Table S2. Positive CUIS. A dictionary of CUISs and the corresponding CUI preferred name that were... more Table S2. Positive CUIS. A dictionary of CUISs and the corresponding CUI preferred name that were retained after filtering. (XLS 23 kb)
Current Opinion in Plant Biology, 2021
Trichomes show 47 morphological phenotypes, while literature reports only two root hair phenotype... more Trichomes show 47 morphological phenotypes, while literature reports only two root hair phenotypes in all plants. However, could hair-like structures exist below-ground in a similar wide range of morphologies like trichomes? Genetic mutants and root hair stress phenotypes point to the possibility of uncharacterized morphological variation existing belowground. For example, such root hairs in Arabidopsis (Arabidopsis thaliana) can be wavy, curled, or branched. We found hints in the literature about hair-like structures that emerge before root hairs belowground. As such, these early emerging hair structures can be potential exceptions to the contrasting morphological variation between trichomes and root hairs. Here, we show a previously unreported 'hooked' hair structure growing below-ground in common bean. The unique 'hooking' shape distinguishes the 'hooked hair' morphologically from root hairs. Currently, we cannot fully characterize the phenotype of our observation due to the lack of automated methods for phenotyping root hairs. This phenotyping bottleneck also handicaps the discovery of more morphology types that might exist below-ground as manual screening across species is slower than computer-assisted high-throughput screening.
Engineering Failure Analysis, 2020
This is a PDF file of an article that has undergone enhancements after acceptance, such as the ad... more This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. This version will undergo additional copyediting, typesetting and review before it is published in its final form, but we are providing this version to give early visibility of the article. Please note that, during the production process, errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.
Journal of Molecular Structure, 2019
We report here the synthesis, characterization and pH sensing properties of a Schiff-base molecul... more We report here the synthesis, characterization and pH sensing properties of a Schiff-base molecule, 2hydroxy-5-methyl-3-((quinolin-2-ylimino)methyl)benzaldehyde (HL-2-qui) to compare the results observed for its isomers having different position of imino linkage on the quinoline unit. Fluorescence intensity of HL-2-qui at 530 nm enhanced gradually with the increase in pH of the media whereas its isomers showed ratiometric pH sensing behavior under similar conditions. HL-2-qui was colorless in acidic condition and yellow in alkaline medium under visible light while under UV light, the colors of the probe changed to indigo and fluorescent green, respectively. The chemosensor was applied in the detection of different pH regions using lemon juice and river water as the real sample.
Journal of Healthcare Informatics Research, 2019
Accurately identifying distant recurrences in breast cancer from the electronic health records (E... more Accurately identifying distant recurrences in breast cancer from the electronic health records (EHR) is important for both clinical care and secondary analysis. Although multiple applications have been developed for computational phenotyping in breast cancer, distant recurrence identification still relies heavily on manual chart review. In this study, we aim to develop a model that identifies distant recurrences in breast cancer using clinical narratives and structured data from EHR. We applied MetaMap to extract features from clinical narratives and also retrieved structured clinical data from EHR. Using these features, we trained a support vector machine model to identify distant recurrences in breast cancer patients. We trained the model using 1396 doubleannotated subjects and validated the model using 599 double-annotated subjects. In addition, we validated the model on a set of 4904 single-annotated subjects as a generalization test. In the held-out test and generalization test, we obtained F-measure scores of 0.78 and 0.74, area under curve (AUC) scores of 0.95 and 0.93, respectively. To explore the representation learning utility of deep neural networks, we designed multiple convolutional neural networks and multilayer neural networks to identify distant recurrences. Using the same test set and generalizability test set, we obtained F-measure scores of 0.79 ± 0.02 and 0.74 ± 0.004, AUC scores of 0.95 ± 0.002 and 0.95 ± 0.01, respectively. Our model can accurately and efficiently identify distant recurrences in breast cancer by combining features extracted from unstructured clinical narratives and structured clinical data.
Journal of Luminescence, 2017
We have synthesized and characterized three Schiff-base molecules, namely, 1-(((2hydroxybenzylide... more We have synthesized and characterized three Schiff-base molecules, namely, 1-(((2hydroxybenzylidene)hydrazono)methyl)naphthalen-2-ol (H 2 L), (1-(((2-hydroxy-5nitrobenzylidene)hydrazono)methyl)naphthalen-2-ol (H 2 L-NO 2) and 1-(((2-hydroxy-5methylbenzylidene)hydrazono)methyl)naphthalen-2-ol) (H 2 L-Me). Out of these three compounds, H 2 L-NO 2 has been found to be a selective fluorescent chemosensor for Al 3+. Fluorescence intensity of H 2 L-NO 2 at 517 nm (λ ex = 390 nm) is increased significantly in the presence of Al 3+. Other relevant metal ions cannot induce considerable enhancement in its emission intensity. The enhancement has been explained using PET and CHEF mechanism. Quantum yield and lifetime of H 2 L-NO 2 have increased in the presence of one equivalent of Al 3+. H 2 L-NO 2 forms 1:1 complex with the metal ion which is confirmed from Job's plot and ESI mass spectral analysis. Its sensitivity has been determined by 3σ method and found to be moderate. Emission intensity of H 2 L and H 2 L-Me does not increase appreciably in the presence of Al 3+. Presence of electron withdrawing group in H 2 L-NO 2 may be responsible for its aluminum sensing properties.
Sensors and Actuators B: Chemical, 2016
Abstract 1-((quinolin-3-ylimino)methyl)naphthalen-2-ol (HL) has been synthesized by one step Schi... more Abstract 1-((quinolin-3-ylimino)methyl)naphthalen-2-ol (HL) has been synthesized by one step Schiff-base condensation reaction between 2-hydroxy-naphthaldehyde and 3-aminoquinoline in 1:1 ratio in acetonitrile and characterized by elemental analysis and different spectroscopic techniques. Emission spectrum of HL shows peak at 412 nm with high intensity in methanol when it is excited at 350 nm. In the presence of Al3+ ion, emission intensity of the Schiff-base at 412 nm decreases and a new peak at 464 nm emerges indicating HL as a ratiometric chemosensor for the Al3+ ion. Other metal ions are not able to change the fluorescence intensity or peak position significantly. Job’s plot analysis indicates 1:1 binding with the formation of complex (complex 1) which is supported by mass spectral measurement. Emission intensity of complex 1 at 464 nm (excitation at 350 nm) decreases with the gradual addition of F− ion with the concomitant development of a peak at 412 nm with fast increasing intensity. Small LOD value of HL suggests it is sensitive towards Al3+. Based on change in fluorescence intensity of HL in the presence of Al3+ and F− ions at 412 and 464 nm, INHIBIT and IMPLICATION molecular logic gates have been constructed and interpreted.
This research using Hyperspectral imaging involves recognizing targets through spatial and spectr... more This research using Hyperspectral imaging involves recognizing targets through spatial and spectral matching and spectral un-mixing of data ranging from remote sensing to medical imaging kernels for clinical studies based on Hyperspectral data-sets generated using the VFTHSI ...
Journal of the Textile Institute Transactions, 1954
It has been shown that the lignin contents of partially delignified jute, determined with 72 per ... more It has been shown that the lignin contents of partially delignified jute, determined with 72 per cent sulphuric acid either at 2°C or at 22°C, are almost the same as the calculated values obtained by applying the necessary correction factors described in a previous communication.
The FASEB Journal, 2012
ABSTRACT Aldosterone stimulates NaCl reabsorption in the distal nephron in part by increasing thi... more ABSTRACT Aldosterone stimulates NaCl reabsorption in the distal nephron in part by increasing thiazide-sensitive cotransporter (NCC) phosphorylation. Through undefined upstream mechanisms, WNK1 kinase participates in this process by activating SPAK and OSR1, which phosphorylate NCC directly. In the kidney, WNK1 is expressed as kinase active (L-WNK1) and defective (KS-WNK1) isoforms; exons 11 and 12 are differentially spliced into both gene products, but the role of these events in WNK1 function is unclear. Here, we explore how exons 11 and 12 link WNK1 to aldosterone action. Both exons harbor PY motifs ([L/P]PXY); these conserved sequences are absent from the rest of WNK1 and are binding sites for Nedd4-2, an E3 ligase which is inhibited by the aldo-induced kinase SGK1. In mammalian cells, Nedd 4-2 associated with WNK1, accelerating its degradation by the ubiquitin proteasome pathway in a PY motif dependent manner. In mpkCCD cells, 100nM aldosterone increased L-WNK and KS-WNK1 protein abundance within 2h, and both isoforms formed an endogenous complex with Nedd 4-2 and SGK1. Antisera specific to exon 12 confirmed the enrichment of Nedd4-2 sensitive WNK1 isoforms in the distal nephron. These results suggest that exons 11 and 12 function as modular "PY cassettes" that alter WNK1 abundance in response to aldosterone via Nedd4-2, revealing a mechanism that directly connects aldosterone signaling to NCC phosphorylation.