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Article ; Online: Chiral Induction in 2D Borophene Nanoplatelets through Stereoselective Boron-Sulfur Conjugation.

Aditya, Teresa / Moitra, Parikshit / Alafeef, Maha / Skrodzki, David / Pan, Dipanjan

ACS nano

2024

Abstract: Chirality is a structural metric that connects biological and abiological forms of matter. Although much progress has been made in understanding the chemistry and physics of chiral inorganic nanoparticles over the past decade, almost nothing is known ... ...

Abstract	Chirality is a structural metric that connects biological and abiological forms of matter. Although much progress has been made in understanding the chemistry and physics of chiral inorganic nanoparticles over the past decade, almost nothing is known about chiral two-dimensional (2D) borophene nanoplatelets and their influence on complex biological networks. Borophene's polymorphic nature, derived from the bonding configurations among boron atoms, distinguishes it from other 2D materials and allows for further customization of its material properties. In this study, we describe a synthetic methodology for producing chiral 2D borophene nanoplatelets applicable to a variety of structural polymorphs. Using this methodology, we demonstrate feasibility of top-down synthesis of chiral χ3 and β
Language	English
Publishing date	2024-04-23
Publishing country	United States
Document type	Journal Article
ISSN	1936-086X
ISSN (online)	1936-086X
DOI	10.1021/acsnano.4c01792
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Article ; Online: Diagnostic Approaches For COVID-19: Lessons Learned and the Path Forward.

Alafeef, Maha / Pan, Dipanjan

ACS nano

2022 Volume 16, Issue 8, Page(s) 11545–11576

Abstract: Coronavirus disease 2019 (COVID-19) is a transmitted respiratory disease caused by the infection of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Although humankind has experienced several outbreaks of infectious diseases, the COVID- ... ...

Abstract	Coronavirus disease 2019 (COVID-19) is a transmitted respiratory disease caused by the infection of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Although humankind has experienced several outbreaks of infectious diseases, the COVID-19 pandemic has the highest rate of infection and has had high levels of social and economic repercussions. The current COVID-19 pandemic has highlighted the limitations of existing virological tests, which have failed to be adopted at a rate to properly slow the rapid spread of SARS-CoV-2. Pandemic preparedness has developed as a focus of many governments around the world in the event of a future outbreak. Despite the largely widespread availability of vaccines, the importance of testing has not diminished to monitor the evolution of the virus and the resulting stages of the pandemic. Therefore, developing diagnostic technology that serves as a line of defense has become imperative. In particular, that test should satisfy three criteria to be widely adopted: simplicity, economic feasibility, and accessibility. At the heart of it all, it must enable early diagnosis in the course of infection to reduce spread. However, diagnostic manufacturers need guidance on the optimal characteristics of a virological test to ensure pandemic preparedness and to aid in the effective treatment of viral infections. Nanomaterials are a decisive element in developing COVID-19 diagnostic kits as well as a key contributor to enhance the performance of existing tests. Our objective is to develop a profile of the criteria that should be available in a platform as the target product. In this work, virus detection tests were evaluated from the perspective of the COVID-19 pandemic, and then we generalized the requirements to develop a target product profile for a platform for virus detection.
MeSH term(s)	Humans ; COVID-19/diagnosis ; Pandemics/prevention & control ; SARS-CoV-2 ; COVID-19 Testing
Language	English
Publishing date	2022-08-03
Publishing country	United States
Document type	Journal Article ; Review ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ISSN	1936-086X
ISSN (online)	1936-086X
DOI	10.1021/acsnano.2c01697
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Article ; Online: Carbon Dots: From Synthesis to Unraveling the Fluorescence Mechanism.

Alafeef, Maha / Srivastava, Indrajit / Aditya, Teresa / Pan, Dipanjan

Small (Weinheim an der Bergstrasse, Germany)

2023 Volume 20, Issue 4, Page(s) e2303937

Abstract: Carbon dots (CDs) being a new type of carbon-based nanomaterial have attracted intensive interest from researchers owing to their excellent biophysical properties. CDs are a class of fluorescent carbon nanomaterials that have emerged as a promising ... ...

Abstract	Carbon dots (CDs) being a new type of carbon-based nanomaterial have attracted intensive interest from researchers owing to their excellent biophysical properties. CDs are a class of fluorescent carbon nanomaterials that have emerged as a promising alternative to traditional quantum dots and organic dyes in applications including bioimaging, sensing, and optoelectronics. CDs possess unique optical properties, such as tunable emission, facile synthesis, and low toxicity, making them attractive for many applications in biology, medicine, and environmental areas. The synthesis of CDs is achievable by a variety of methods, including bottom-up and top-down approaches, involving the use of different carbon sources and surface functionalization strategies. However, understanding the fluorescence mechanism of CDs remains a challenge. Various mechanistic models have been proposed to explain their origin of luminescence. This review summarizes the recent developments in the synthesis and functionalization of CDs and provides an overview of the current understanding of the fluorescence mechanism.
Language	English
Publishing date	2023-09-15
Publishing country	Germany
Document type	Journal Article ; Review
ZDB-ID	2168935-0
ISSN	1613-6829 ; 1613-6810
ISSN (online)	1613-6829
ISSN	1613-6810
DOI	10.1002/smll.202303937
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Article ; Online: Smartphone-based photoplethysmographic imaging for heart rate monitoring.

Alafeef, Maha

Journal of medical engineering & technology

2017 Volume 41, Issue 5, Page(s) 387–395

Abstract: The purpose of this study is to make use of visible light reflected mode photoplethysmographic (PPG) imaging for heart rate (HR) monitoring via smartphones. The system uses the built-in camera feature in mobile phones to capture video from the subject's ... ...

Abstract	The purpose of this study is to make use of visible light reflected mode photoplethysmographic (PPG) imaging for heart rate (HR) monitoring via smartphones. The system uses the built-in camera feature in mobile phones to capture video from the subject's index fingertip. The video is processed, and then the PPG signal resulting from the video stream processing is used to calculate the subject's heart rate. Records from 19 subjects were used to evaluate the system's performance. The HR values obtained by the proposed method were compared with the actual HR. The obtained results show an accuracy of 99.7% and a maximum absolute error of 0.4 beats/min where most of the absolute errors lay in the range of 0.04-0.3 beats/min. Given the encouraging results, this type of HR measurement can be adopted with great benefit, especially in the conditions of personal use or home-based care. The proposed method represents an efficient portable solution for HR accurate detection and recording.
Language	English
Publishing date	2017-07
Publishing country	England
Document type	Journal Article
ZDB-ID	243092-7
ISSN	1464-522X ; 0309-1902
ISSN (online)	1464-522X
ISSN	0309-1902
DOI	10.1080/03091902.2017.1299233
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Article ; Online: Binding-Induced Folding of DNA Oligonucleotides Targeted to the Nucleocapsid Gene Enables Electrochemical Sensing of SARS-CoV-2.

Alafeef, Maha / Skrodzki, David / Moitra, Parikshit / Gunaseelan, Nivetha / Pan, Dipanjan

ACS applied bio materials

2023 Volume 6, Issue 3, Page(s) 1133–1145

Abstract: In the wake of the COVID-19 pandemic, millions of confirmed cases and deaths have been reported around the world. COVID-19 spread can be slowed and eventually stopped by a rapid test to diagnose positive cases of the disease on the spot. It is still ... ...

Abstract	In the wake of the COVID-19 pandemic, millions of confirmed cases and deaths have been reported around the world. COVID-19 spread can be slowed and eventually stopped by a rapid test to diagnose positive cases of the disease on the spot. It is still important to test for COVID-19 quickly regardless of the availability of the vaccine. Using the binding-induced folding principle, we developed an electrochemical test for detecting SARS-CoV-2 with no RNA extraction or nucleic acid amplification. The test showed high sensitivity with a limit of detection of 2.5 copies/μL. An electrode mounted with a capture probe and a portable potentiostat are used to conduct the test. To target the N-gene of SARS-CoV-2, a highly specific oligo-capturing probe was used. Based on the binding-induced "folding" principle, the sensor detects binding between the oligo and RNA. When the target is absent, the capture probe tends to form a hairpin as a secondary structure, retaining the redox reporter close to the surface. This can be seen as a large anodic and cathodic peak current. When the target RNA is present, the hairpin structure will open to hybridize with its complementary sequence, causing the redox reporter to pull away from the electrode. Consequently, the anodic/cathodic peak currents are reduced, indicating the presence of the SARS-CoV-2 genetic material. Validation of the test performance was performed using 122 COVID-19 clinical samples (55 positives and 67 negatives) and benchmarked to the gold standard reverse transcription-polymerase chain reaction (RT-PCR) test. As a result of our test, the accuracy, sensitivity, and specificity have been measured at 98.4%, 98.2%, and 98.5%, respectively.
MeSH term(s)	Humans ; SARS-CoV-2/genetics ; COVID-19/diagnosis ; Pandemics ; Sensitivity and Specificity ; Nucleocapsid ; DNA ; RNA ; Oligonucleotides
Chemical Substances	DNA (9007-49-2) ; RNA (63231-63-0) ; Oligonucleotides
Language	English
Publishing date	2023-03-06
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ISSN	2576-6422
ISSN (online)	2576-6422
DOI	10.1021/acsabm.2c00984
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Article ; Online: Single-gene diagnostic assay for rapid subclassification of basal like breast cancer with mRNA targeted antisense oligonucleotide capped molecular probe.

Moitra, Parikshit / Alafeef, Maha / Dighe, Ketan / Pan, Dipanjan

Biosensors & bioelectronics

2022 Volume 207, Page(s) 114178

Abstract: Basal-like breast cancers (BLBCs) represent a subset of ∼70% of triple negative breast cancers (TNBCs) and is significantly more aggressive than tumors of other molecular subtypes. The primary hurdle to develop an effective therapeutic possibility for ... ...

Abstract	Basal-like breast cancers (BLBCs) represent a subset of ∼70% of triple negative breast cancers (TNBCs) and is significantly more aggressive than tumors of other molecular subtypes. The primary hurdle to develop an effective therapeutic possibility for BLBC lies in the failure to accurately classify this molecular subtype using typical histopathological practices. A clear clinical unmet need is therefore to develop a simple robust diagnostic assay for BLBC that can be made widely available to every pathology laboratory. Elevated expression of transcription factor Forkhead box C1 (FOXC1) has recently been reported as an important prognostic biomarker and functional regulator of BLBC. We herein developed a new nanotechnology-enabled molecular diagnostic assay that will target FOXC1 to directly classify BLBC types from tissue extracts. The molecular assay is comprised of unique antisense oligonucleotide (ASO) guided nanoprobe designed for specific targeting of FOXC1 mRNA. The developed assay has been optimized and validated analytically and demonstrated for its clinical applicability in a small cohort of breast cancer tissues. The significance of the results was further established and corroborated using FOXC1 protein-based ELISA, RT-PCR and fluorescence in-situ hybridization (FISH) assay by detecting the endogenous mRNAs at the ultrastructural level. The results reported herein could greatly improve accessibility of single gene based oncologic assay and help accelerate the accurate identification of this aggressive disease.
MeSH term(s)	Biomarkers, Tumor/analysis ; Biosensing Techniques ; Breast Neoplasms/diagnosis ; Breast Neoplasms/genetics ; Breast Neoplasms/metabolism ; Female ; Humans ; Molecular Probes ; Oligonucleotides, Antisense/genetics ; RNA, Messenger/genetics ; Triple Negative Breast Neoplasms
Chemical Substances	Biomarkers, Tumor ; Molecular Probes ; Oligonucleotides, Antisense ; RNA, Messenger
Language	English
Publishing date	2022-03-16
Publishing country	England
Document type	Journal Article
ZDB-ID	1011023-9
ISSN	1873-4235 ; 0956-5663
ISSN (online)	1873-4235
ISSN	0956-5663
DOI	10.1016/j.bios.2022.114178
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Jg. 1995 - 2021: Lesesall (2.OG)
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Article ; Online: Diagnosis of COVID-19 with simultaneous accurate prediction of cardiac abnormalities from chest computed tomographic images.

Moitra, Moumita / Alafeef, Maha / Narasimhan, Arjun / Kakaria, Vikram / Moitra, Parikshit / Pan, Dipanjan

PloS one

2023 Volume 18, Issue 12, Page(s) e0290494

Abstract: COVID-19 has potential consequences on the pulmonary and cardiovascular health of millions of infected people worldwide. Chest computed tomographic (CT) imaging has remained the first line of diagnosis for individuals infected with SARS-CoV-2. However, ... ...

Abstract	COVID-19 has potential consequences on the pulmonary and cardiovascular health of millions of infected people worldwide. Chest computed tomographic (CT) imaging has remained the first line of diagnosis for individuals infected with SARS-CoV-2. However, differentiating COVID-19 from other types of pneumonia and predicting associated cardiovascular complications from the same chest-CT images have remained challenging. In this study, we have first used transfer learning method to distinguish COVID-19 from other pneumonia and healthy cases with 99.2% accuracy. Next, we have developed another CNN-based deep learning approach to automatically predict the risk of cardiovascular disease (CVD) in COVID-19 patients compared to the normal subjects with 97.97% accuracy. Our model was further validated against cardiac CT-based markers including cardiac thoracic ratio (CTR), pulmonary artery to aorta ratio (PA/A), and presence of calcified plaque. Thus, we successfully demonstrate that CT-based deep learning algorithms can be employed as a dual screening diagnostic tool to diagnose COVID-19 and differentiate it from other pneumonia, and also predicts CVD risk associated with COVID-19 infection.
MeSH term(s)	Humans ; COVID-19/diagnostic imaging ; SARS-CoV-2 ; Deep Learning ; Pneumonia ; Tomography, X-Ray Computed/methods ; Heart Defects, Congenital ; COVID-19 Testing
Language	English
Publishing date	2023-12-14
Publishing country	United States
Document type	Journal Article
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0290494
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Article ; Online: Highly-Specific Single-Stranded Oligonucleotides and Functional Nanoprobes for Clinical Determination of Chlamydia Trachomatis and Neisseria Gonorrhoeae Infections.

Dighe, Ketan / Moitra, Parikshit / Gunaseelan, Nivetha / Alafeef, Maha / Jensen, Tor / Rafferty, Carla / Pan, Dipanjan

Advanced science (Weinheim, Baden-Wurttemberg, Germany)

2023 Volume 10, Issue 36, Page(s) e2304009

Abstract: Early detection of Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) is the key to controlling the spread of these bacterial infections. An important step in developing biosensors involves identifying reliable sensing probes against specific ... ...

Abstract	Early detection of Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) is the key to controlling the spread of these bacterial infections. An important step in developing biosensors involves identifying reliable sensing probes against specific genetic targets for CT and NG. Here, the authors have designed single-stranded oligonucleotides (ssDNAs) targeting mutually conserved genetic regions of cryptic plasmid and chromosomal DNA of both CT and NG. The 5'- and 3'- ends of these ssDNAs are differentially functionalized with thiol groups and coupled with gold nanoparticles (AuNP) to develop absorbance-based assay. The AuNPs agglomerate selectively in the presence of its target DNA sequence and demonstrate a change in their surface plasmon resonance. The optimized assay is then used to detect both CT and NG DNA extracted from 60 anonymized clinical samples with a clinical sensitivity of ∼100%. The limit of detection of the assays are found to be 7 and 5 copies/µL for CT and NG respectively. Furthermore, it can successfully detect the DNA levels of these two bacteria without the need for DNA extraction and via a lateral flow-based platform. These assays thus hold the potential to be employed in clinics for rapid and efficient monitoring of sexually transmitted infections.
MeSH term(s)	Humans ; Neisseria gonorrhoeae/genetics ; Chlamydia trachomatis/genetics ; Gold ; Oligonucleotides ; Chlamydia Infections/diagnosis ; Chlamydia Infections/microbiology ; Sensitivity and Specificity ; Metal Nanoparticles ; Gonorrhea/diagnosis ; Gonorrhea/microbiology ; DNA
Chemical Substances	Gold (7440-57-5) ; Oligonucleotides ; DNA (9007-49-2)
Language	English
Publishing date	2023-10-23
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2808093-2
ISSN	2198-3844 ; 2198-3844
ISSN (online)	2198-3844
ISSN	2198-3844
DOI	10.1002/advs.202304009
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Article ; Online: Diagnosis of COVID-19 with simultaneous accurate prediction of cardiac abnormalities from chest computed tomographic images

Moumita Moitra / Maha Alafeef / Arjun Narasimhan / Vikram Kakaria / Parikshit Moitra / Dipanjan Pan

PLoS ONE, Vol 18, Iss

2023 Volume 12

Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2023-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: N-gene-complementary antisense-oligonucleotide directed molecular aggregation of dual-colour carbon dots, leading to efficient fluorometric sensing of SARS-COV-2 RNA.

Sheffield, Zach / Alafeef, Maha / Moitra, Parikshit / Ray, Priyanka / Pan, Dipanjan

Nanoscale

2022 Volume 14, Issue 13, Page(s) 5112–5120

Abstract: The early stages of the COVID-19 pandemic punctuated the need for rapid, mass testing for early detection of viral infection. Carbon dots are easily synthesized, cost-effective fluorescent nanoparticles whose surface functionalities enable facile ... ...

Abstract	The early stages of the COVID-19 pandemic punctuated the need for rapid, mass testing for early detection of viral infection. Carbon dots are easily synthesized, cost-effective fluorescent nanoparticles whose surface functionalities enable facile conjugation with biorecognition elements suitable for molecular detection of viral RNA. Herein, we report that a pair of complementary antisense oligonucleotide (ASO) sequences can lead to a highly specific molecular aggregation of dual colour carbon dots (CDs) in the presence of SARS-CoV-2 RNA. The nanoprobes used ASOs highly specific to the N-gene of SARS-COV-2. When the ASOs are conjugated to blue and yellow citric acid-derived CDs, the combination of the ASO-CD pairs facilitates aggregation-induced emission enhancement (AIEE) of the measured fluorescence after hybridization with SARS-CoV-2 RNA. We found the sensor capable of differentiating between MERS-CoV and SARS-CoV-2 samples and was found to have a limit of detection of 81 copies per μL. Additionally, we used dialysis to demonstrate that the change in emission upon aggregation is dependent on the compositional heterogeneity of the conjugated-carbon dot mixture.
MeSH term(s)	COVID-19/diagnosis ; Carbon ; Color ; Humans ; Oligonucleotides ; Oligonucleotides, Antisense ; Pandemics ; RNA, Viral/genetics ; SARS-CoV-2/genetics
Chemical Substances	Oligonucleotides ; Oligonucleotides, Antisense ; RNA, Viral ; Carbon (7440-44-0)
Language	English
Publishing date	2022-03-31
Publishing country	England
Document type	Journal Article
ZDB-ID	2515664-0
ISSN	2040-3372 ; 2040-3364
ISSN (online)	2040-3372
ISSN	2040-3364
DOI	10.1039/d1nr07169f
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