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Article: Efficient imputation methods in case of measurement errors.

Kumar, Anoop / Bhushan, Shashi / Shukla, Shivam / Bakr, M E / Alshangiti, Arwa M / Balogun, Oluwafemi Samson

2024 Volume 10, Issue 6, Page(s) e26864

Abstract: This manuscript develops few efficient difference and ratio kinds of imputations to handle the situation of missing observations given that these observations are polluted by the measurement errors (ME). The mean square errors of the developed ... ...

Abstract	This manuscript develops few efficient difference and ratio kinds of imputations to handle the situation of missing observations given that these observations are polluted by the measurement errors (ME). The mean square errors of the developed imputations are studied to the primary degree approximation by adopting Taylor series expansion. The proposed imputations are equated with the latest existing imputations presented in the literature. The execution of the proposed imputations is assessed by utilizing a broad empirical study utilizing some real and hypothetically created populations. Appropriate remarks are made for sampling respondents regarding practical applications.
Language	English
Publishing date	2024-02-28
Publishing country	England
Document type	Journal Article
ZDB-ID	2835763-2
ISSN	2405-8440
ISSN	2405-8440
DOI	10.1016/j.heliyon.2024.e26864
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Article ; Online: Study on damage of Gd

Haq, Waseem Ul / Grover, V / Kalita, Parswajit / Shukla, Rakesh / Singh, Fouran / Srivastava, Sanjeev Kumar / Shukla, Shivam / Ghosh, Santanu

Physical chemistry chemical physics : PCCP

2024 Volume 26, Issue 6, Page(s) 5311–5322

Abstract: To understand the physical phenomena responsible for radiation damage of the materials used in nuclear reactors, and thus study their operation life and/or efficiency, it is required to simulate the conditions by exposing the materials to energetic ions. ...

Abstract	To understand the physical phenomena responsible for radiation damage of the materials used in nuclear reactors, and thus study their operation life and/or efficiency, it is required to simulate the conditions by exposing the materials to energetic ions. Ceria (CeO
Language	English
Publishing date	2024-02-07
Publishing country	England
Document type	Journal Article
ZDB-ID	1476244-4
ISSN	1463-9084 ; 1463-9076
ISSN (online)	1463-9084
ISSN	1463-9076
DOI	10.1039/d3cp05252d
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Article ; Online: Smartphone-based fluorescence spectroscopic device for cervical precancer diagnosis: a random forest classification of in vitro data.

Shukla, Shivam / Vishwakarma, Chaitanya / Sah, Amar Nath / Ahirwar, Shikha / Pandey, Kiran / Pradhan, Asima

Applied optics

2023 Volume 62, Issue 25, Page(s) 6826–6834

Abstract: Cervical cancer can be treated and cured if diagnosed at an early stage. Optical devices, developed on smartphone-based platforms, are being tested for this purpose as they are cost-effective, robust, and field portable, showing good efficiency compared ... ...

Abstract	Cervical cancer can be treated and cured if diagnosed at an early stage. Optical devices, developed on smartphone-based platforms, are being tested for this purpose as they are cost-effective, robust, and field portable, showing good efficiency compared to the existing commercial devices. This study reports on the applicability of a 3D printed smartphone-based spectroscopic device (3D-SSD) for the early diagnosis of cervical cancer. The proposed device has the ability to evaluate intrinsic fluorescence (IF) from the collected polarized fluorescence (PF) and elastic-scattering (ES) spectra from cervical tissue samples of different grades. IF spectra of 30 cervical tissue samples have been analyzed and classified using a combination of principal component analysis (PCA) and random forest (RF)-based multi-class classification algorithm with an overall accuracy above 90%. The usage of smartphone for image collection, spectral data analysis, and display makes this device a potential contender for use in clinics as a regular screening tool.
MeSH term(s)	Female ; Humans ; Uterine Cervical Neoplasms/diagnosis ; Random Forest ; Smartphone ; Spectrometry, Fluorescence ; Algorithms
Language	English
Publishing date	2023-09-14
Publishing country	United States
Document type	Journal Article
ISSN	1539-4522
ISSN (online)	1539-4522
DOI	10.1364/AO.496543
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Article ; Online: Design, fabrication and testing of 3D printed smartphone-based device for collection of intrinsic fluorescence from human cervix.

Shukla, Shivam / Sah, Amar Nath / Hatiboruah, Diganta / Ahirwar, Shikha / Nath, Pabitra / Pradhan, Asima

Scientific reports

2022 Volume 12, Issue 1, Page(s) 11192

Abstract: Fluorescence spectroscopy has the potential to identify discriminatory signatures, crucial for early diagnosis of cervical cancer. We demonstrate here the design, fabrication and testing of a 3D printed smartphone based spectroscopic device. Polarized ... ...

Abstract	Fluorescence spectroscopy has the potential to identify discriminatory signatures, crucial for early diagnosis of cervical cancer. We demonstrate here the design, fabrication and testing of a 3D printed smartphone based spectroscopic device. Polarized fluorescence and elastic scattering spectra are captured through the device using a 405 nm laser and a white LED source respectively. The device has been calibrated by comparison of spectra of standard fluorophores (Flavin adenine dinucleotide, fluorescein, rhodamine, and porphyrin) with the corresponding spectra collected from a commercial spectrometer. A few cervical tissue spectra have also been captured for proof of its applicability as a portable, standalone device for the collection of intrinsic fluorescence spectra from human cervix.
MeSH term(s)	Cervix Uteri/chemistry ; Female ; Humans ; Printing, Three-Dimensional ; Smartphone ; Spectrometry, Fluorescence/methods ; Uterine Cervical Neoplasms/diagnosis
Language	English
Publishing date	2022-07-01
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-022-15007-x
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Article ; Online: Cervical pre-cancer classification using entropic features and CNN: In vivo validation with a handheld fluorescence probe.

Deo, Bhaswati Singha / Sah, Amar Nath / Shukla, Shivam / Pandey, Kiran / Singh, Sweta / Pal, Mayukha / Panigrahi, Prasanta K / Pradhan, Asima

Journal of biophotonics

2023 Volume 17, Issue 3, Page(s) e202300363

Abstract: Cervical cancer is one of the most prevalent forms of cancer, with a lengthy latent period and a gradual onset phase. Conventional techniques are found to be severely lacking in real time detection of disease progression which can greatly enhance the ... ...

Abstract	Cervical cancer is one of the most prevalent forms of cancer, with a lengthy latent period and a gradual onset phase. Conventional techniques are found to be severely lacking in real time detection of disease progression which can greatly enhance the cure rate. Due to their high sensitivity and specificity, optical techniques are emerging as reliable tools, particularly in case of cancer. It has been seen that biochemical changes are better highlighted through intrinsic fluorescence devoid of interference from absorption and scattering. Its effectiveness in in-vivo conditions is affected by the fact that the intrinsic spectral signatures vary from patient to patient, as well as in different population groups. Here, we overcome this limitation by collectively enumerating the subtle changes in the spectral profiles and correlations through an information theory based entropic approach, which significantly amplifies the minute spectral variations. In conjunction with artificial intelligence (AI)/machine learning (ML) tools, it yields high specificity and sensitivity with a small dataset from patients in clinical conditions, without artificial augmentation. We have used an in-house developed handheld probe (i-HHP) for extracting intrinsic fluorescence spectra of human cervix from 110 different subjects drawn from diverse population groups. The average classification accuracy of the proposed methodology using 10-fold cross validation is 93.17%. A combination of polarised fluorescence spectra from i-HHP and the proposed classifier is proven to be minimally invasive with the ability to diagnose patients in real time. This paves the way for effective use of relatively smaller sized sensitive fluorescence data with advanced AI/ML tools for early cervical cancer detection in clinics.
MeSH term(s)	Female ; Humans ; Uterine Cervical Neoplasms/diagnostic imaging ; Cervix Uteri ; Artificial Intelligence ; Neural Networks, Computer ; Machine Learning
Language	English
Publishing date	2023-12-20
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2390063-5
ISSN	1864-0648 ; 1864-063X
ISSN (online)	1864-0648
ISSN	1864-063X
DOI	10.1002/jbio.202300363
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Article ; Online: In‐solution structure and oligomerization of human histone deacetylase 6 – an integrative approach

Shukla, Shivam / Komárek, Jan / Novakova, Zora / Nedvedova, Jana / Ustinova, Kseniya / Vankova, Pavla / Kadek, Alan / Uetrecht, Charlotte / Mertens, Haydyn / Barinka, Cyril

The FEBS Journal. 2023 Feb., v. 290, no. 3 p.821-836

2023

Abstract: Human histone deacetylase 6 (HDAC6) is a structurally unique, multidomain protein implicated in a variety of physiological processes including cytoskeletal remodelling and the maintenance of cellular homeostasis. Our current understanding of the HDAC6 ... ...

Abstract	Human histone deacetylase 6 (HDAC6) is a structurally unique, multidomain protein implicated in a variety of physiological processes including cytoskeletal remodelling and the maintenance of cellular homeostasis. Our current understanding of the HDAC6 structure is limited to isolated domains, and a holistic picture of the full‐length protein structure, including possible domain interactions, is missing. Here, we used an integrative structural biology approach to build a solution model of HDAC6 by combining experimental data from several orthogonal biophysical techniques complemented by molecular modelling. We show that HDAC6 is best described as a mosaic of folded and intrinsically disordered domains that in‐solution adopts an ensemble of conformations without any stable interactions between structured domains. Furthermore, HDAC6 forms dimers/higher oligomers in a concentration‐dependent manner, and its oligomerization is mediated via the positively charged N‐terminal microtubule‐binding domain. Our findings provide the first insights into the structure of full‐length human HDAC6 and can be used as a basis for further research into structure function and physiological studies of this unique deacetylase.
Keywords	cytoskeleton ; histone deacetylase ; homeostasis ; humans ; models ; oligomerization ; protein structure ; structural biology
Language	English
Dates of publication	2023-02
Size	p. 821-836.
Publishing place	John Wiley & Sons, Ltd
Document type	Article ; Online
Note	JOURNAL ARTICLE
ZDB-ID	2173655-8
ISSN	1742-4658 ; 1742-464X
ISSN (online)	1742-4658
ISSN	1742-464X
DOI	10.1111/febs.16616
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Article ; Online: Structural, Biochemical, and Computational Characterization of Sulfamides as Bimetallic Peptidase Inhibitors.

Novakova, Zora / Tehrani, Zahra Aliakbar / Jurok, Radek / Motlova, Lucia / Kutil, Zsofia / Pavlicek, Jiri / Shukla, Shivam / Choy, Cindy J / Havlinova, Barbora / Baranova, Petra / Berkman, Clifford E / Kuchar, Martin / Cerny, Jiri / Barinka, Cyril

Journal of chemical information and modeling

2024 Volume 64, Issue 3, Page(s) 1030–1042

Abstract: The sulfonamide function is used extensively as a general building block in various inhibitory scaffolds and, more specifically, as a zinc-binding group (ZBG) of metalloenzyme inhibitors. Here, we provide biochemical, structural, and computational ... ...

Abstract	The sulfonamide function is used extensively as a general building block in various inhibitory scaffolds and, more specifically, as a zinc-binding group (ZBG) of metalloenzyme inhibitors. Here, we provide biochemical, structural, and computational characterization of a metallopeptidase in complex with inhibitors, where the mono- and bisubstituted sulfamide functions are designed to directly engage zinc ions of a bimetallic enzyme site. Structural data showed that while monosubstituted sulfamides coordinate active-site zinc ions via the free negatively charged amino group in a canonical manner, their bisubstituted counterparts adopt an atypical binding pattern divergent from expected positioning of corresponding tetrahedral reaction intermediates. Accompanying quantum mechanics calculations revealed that electroneutrality of the sulfamide function is a major factor contributing to the markedly lower potency of bisubstituted compounds by considerably lowering their interaction energy with the enzyme. Overall, while bisubstituted uncharged sulfamide functions can bolster favorable pharmacological properties of a given inhibitor, their use as ZBGs in metalloenzyme inhibitors might be less advantageous due to their suboptimal metal-ligand properties.
MeSH term(s)	Protease Inhibitors/pharmacology ; Metalloproteins/chemistry ; Zinc/metabolism ; Ions
Chemical Substances	Protease Inhibitors ; Metalloproteins ; Zinc (J41CSQ7QDS) ; Ions
Language	English
Publishing date	2024-01-15
Publishing country	United States
Document type	Journal Article
ZDB-ID	190019-5
ISSN	1549-960X ; 0095-2338
ISSN (online)	1549-960X
ISSN	0095-2338
DOI	10.1021/acs.jcim.3c01542
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Article ; Online: A smartphone-based standalone fluorescence spectroscopy tool for cervical precancer diagnosis in clinical conditions.

Shukla, Shivam / Deo, Bhaswati Singha / Vishwakarma, Chaitanya / Mishra, Subrata / Ahirwar, Shikha / Sah, Amar Nath / Pandey, Kiran / Singh, Sweta / Prasad, S N / Padhi, Ashok Kumar / Pal, Mayukha / Panigrahi, Prasanta K / Pradhan, Asima

Journal of biophotonics

2024 , Page(s) e202300468

Abstract: Real-time prediction about the severity of noncommunicable diseases like cancers is a boon for early diagnosis and timely cure. Optical techniques due to their minimally invasive nature provide better alternatives in this context than the conventional ... ...

Abstract	Real-time prediction about the severity of noncommunicable diseases like cancers is a boon for early diagnosis and timely cure. Optical techniques due to their minimally invasive nature provide better alternatives in this context than the conventional techniques. The present study talks about a standalone, field portable smartphone-based device which can classify different grades of cervical cancer on the basis of the spectral differences captured in their intrinsic fluorescence spectra with the help of AI/ML technique. In this study, a total number of 75 patients and volunteers, from hospitals at different geographical locations of India, have been tested and classified with this device. A classification approach employing a hybrid mutual information long short-term memory model has been applied to categorize various subject groups, resulting in an average accuracy, specificity, and sensitivity of 96.56%, 96.76%, and 94.37%, respectively using 10-fold cross-validation. This exploratory study demonstrates the potential of combining smartphone-based technology with fluorescence spectroscopy and artificial intelligence as a diagnostic screening approach which could enhance the detection and screening of cervical cancer.
Language	English
Publishing date	2024-03-17
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2390063-5
ISSN	1864-0648 ; 1864-063X
ISSN (online)	1864-0648
ISSN	1864-063X
DOI	10.1002/jbio.202300468
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Article ; Online: In-solution structure and oligomerization of human histone deacetylase 6 - an integrative approach.

Shukla, Shivam / Komarek, Jan / Novakova, Zora / Nedvedova, Jana / Ustinova, Kseniya / Vankova, Pavla / Kadek, Alan / Uetrecht, Charlotte / Mertens, Haydyn / Barinka, Cyril

The FEBS journal

2022 Volume 290, Issue 3, Page(s) 821–836

Abstract	Human histone deacetylase 6 (HDAC6) is a structurally unique, multidomain protein implicated in a variety of physiological processes including cytoskeletal remodelling and the maintenance of cellular homeostasis. Our current understanding of the HDAC6 structure is limited to isolated domains, and a holistic picture of the full-length protein structure, including possible domain interactions, is missing. Here, we used an integrative structural biology approach to build a solution model of HDAC6 by combining experimental data from several orthogonal biophysical techniques complemented by molecular modelling. We show that HDAC6 is best described as a mosaic of folded and intrinsically disordered domains that in-solution adopts an ensemble of conformations without any stable interactions between structured domains. Furthermore, HDAC6 forms dimers/higher oligomers in a concentration-dependent manner, and its oligomerization is mediated via the positively charged N-terminal microtubule-binding domain. Our findings provide the first insights into the structure of full-length human HDAC6 and can be used as a basis for further research into structure function and physiological studies of this unique deacetylase.
MeSH term(s)	Humans ; Histone Deacetylase 6/genetics ; Histone Deacetylase 6/chemistry ; Histone Deacetylase 6/metabolism ; Histone Deacetylases/metabolism ; Microtubules/metabolism ; Histone Deacetylase Inhibitors ; Acetylation
Chemical Substances	Histone Deacetylase 6 (EC 3.5.1.98) ; Histone Deacetylases (EC 3.5.1.98) ; Histone Deacetylase Inhibitors
Language	English
Publishing date	2022-09-19
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2173655-8
ISSN	1742-4658 ; 1742-464X
ISSN (online)	1742-4658
ISSN	1742-464X
DOI	10.1111/febs.16616
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Article ; Online: Heterologous expression and purification of recombinant human protoporphyrinogen oxidase IX: A comparative study.

Novakova, Zora / Khuntsaria, Daria / Gresova, Marketa / Mikesova, Jana / Havlinova, Barbora / Shukla, Shivam / Kolarova, Lucie / Vesela, Katerina / Martasek, Pavel / Barinka, Cyril

PloS one

2021 Volume 16, Issue 11, Page(s) e0259837

Abstract: Human protoporphyrinogen oxidase IX (hPPO) is an oxygen-dependent enzyme catalyzing the penultimate step in the heme biosynthesis pathway. Mutations in the enzyme are linked to variegate porphyria, an autosomal dominant metabolic disease. Here we ... ...

Abstract	Human protoporphyrinogen oxidase IX (hPPO) is an oxygen-dependent enzyme catalyzing the penultimate step in the heme biosynthesis pathway. Mutations in the enzyme are linked to variegate porphyria, an autosomal dominant metabolic disease. Here we investigated eukaryotic cells as alternative systems for heterologous expression of hPPO, as the use of a traditional bacterial-based system failed to produce several clinically relevant hPPO variants. Using bacterially-produced hPPO, we first analyzed the impact of N-terminal tags and various detergent on hPPO yield, and specific activity. Next, the established protocol was used to compare hPPO constructs heterologously expressed in mammalian HEK293T17 and insect Hi5 cells with prokaryotic overexpression. By attaching various fusion partners at the N- and C-termini of hPPO we also evaluated the influence of the size and positioning of fusion partners on expression levels, specific activity, and intracellular targeting of hPPO fusions in mammalian cells. Overall, our results suggest that while enzymatically active hPPO can be heterologously produced in eukaryotic systems, the limited availability of the intracellular FAD co-factor likely negatively influences yields of a correctly folded protein making thus the E.coli a system of choice for recombinant hPPO overproduction. At the same time, PPO overexpression in eukaryotic cells might be preferrable in cases when the effects of post-translational modifications (absent in bacteria) on target protein functions are studied.
MeSH term(s)	Animals ; Cell Line ; Escherichia coli/genetics ; Flavoproteins/biosynthesis ; Flavoproteins/genetics ; Flavoproteins/isolation & purification ; HEK293 Cells ; Humans ; Mitochondrial Proteins/biosynthesis ; Mitochondrial Proteins/genetics ; Mitochondrial Proteins/isolation & purification ; Protoporphyrinogen Oxidase/biosynthesis ; Protoporphyrinogen Oxidase/genetics ; Protoporphyrinogen Oxidase/isolation & purification ; Recombinant Fusion Proteins/biosynthesis ; Recombinant Fusion Proteins/genetics ; Recombinant Fusion Proteins/isolation & purification ; Sf9 Cells
Chemical Substances	Flavoproteins ; Mitochondrial Proteins ; Recombinant Fusion Proteins ; PPOX protein, human (EC 1.3.3.4) ; Protoporphyrinogen Oxidase (EC 1.3.3.4)
Language	English
Publishing date	2021-11-18
Publishing country	United States
Document type	Comparative Study ; Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0259837
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