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Article ; Online: Resolution of inter/intraspecies variation in Weissella group requires multigene analysis and functional characterization

Joglekar, Amruta / Nimonkar, Yogesh / Bajaj, Abhay / Prakash, Om

Journal of Basic Microbiology. 2023 Feb., v. 63, no. 2 p.140-155

2023

Abstract: Weissella confusa and Weissella cibaria strains isolated from the human‐ gut are considered as potential probiotics, but remain under‐explored owing to their ambiguous taxonomic assignment. The present study assesses the taxonomic resolution of 11 ... ...

Abstract	Weissella confusa and Weissella cibaria strains isolated from the human‐ gut are considered as potential probiotics, but remain under‐explored owing to their ambiguous taxonomic assignment. The present study assesses the taxonomic resolution of 11 strains belonging to W. confusa and W. cibaria species and highlights the inter‐ and intraspecies variations using an array of phenetic and molecular methods. Remarkable genomic variability among the strains was observed by phylogenetic analysis using concatenated housekeeping genes (pheS, gyrB, and dnaA) along with 16S rRNA gene sequence, suggesting intraspecies variations; which is also supported by the phenetic data. Analysis showed that 16S rRNA gene sequence alone could not resolve the variation, and among the tested marker genes, signals from pheS gene provide better taxonomic resolution. The biochemical and antibiotic susceptibility tests also showed considerable variations among the isolates. Additionally, 'quick' identification using mass spectroscopy‐based matrix‐assisted laser desorption/ionization‐time of flight mass spectra was accurate up to genus only, and not species level, for the Weissella group. The study highlights need for inclusion of functional, phenetic, and multigene phylogenetic analysis in addition to 16S rRNA gene‐based identification for the Weissella group, to provide better resolution in taxonomic assignments, which is often a prerequisite for the selection of potential strains with biotechnological applications.
Keywords	Weissella cibaria ; Weissella confusa ; antibiotic resistance ; digestive system ; genes ; genetic variation ; nucleotide sequences ; phylogeny ; probiotics
Language	English
Dates of publication	2023-02
Size	p. 140-155.
Publishing place	John Wiley & Sons, Ltd
Document type	Article ; Online
Note	JOURNAL ARTICLE
ZDB-ID	632513-0
ISSN	1521-4028 ; 0233-111X
ISSN (online)	1521-4028
ISSN	0233-111X
DOI	10.1002/jobm.202200357
Database	NAL-Catalogue (AGRICOLA)

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Article: Risk factors and outcome of antenatally diagnosed congenital diaphragmatic hernia following in-utero transfer in a busy public-sector tertiary care center in North India.

Joglekar, Abhay / Roy Choudhury, Subhasis / Vibhash, Chandra / Kumar, Manisha / Gupta, Amit

Monaldi archives for chest disease = Archivio Monaldi per le malattie del torace

2024

Abstract: We analyzed the risk factors and outcomes of antenatally diagnosed congenital diaphragmatic hernia (CDH) from a tertiary-care children's hospital following in-utero transfer. A total of 41 antenatally detected cases of CDH were included; 30 were live- ... ...

Abstract	We analyzed the risk factors and outcomes of antenatally diagnosed congenital diaphragmatic hernia (CDH) from a tertiary-care children's hospital following in-utero transfer. A total of 41 antenatally detected cases of CDH were included; 30 were live-born and 11 were still-born. The primary outcome was postnatal survival. The secondary outcome was the probable factor affecting survival. No medical termination of the pregnancy was done. The mean gestational age at diagnosis was 23 weeks. The diagnostic accuracy of antenatal ultrasonography was 40/41 (97.5%). Lung-to-head ratio (LHR) was <1 in 20 cases (survived 2), LHR was >1 in 10 cases (survived 8), and LHR was not recorded in 11 cases (survived 4). Overall survival was 14/41 (34.1%). Survival in fetuses with polyhydramnios was 0% (n=3; survived 0), associated anomalies were 33.3% (n=3; survived 1), and liver herniation was 22.2% (n=9; survived 2). Postnatally, significant risk factors included a low Apgar score, the need for ventilation, and neonatal intensive care unit (NICU) management. Survival in live-born cases was 14/30 (46.6%) and in operated cases was 14/19 (73.6%). We concluded that antenatal ultrasound had a high accuracy rate for detecting CDH. Antenatal risk factors affecting outcomes were low LHR, maternal polyhydramnios, liver herniation, and associated malformations. Postnatal risk factors included a low Apgar score, NICU admission, and a need for ventilation. The overall survival rate, as well as the survival rates for live-borns and those undergoing surgery, were 34.1%, 46.6%, and 73.6%, respectively. This data will guide clinicians in counseling the families of antenatally diagnosed CDH.
Language	English
Publishing date	2024-04-30
Publishing country	Italy
Document type	Journal Article
ZDB-ID	1160940-0
ISSN	1122-0643 ; 1120-0391
ISSN	1122-0643 ; 1120-0391
DOI	10.4081/monaldi.2024.2880
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Book ; Online: On Speech Pre-emphasis as a Simple and Inexpensive Method to Boost Speech Enhancement

López-Espejo, Iván / Joglekar, Aditya / Peinado, Antonio M. / Jensen, Jesper

2024

Abstract: Pre-emphasis filtering, compensating for the natural energy decay of speech at higher frequencies, has been considered as a common pre-processing step in a number of speech processing tasks over the years. In this work, we demonstrate, for the first time, ...

Abstract	Pre-emphasis filtering, compensating for the natural energy decay of speech at higher frequencies, has been considered as a common pre-processing step in a number of speech processing tasks over the years. In this work, we demonstrate, for the first time, that pre-emphasis filtering may also be used as a simple and computationally-inexpensive way to leverage deep neural network-based speech enhancement performance. Particularly, we look into pre-emphasizing the estimated and actual clean speech prior to loss calculation so that different speech frequency components better mirror their perceptual importance during the training phase. Experimental results on a noisy version of the TIMIT dataset show that integrating the pre-emphasis-based methodology at hand yields relative estimated speech quality improvements of up to 4.6% and 3.4% for noise types seen and unseen, respectively, during the training phase. Similar to the case of pre-emphasis being considered as a default pre-processing step in classical automatic speech recognition and speech coding systems, the pre-emphasis-based methodology analyzed in this article may potentially become a default add-on for modern speech enhancement.
Keywords	Electrical Engineering and Systems Science - Audio and Speech Processing
Subject code	410
Publishing date	2024-01-17
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Resolution of inter/intraspecies variation in Weissella group requires multigene analysis and functional characterization.

Joglekar, Amruta / Nimonkar, Yogesh / Bajaj, Abhay / Prakash, Om

Journal of basic microbiology

2022 Volume 63, Issue 2, Page(s) 140–155

Abstract: Weissella confusa and Weissella cibaria strains isolated from the human- gut are considered as potential probiotics, but remain under-explored owing to their ambiguous taxonomic assignment. The present study assesses the taxonomic resolution of 11 ... ...

Abstract	Weissella confusa and Weissella cibaria strains isolated from the human- gut are considered as potential probiotics, but remain under-explored owing to their ambiguous taxonomic assignment. The present study assesses the taxonomic resolution of 11 strains belonging to W. confusa and W. cibaria species and highlights the inter- and intraspecies variations using an array of phenetic and molecular methods. Remarkable genomic variability among the strains was observed by phylogenetic analysis using concatenated housekeeping genes (pheS, gyrB, and dnaA) along with 16S rRNA gene sequence, suggesting intraspecies variations; which is also supported by the phenetic data. Analysis showed that 16S rRNA gene sequence alone could not resolve the variation, and among the tested marker genes, signals from pheS gene provide better taxonomic resolution. The biochemical and antibiotic susceptibility tests also showed considerable variations among the isolates. Additionally, 'quick' identification using mass spectroscopy-based matrix-assisted laser desorption/ionization-time of flight mass spectra was accurate up to genus only, and not species level, for the Weissella group. The study highlights need for inclusion of functional, phenetic, and multigene phylogenetic analysis in addition to 16S rRNA gene-based identification for the Weissella group, to provide better resolution in taxonomic assignments, which is often a prerequisite for the selection of potential strains with biotechnological applications.
MeSH term(s)	Humans ; Weissella/genetics ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; Genomics ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods ; Sequence Analysis, DNA
Chemical Substances	RNA, Ribosomal, 16S
Language	English
Publishing date	2022-11-03
Publishing country	Germany
Document type	Journal Article
ZDB-ID	632513-0
ISSN	1521-4028 ; 0233-111X
ISSN (online)	1521-4028
ISSN	0233-111X
DOI	10.1002/jobm.202200357
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Book ; Online: Topology Optimization using Neural Networks with Conditioning Field Initialization for Improved Efficiency

Chen, Hongrui / Joglekar, Aditya / Kara, Levent Burak

2023

Abstract: We propose conditioning field initialization for neural network based topology optimization. In this work, we focus on (1) improving upon existing neural network based topology optimization, (2) demonstrating that by using a prior initial field on the ... ...

Abstract	We propose conditioning field initialization for neural network based topology optimization. In this work, we focus on (1) improving upon existing neural network based topology optimization, (2) demonstrating that by using a prior initial field on the unoptimized domain, the efficiency of neural network based topology optimization can be further improved. Our approach consists of a topology neural network that is trained on a case by case basis to represent the geometry for a single topology optimization problem. It takes in domain coordinates as input to represent the density at each coordinate where the topology is represented by a continuous density field. The displacement is solved through a finite element solver. We employ the strain energy field calculated on the initial design domain as an additional conditioning field input to the neural network throughout the optimization. The addition of the strain energy field input improves the convergence speed compared to standalone neural network based topology optimization.
Keywords	Computer Science - Machine Learning
Subject code	006 ; 510
Publishing date	2023-05-17
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Book ; Online: DMF-TONN

Joglekar, Aditya / Chen, Hongrui / Kara, Levent Burak

Direct Mesh-free Topology Optimization using Neural Networks

2023

Abstract: We propose a direct mesh-free method for performing topology optimization by integrating a density field approximation neural network with a displacement field approximation neural network. We show that this direct integration approach can give ... ...

Abstract	We propose a direct mesh-free method for performing topology optimization by integrating a density field approximation neural network with a displacement field approximation neural network. We show that this direct integration approach can give comparable results to conventional topology optimization techniques, with an added advantage of enabling seamless integration with post-processing software, and a potential of topology optimization with objectives where meshing and Finite Element Analysis (FEA) may be expensive or not suitable. Our approach (DMF-TONN) takes in as inputs the boundary conditions and domain coordinates and finds the optimum density field for minimizing the loss function of compliance and volume fraction constraint violation. The mesh-free nature is enabled by a physics-informed displacement field approximation neural network to solve the linear elasticity partial differential equation and replace the FEA conventionally used for calculating the compliance. We show that using a suitable Fourier Features neural network architecture and hyperparameters, the density field approximation neural network can learn the weights to represent the optimal density field for the given domain and boundary conditions, by directly backpropagating the loss gradient through the displacement field approximation neural network, and unlike prior work there is no requirement of a sensitivity filter, optimality criterion method, or a separate training of density network in each topology optimization iteration.
Keywords	Computer Science - Computational Engineering ; Finance ; and Science ; Computer Science - Machine Learning
Subject code	006
Publishing date	2023-05-06
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: From words to complete phrases: insight into single-cell isoforms using short and long reads.

Joglekar, Anoushka / Foord, Careen / Jarroux, Julien / Pollard, Shaun / Tilgner, Hagen U

Transcription

2023 Volume 14, Issue 3-5, Page(s) 92–104

Abstract: The profiling of gene expression patterns to glean biological insights from single cells has become commonplace over the last few years. However, this approach overlooks the transcript contents that can differ between individual cells and cell ... ...

Abstract	The profiling of gene expression patterns to glean biological insights from single cells has become commonplace over the last few years. However, this approach overlooks the transcript contents that can differ between individual cells and cell populations. In this review, we describe early work in the field of single-cell short-read sequencing as well as full-length isoforms from single cells. We then describe recent work in single-cell long-read sequencing wherein some transcript elements have been observed to work in tandem. Based on earlier work in bulk tissue, we motivate the study of combination patterns of other RNA variables. Given that we are still blind to some aspects of isoform biology, we suggest possible future avenues such as CRISPR screens which can further illuminate the function of RNA variables in distinct cell populations.
MeSH term(s)	Gene Expression Profiling ; Transcriptome ; Alternative Splicing ; Protein Isoforms/genetics ; Protein Isoforms/metabolism ; RNA/genetics ; Sequence Analysis, RNA ; High-Throughput Nucleotide Sequencing
Chemical Substances	Protein Isoforms ; RNA (63231-63-0)
Language	English
Publishing date	2023-06-14
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	2646974-1
ISSN	2154-1272 ; 2154-1264
ISSN (online)	2154-1272
ISSN	2154-1264
DOI	10.1080/21541264.2023.2213514
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Article ; Online: Sequencing of individual barcoded cDNAs using Pacific Biosciences and Oxford Nanopore Technologies reveals platform-specific error patterns.

Mikheenko, Alla / Prjibelski, Andrey D / Joglekar, Anoushka / Tilgner, Hagen U

Genome research

2022 Volume 32, Issue 4, Page(s) 726–737

Abstract: Long-read transcriptomics require understanding error sources inherent to technologies. Current approaches cannot compare methods for an individual RNA molecule. Here, we present a novel platform-comparison method that combines barcoding strategies and ... ...

Abstract	Long-read transcriptomics require understanding error sources inherent to technologies. Current approaches cannot compare methods for an individual RNA molecule. Here, we present a novel platform-comparison method that combines barcoding strategies and long-read sequencing to sequence cDNA copies representing an individual RNA molecule on both Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT). We compare these long-read pairs in terms of sequence content and isoform patterns. Although individual read pairs show high similarity, we find differences in (1) aligned length, (2) transcription start site (TSS), (3) polyadenylation site (poly(A)-site) assignment, and (4) exon-intron structures. Overall, 25% of read pairs disagree on either TSS, poly(A)-site, or splice site. Intron-chain disagreement typically arises from alignment errors of microexons and complicated splice sites. Our single-molecule technology comparison reveals that inconsistencies are often caused by sequencing error-induced inaccurate ONT alignments, especially to downstream GUNNGU donor motifs. However, annotation-disagreeing upstream shifts in NAGNAG acceptors in ONT are often confirmed by PacBio and are thus likely real. In both barcoded and nonbarcoded ONT reads, we find that intron number and proximity of GU/AGs better predict inconsistencies with the annotation than read quality alone. We summarize these findings in an annotation-based algorithm for spliced alignment correction that improves subsequent transcript construction with ONT reads.
MeSH term(s)	DNA, Complementary ; High-Throughput Nucleotide Sequencing/methods ; Nanopores ; RNA ; Sequence Analysis, DNA/methods ; Technology
Chemical Substances	DNA, Complementary ; RNA (63231-63-0)
Language	English
Publishing date	2022-03-17
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1284872-4
ISSN	1549-5469 ; 1088-9051 ; 1054-9803
ISSN (online)	1549-5469
ISSN	1088-9051 ; 1054-9803
DOI	10.1101/gr.276405.121
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Article ; Online: ScisorWiz: visualizing differential isoform expression in single-cell long-read data.

Stein, Alexander N / Joglekar, Anoushka / Poon, Chi-Lam / Tilgner, Hagen U

Bioinformatics (Oxford, England)

2022 Volume 38, Issue 13, Page(s) 3474–3476

Abstract: Summary: RNA isoforms contribute to the diverse functionality of the proteins they encode within the cell. Visualizing how isoform expression differs across cell types and brain regions can inform our understanding of disease and gain or loss of ... ...

Abstract	Summary: RNA isoforms contribute to the diverse functionality of the proteins they encode within the cell. Visualizing how isoform expression differs across cell types and brain regions can inform our understanding of disease and gain or loss of functionality caused by alternative splicing with potential negative impacts. However, the extent to which this occurs in specific cell types and brain regions is largely unknown. This is the kind of information that ScisorWiz plots can provide in an informative and easily communicable manner. ScisorWiz affords its user the opportunity to visualize specific genes across any number of cell types, and provides various sorting options for the user to gain different ways to understand their data. ScisorWiz provides a clear picture of differential isoform expression through various clustering methods and highlights features such as alternative exons and single-nucleotide variants. Tools like ScisorWiz are key for interpreting single-cell isoform sequencing data. This tool applies to any single-cell long-read RNA sequencing data in any cell type, tissue or species. Availability and implementation: Source code is available at http://github.com/ans4013/ScisorWiz. No new data were generated for this publication. Data used to generate figures was sourced from GEO accession token GSE158450 and available on GitHub as example data.
MeSH term(s)	Protein Isoforms/genetics ; Protein Isoforms/metabolism ; Alternative Splicing ; Software ; RNA Isoforms/metabolism ; Exons ; Sequence Analysis, RNA
Chemical Substances	Protein Isoforms ; RNA Isoforms
Language	English
Publishing date	2022-05-19
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btac340
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Article ; Online: Three new and notes on two other jumping spider species of the genus Stenaelurillus Simon, 1886 (Salticidae: Aelurillina) from the Deccan Plateau, India.

Marathe, Kiran / Sanap, Rajesh / Joglekar, Anuradha / Caleb, John T D / Maddison, Wayne P

Zootaxa

2022 Volume 5125, Issue 1, Page(s) 1–19

Abstract: We describe three new species of Stenaelurillus Simon, 1886 from the Deccan Plateau of India, and report on populations of S. sarojinae Caleb Mathai, 2014 and S. marusiki Logunov, 2001. One of the new species, S. shwetamukhi Marathe, Sanap, Maddison, sp. ...

Abstract	We describe three new species of Stenaelurillus Simon, 1886 from the Deccan Plateau of India, and report on populations of S. sarojinae Caleb Mathai, 2014 and S. marusiki Logunov, 2001. One of the new species, S. shwetamukhi Marathe, Sanap, Maddison, sp. nov., has black-and-white markings, characteristic of several other Indian Stenaelurillus species. The other two new species, S. tamravarni Marathe Maddison, sp. nov., and S. vyaghri Sanap, Joglekar, Caleb, sp. nov., are colourful and with fringed male abdomens, like several other Indian species including S. sarojinae. The population of S. sarojinae from Mysuru, Karnataka, shows colours distinct from the population at the type locality. The female of S. marusiki is described for the first time.
MeSH term(s)	Animal Distribution ; Animals ; Female ; India ; Male ; Spiders
Language	English
Publishing date	2022-04-07
Publishing country	New Zealand
Document type	Journal Article
ISSN	1175-5334
ISSN (online)	1175-5334
DOI	10.11646/zootaxa.5125.1.1
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