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Article ; Online: Single-nucleus multiomic mapping of m

Hamashima, Kiyofumi / Wong, Ka Wai / Sam, Tsz Wing / Teo, Jia Hao Jackie / Taneja, Reshma / Le, Minh T N / Li, Qi-Jing / Hanna, Jacob H / Li, Hu / Loh, Yuin-Han

Molecular cell

2023

Abstract: ... ...

Abstract	N
Language	English
Publishing date	2023-08-25
Publishing country	United States
Document type	Journal Article
ZDB-ID	1415236-8
ISSN	1097-4164 ; 1097-2765
ISSN (online)	1097-4164
ISSN	1097-2765
DOI	10.1016/j.molcel.2023.08.010
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Article: Independent regulation of Z-lines and M-lines during sarcomere assembly in cardiac myocytes revealed by the automatic image analysis software sarcApp.

Neininger-Castro, Abigail C / Hayes, James B / Sanchez, Zachary C / Taneja, Nilay / Fenix, Aidan M / Moparthi, Satish / Vassilopoulos, Stéphane / Burnette, Dylan T

bioRxiv : the preprint server for biology

2023

Abstract: ... of both precursors and sarcomeres/myofibrils. We then expanded sarcApp to analyze "M-Lines" using the localization ... of myomesin and a protein that connects the Z-Lines to the M-Line (titin). sarcApp produces 33 distinct ... perturbations that affected Z-Lines and M-Lines differently, suggesting that they may be regulated independently ...

Abstract	Sarcomeres are the basic contractile units within cardiac myocytes, and the collective shortening of sarcomeres aligned along myofibrils generates the force driving the heartbeat. The alignment of the individual sarcomeres is important for proper force generation, and misaligned sarcomeres are associated with diseases including cardiomyopathies and COVID-19. The actin bundling protein, α-actinin-2, localizes to the "Z-Bodies" of sarcomere precursors and the "Z-Lines" of sarcomeres, and has been used previously to assess sarcomere assembly and maintenance. Previous measurements of α-actinin-2 organization have been largely accomplished manually, which is time-consuming and has hampered research progress. Here, we introduce sarcApp, an image analysis tool that quantifies several components of the cardiac sarcomere and their alignment in muscle cells and tissue. We first developed sarcApp to utilize deep learning-based segmentation and real space quantification to measure α-actinin-2 structures and determine the organization of both precursors and sarcomeres/myofibrils. We then expanded sarcApp to analyze "M-Lines" using the localization of myomesin and a protein that connects the Z-Lines to the M-Line (titin). sarcApp produces 33 distinct measurements per cell and 24 per myofibril that allow for precise quantification of changes in sarcomeres, myofibrils, and their precursors. We validated this system with perturbations to sarcomere assembly. We found perturbations that affected Z-Lines and M-Lines differently, suggesting that they may be regulated independently during sarcomere assembly.
Language	English
Publishing date	2023-10-06
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.01.11.523681
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Article ; Online: Independent regulation of Z-lines and M-lines during sarcomere assembly in cardiac myocytes revealed by the automatic image analysis software sarcApp.

Neininger-Castro, Abigail C / Hayes, James B / Sanchez, Zachary C / Taneja, Nilay / Fenix, Aidan M / Moparthi, Satish / Vassilopoulos, Stéphane / Burnette, Dylan Tyler

eLife

2023 Volume 12

Abstract: ... of myomesin and a protein that connects the Z-Lines to the M-Line (titin). sarcApp produces 33 distinct ... perturbations that affected Z-Lines and M-Lines differently, suggesting that they may be regulated independently ... of both precursors and sarcomeres/myofibrils. We then expanded sarcApp to analyze 'M-Lines' using the localization ...

Abstract	Sarcomeres are the basic contractile units within cardiac myocytes, and the collective shortening of sarcomeres aligned along myofibrils generates the force driving the heartbeat. The alignment of the individual sarcomeres is important for proper force generation, and misaligned sarcomeres are associated with diseases, including cardiomyopathies and COVID-19. The actin bundling protein, α-actinin-2, localizes to the 'Z-Bodies" of sarcomere precursors and the 'Z-Lines' of sarcomeres, and has been used previously to assess sarcomere assembly and maintenance. Previous measurements of α-actinin-2 organization have been largely accomplished manually, which is time-consuming and has hampered research progress. Here, we introduce sarcApp, an image analysis tool that quantifies several components of the cardiac sarcomere and their alignment in muscle cells and tissue. We first developed sarcApp to utilize deep learning-based segmentation and real space quantification to measure α-actinin-2 structures and determine the organization of both precursors and sarcomeres/myofibrils. We then expanded sarcApp to analyze 'M-Lines' using the localization of myomesin and a protein that connects the Z-Lines to the M-Line (titin). sarcApp produces 33 distinct measurements per cell and 24 per myofibril that allow for precise quantification of changes in sarcomeres, myofibrils, and their precursors. We validated this system with perturbations to sarcomere assembly. We found perturbations that affected Z-Lines and M-Lines differently, suggesting that they may be regulated independently during sarcomere assembly.
MeSH term(s)	Sarcomeres/metabolism ; Myocytes, Cardiac/metabolism ; Actinin/metabolism ; Myofibrils/metabolism ; Connectin/metabolism ; Software
Chemical Substances	Actinin (11003-00-2) ; Connectin
Language	English
Publishing date	2023-11-03
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2687154-3
ISSN	2050-084X ; 2050-084X
ISSN (online)	2050-084X
ISSN	2050-084X
DOI	10.7554/eLife.87065
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Article ; Online: Independent regulation of Z-lines and M-lines during sarcomere assembly in cardiac myocytes revealed by the automatic image analysis software sarcApp

Abigail C Neininger-Castro / James B Hayes / Zachary C Sanchez / Nilay Taneja / Aidan M Fenix / Satish Moparthi / Stéphane Vassilopoulos / Dylan Tyler Burnette

eLife, Vol

2023 Volume 12

Abstract: ... of both precursors and sarcomeres/myofibrils. We then expanded sarcApp to analyze ‘M-Lines’ using the localization ... of myomesin and a protein that connects the Z-Lines to the M-Line (titin). sarcApp produces 33 distinct ... perturbations that affected Z-Lines and M-Lines differently, suggesting that they may be regulated independently ...

Abstract	Sarcomeres are the basic contractile units within cardiac myocytes, and the collective shortening of sarcomeres aligned along myofibrils generates the force driving the heartbeat. The alignment of the individual sarcomeres is important for proper force generation, and misaligned sarcomeres are associated with diseases, including cardiomyopathies and COVID-19. The actin bundling protein, α-actinin-2, localizes to the ‘Z-Bodies” of sarcomere precursors and the ‘Z-Lines’ of sarcomeres, and has been used previously to assess sarcomere assembly and maintenance. Previous measurements of α-actinin-2 organization have been largely accomplished manually, which is time-consuming and has hampered research progress. Here, we introduce sarcApp, an image analysis tool that quantifies several components of the cardiac sarcomere and their alignment in muscle cells and tissue. We first developed sarcApp to utilize deep learning-based segmentation and real space quantification to measure α-actinin-2 structures and determine the organization of both precursors and sarcomeres/myofibrils. We then expanded sarcApp to analyze ‘M-Lines’ using the localization of myomesin and a protein that connects the Z-Lines to the M-Line (titin). sarcApp produces 33 distinct measurements per cell and 24 per myofibril that allow for precise quantification of changes in sarcomeres, myofibrils, and their precursors. We validated this system with perturbations to sarcomere assembly. We found perturbations that affected Z-Lines and M-Lines differently, suggesting that they may be regulated independently during sarcomere assembly.
Keywords	cardiac myocyte ; sarcomere ; myofibril ; Medicine ; R ; Science ; Q ; Biology (General) ; QH301-705.5
Language	English
Publishing date	2023-11-01T00:00:00Z
Publisher	eLife Sciences Publications Ltd
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Comparison of the diagnostic accuracy of 99 m-Tc-MDP bone scintigraphy and 18 F-FDG PET/CT for the detection of skeletal metastases.

Chang, Connie Y / Gill, Corey M / Joseph Simeone, F / Taneja, Atul K / Huang, Ambrose J / Torriani, Martin / Bredella, Miriam A

Acta radiologica (Stockholm, Sweden : 1987)

2016 Volume 57, Issue 1, Page(s) 58–65

Abstract: ... PET/CT and technetium-99 m-bone scintigraphy (bone scan) for the detection of skeletal metastases ...

Abstract	Background: Fluorine-18-fluorodeoxyglucose positron emission tomography/computed tomography (FDG PET/CT) is commonly performed for cancer staging, as it can detect metastatic disease in multiple organ systems. However, there has been some controversy in the scientific literature when comparing FDG PET/CT and technetium-99 m-bone scintigraphy (bone scan) for the detection of skeletal metastases. Purpose: To compare the accuracy of FDG PET/CT with bone scan for the detection of skeletal metastases. Material and methods: The study group comprised 202 adult cancer patients who underwent both FDG PET/CT and bone scan within 31 days for staging. Bone scans and FDG PET/CT were evaluated by two musculoskeletal radiologists for the presence and location of skeletal metastatic disease. Confirmation of the final diagnosis was based on the CT or magnetic resonance imaging (MRI) appearance, follow-up imaging, or histology. Results: The sensitivity, specificity, and accuracy for detecting skeletal metastatic disease of FDG PET/CT were 97%, 98%, and 98%, respectively, and of bone scan were 83%, 98%, and 93%, respectively. The lesions that bone scan most commonly missed were located in the pelvis, spine, and sacrum. FDG PET/CT missed mostly lesions that were outside of the field of view, but in all of these cases the patient had additional sites of skeletal metastatic disease. Bone scan falsely identified six metastatic lesions and FDG PET/CT falsely identified three metastatic lesions. Conclusion: FDG PET/CT is an accurate technique for detection of skeletal metastases, and is superior to bone scan, especially in the spine and pelvis.
MeSH term(s)	Adolescent ; Adult ; Aged ; Aged, 80 and over ; Bone Neoplasms/diagnostic imaging ; Bone Neoplasms/secondary ; Child ; Female ; Fluorodeoxyglucose F18 ; Humans ; Magnetic Resonance Imaging ; Male ; Middle Aged ; Multimodal Imaging ; Neoplasm Staging ; Positron-Emission Tomography ; Radiopharmaceuticals ; Sensitivity and Specificity ; Technetium Tc 99m Medronate ; Tomography, X-Ray Computed
Chemical Substances	Radiopharmaceuticals ; Fluorodeoxyglucose F18 (0Z5B2CJX4D) ; Technetium Tc 99m Medronate (X89XV46R07)
Language	English
Publishing date	2016-01
Publishing country	England
Document type	Comparative Study ; Journal Article
ZDB-ID	105-3
ISSN	1600-0455 ; 0284-1851 ; 0349-652X
ISSN (online)	1600-0455
ISSN	0284-1851 ; 0349-652X
DOI	10.1177/0284185114564438
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Article: Iodobenzene and m-chloroperbenzoic acid mediated oxidative dearomatization of phenols

Taneja, Neha / Rama Krishna Peddinti

Tetrahedron letters. 2016 Aug. 31, v. 57

2016

Abstract: ... monoketals by catalytic amount of iodobenzene, and m-CPBA as a co-oxidant has been achieved via in situ ...

Abstract	Oxidative dearomatization of 2- and 4-substituted phenols to their corresponding benzoquinone monoketals by catalytic amount of iodobenzene, and m-CPBA as a co-oxidant has been achieved via in situ generation of PhIO2, a hypervalent iodine(V) species. The transiently generated orthobenzoquinone monoketals further underwent DielsâAlder reaction with various dienophiles to furnish densely substituted bicyclo[2.2.2]octenones in high selectivities and yields. This methodology features ready availability of reagents, cost effectiveness, safety, brevity, selectivity, diversity and excellent yields.
Keywords	benzoquinones ; chemical structure ; cost effectiveness ; cycloaddition reactions ; iodine ; phenols
Language	English
Dates of publication	2016-0831
Size	p. 3958-3963.
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	204287-3
ISSN	1873-3581 ; 0040-4039
ISSN (online)	1873-3581
ISSN	0040-4039
DOI	10.1016/j.tetlet.2016.07.078
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Computational screening for new inhibitors of M. tuberculosis mycolyltransferases antigen 85 group of proteins as potential drug targets.

Gahoi, Shachi / Mandal, Rahul Shubhra / Ivanisenko, Nikita / Shrivastava, Priyanka / Jain, Sriyans / Singh, Ashish Kumar / Raghunandanan, Muthukurrusi Varieth / Kanchan, Swarna / Taneja, Bhupesh / Mandal, Chhabinath / Ivanisenko, Vladimir A / Kumar, Anil / Kumar, Rita / Ramachandran, Srinivasan

Journal of biomolecular structure & dynamics

2013 Volume 31, Issue 1, Page(s) 30–43

Abstract: The group of antigen 85 proteins of Mycobacterium tuberculosis is responsible for converting trehalose monomycolate to trehalose dimycolate, which contributes to cell wall stability. Here, we have used a serial enrichment approach to identify new ... ...

Abstract	The group of antigen 85 proteins of Mycobacterium tuberculosis is responsible for converting trehalose monomycolate to trehalose dimycolate, which contributes to cell wall stability. Here, we have used a serial enrichment approach to identify new potential inhibitors by searching the libraries of compounds using both 2D atom pair descriptors and binary fingerprints followed by molecular docking. Three different docking softwares AutoDock, GOLD, and LigandFit were used for docking calculations. In addition, we applied the criteria of selecting compounds with binding efficiency close to the starting known inhibitor and showing potential to form hydrogen bonds with the active site amino acid residues. The starting inhibitor was ethyl-3-phenoxybenzyl-butylphosphonate, which had IC(50) value of 2.0 μM in mycolyltransferase inhibition assay. Our search from more than 34 million compounds from public libraries yielded 49 compounds. Subsequently, selection was restricted to compounds conforming to the Lipinski rule of five and exhibiting hydrogen bonding to any of the amino acid residues in the active site pocket of all three proteins of antigen 85A, 85B, and 85C. Finally, we selected those ligands which were ranked top in the table with other known decoys in all the docking results. The compound NIH415032 from tuberculosis antimicrobial acquisition and coordinating facility was further examined using molecular dynamics simulations for 10 ns. These results showed that the binding is stable, although some of the hydrogen bond atom pairs varied through the course of simulation. The NIH415032 has antitubercular properties with IC(90) at 20 μg/ml (53.023 μM). These results will be helpful to the medicinal chemists for developing new antitubercular molecules for testing.
MeSH term(s)	Acyltransferases/chemistry ; Acyltransferases/metabolism ; Antigens, Bacterial/chemistry ; Antigens, Bacterial/metabolism ; Antitubercular Agents/chemistry ; Antitubercular Agents/metabolism ; Bacterial Proteins/chemistry ; Bacterial Proteins/metabolism ; Binding Sites ; Drug Design ; Hydrogen Bonding ; Ligands ; Molecular Docking Simulation ; Mycobacterium tuberculosis/enzymology
Chemical Substances	Antigens, Bacterial ; Antitubercular Agents ; Bacterial Proteins ; Ligands ; Acyltransferases (EC 2.3.-) ; antigen 85B, Mycobacterium tuberculosis (EC 2.3.1.-)
Language	English
Publishing date	2013
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2012.691343
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Article ; Online: Commentary: Renewed interest in off-axis retinoscopy and peripheral refraction for it's role in control of myopia progression.

Taneja, Mukesh

Indian journal of ophthalmology

2022 Volume 70, Issue 3, Page(s) 781–782

MeSH term(s)	Humans ; Myopia/diagnosis ; Refraction, Ocular ; Retinoscopy ; Vision Tests
Language	English
Publishing date	2022-03-10
Publishing country	India
Document type	Journal Article ; Comment
ZDB-ID	187392-1
ISSN	1998-3689 ; 0301-4738
ISSN (online)	1998-3689
ISSN	0301-4738
DOI	10.4103/ijo.IJO_2842_21
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Article ; Online: Commentary: Effect of dry eyes on the corneal diagnostic measurements.

Taneja, Mukesh

Indian journal of ophthalmology

2022 Volume 70, Issue 4, Page(s) 1157–1158

MeSH term(s)	Corneal Topography ; Dry Eye Syndromes/diagnosis ; Humans
Language	English
Publishing date	2022-03-24
Publishing country	India
Document type	Journal Article ; Comment
ZDB-ID	187392-1
ISSN	1998-3689 ; 0301-4738
ISSN (online)	1998-3689
ISSN	0301-4738
DOI	10.4103/ijo.IJO_3119_21
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Book ; Online: Ports and Waterways

van Koningsveld, Mark / Verheij, Henk / Taneja, Poonam / de Vriend, Huib

Navigating the changing world

2023

Keywords	Harbours & ports ; Maritime / nautical trades ; Hydraulic engineering ; system performance ; waterborne supply chains ; port development ; port planning ; container terminals ; waterway transport
Language	English
Size	1 electronic resource (517 pages)
Publisher	TU Delft Open
Publishing place	Delft
Document type	Book ; Online
Note	English
HBZ-ID	HT030649901
ISBN	9789463664448 ; 9463664440
Database	ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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