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Sternak M, Stojak M, Banasik T, Kij A, Bar A, Pacia MZ, Wojnar-Lason K, Chorazy N, Mohaissen T, Marczyk B, Czyzynska-Cichon I, Berkimbayeva Z, Mika A, Chlopicki S. Vascular ATGL-dependent lipolysis and the activation of cPLA 2-PGI 2 pathway protect against postprandial endothelial dysfunction. Cell Mol Life Sci 2024; 81:125. [PMID: 38467757 PMCID: PMC10927860 DOI: 10.1007/s00018-024-05167-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 01/05/2024] [Accepted: 02/02/2024] [Indexed: 03/13/2024]
Abstract
Adipose triglyceride lipase (ATGL) is involved in lipolysis and displays a detrimental pathophysiological role in cardio-metabolic diseases. However, the organo-protective effects of ATGL-induced lipolysis were also suggested. The aim of this work was to characterize the function of lipid droplets (LDs) and ATGL-induced lipolysis in the regulation of endothelial function. ATGL-dependent LDs hydrolysis and cytosolic phospholipase A2 (cPLA2)-derived eicosanoids production were studied in the aorta, endothelial and smooth muscle cells exposed to exogenous oleic acid (OA) or arachidonic acid (AA). Functional effects of ATGL-dependent lipolysis and subsequent activation of cPLA2/PGI2 pathway were also studied in vivo in relation to postprandial endothelial dysfunction.The formation of LDs was invariably associated with elevated production of endogenous AA-derived prostacyclin (PGI2). In the presence of the inhibitor of ATGL or the inhibitor of cytosolic phospholipase A2, the production of eicosanoids was reduced, with a concomitant increase in the number of LDs. OA administration impaired endothelial barrier integrity in vitro that was further impaired if OA was given together with ATGL inhibitor. Importantly, in vivo, olive oil induced postprandial endothelial dysfunction that was significantly deteriorated by ATGL inhibition, cPLA2 inhibition or by prostacyclin (IP) receptor blockade.In summary, vascular LDs formation induced by exogenous AA or OA was associated with ATGL- and cPLA2-dependent PGI2 production from endogenous AA. The inhibition of ATGL resulted in an impairment of endothelial barrier function in vitro. The inhibition of ATGL-cPLA2-PGI2 dependent pathway resulted in the deterioration of endothelial function upon exposure to olive oil in vivo. In conclusion, vascular ATGL-cPLA2-PGI2 dependent pathway activated by lipid overload and linked to LDs formation in endothelium and smooth muscle cells has a vasoprotective role by counterbalancing detrimental effects of lipid overload on endothelial function.
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Affiliation(s)
- M Sternak
- Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, Bobrzynskiego 14, Krakow, Poland.
| | - M Stojak
- Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, Bobrzynskiego 14, Krakow, Poland
| | - T Banasik
- Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, Bobrzynskiego 14, Krakow, Poland
| | - A Kij
- Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, Bobrzynskiego 14, Krakow, Poland
| | - A Bar
- Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, Bobrzynskiego 14, Krakow, Poland
| | - M Z Pacia
- Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, Bobrzynskiego 14, Krakow, Poland
| | - K Wojnar-Lason
- Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, Bobrzynskiego 14, Krakow, Poland
- Medical College, Chair of Pharmacology, Jagiellonian University, Grzegorzecka 16, Krakow, Poland
| | - N Chorazy
- Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, Bobrzynskiego 14, Krakow, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Lojasiewicza 11, Krakow, Poland
| | - T Mohaissen
- Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, Bobrzynskiego 14, Krakow, Poland
| | - B Marczyk
- Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, Bobrzynskiego 14, Krakow, Poland
| | - I Czyzynska-Cichon
- Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, Bobrzynskiego 14, Krakow, Poland
| | - Z Berkimbayeva
- Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, Bobrzynskiego 14, Krakow, Poland
| | - A Mika
- Department of Environmental Analysis, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, Gdansk, Poland
- Department of Pharmaceutical Biochemistry, Medical University of Gdansk, Debinki 1, Gdansk, Poland
| | - S Chlopicki
- Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, Bobrzynskiego 14, Krakow, Poland.
- Medical College, Chair of Pharmacology, Jagiellonian University, Grzegorzecka 16, Krakow, Poland.
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Bar A, Argaman L, Eldar M, Margalit H. TRS: a method for determining transcript termini from RNAtag-seq sequencing data. Nat Commun 2023; 14:7843. [PMID: 38030608 PMCID: PMC10687069 DOI: 10.1038/s41467-023-43534-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Accepted: 11/12/2023] [Indexed: 12/01/2023] Open
Abstract
In bacteria, determination of the 3' termini of transcripts plays an essential role in regulation of gene expression, affecting the functionality and stability of the transcript. Several experimental approaches were developed to identify the 3' termini of transcripts, however, these were applied only to a limited number of bacteria and growth conditions. Here we present a straightforward approach to identify 3' termini from widely available RNA-seq data without the need for additional experiments. Our approach relies on the observation that the RNAtag-seq sequencing protocol results in overabundance of reads mapped to transcript 3' termini. We present TRS (Termini by Read Starts), a computational pipeline exploiting this property to identify 3' termini in RNAtag-seq data, and show that the identified 3' termini are highly reliable. Since RNAtag-seq data are widely available for many bacteria and growth conditions, our approach paves the way for studying bacterial transcription termination in an unprecedented scope.
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Affiliation(s)
- Amir Bar
- Department of Microbiology and Molecular Genetics IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, 9112102, Israel
| | - Liron Argaman
- Department of Microbiology and Molecular Genetics IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, 9112102, Israel
| | - Michal Eldar
- Department of Microbiology and Molecular Genetics IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, 9112102, Israel
| | - Hanah Margalit
- Department of Microbiology and Molecular Genetics IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, 9112102, Israel.
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3
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Kopacz A, Kloska D, Bar A, Targosz-Korecka M, Chlopicki S, Jozkowicz A, Szade K, Grochot-Przeczek A. MiRNA-34a deficiency impairs endothelial function and stimulates its proliferation - the impact on angiotensin II-induced abdominal aortic aneurysm. Cardiovasc Res 2022. [DOI: 10.1093/cvr/cvac066.191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Funding Acknowledgements
Type of funding sources: Public grant(s) – National budget only. Main funding source(s): This work was supported by National Science Center grant SONATA BIS No. 2016/22/E/NZ3/00405 (AGP) and the project for PhD students and Young Scientists FBBB N19/MNW/000005 (AK).
Background
Abdominal aortic aneurysm (AAA) is a permanent dilatation of the abdominal aorta, which bears a high risk of rupture and sudden death of the patient. The pathogenic mechanisms of AAA remain elusive and surgical intervention represents the only treatment option. The involvement of endothelial cells (ECs) in the formation of aneurysms is still a matter of debate.
Purpose
As AAA is an age-related cardiovascular disease, we aimed to investigate the role of age-related miRNA-34a in ECs in pathogenesis of AAA. The deficiency of this miRNA has been so far proved preventive in several cardiovascular disease settings; however, the detailed mechanisms of protection have not been elucidated and the impact on EC function has not been addressed.
Methods
In vitro experiments were performed on primary human aortic ECs with RNA interference-mediated depletion of miRNA-34a. Animal studies were done on tamoxifen-induced EC-specific knockout of miRNA-34a or Rainbow mice. For aneurysm studies, we used an angiotensin II (AngII)-based model. Aortas and ECs were characterised using intravital microscopy, atomic force microscopy, fluorescent stainings, EPR, blood pressure measurements and Doppler flowmetry.
Results
Deficiency of miRNA-34a in vivo led to age-dependent EC dysfunction, as evidenced by a decreased length and coverage of glycocalyx and reduced NO production, with a concomitant increase in arterial stiffness, leukocyte adhesion and prothrombotic phenotype. However, despite detrimental effects of miRNA-34a deficiency on EC function, it did not result in a higher aneurysm incidence in young mice in AngII model. Quite surprisingly, the formation of the aneurysm was abrogated in older miRNA-34aEC-KO animals. Changes in expression of AngII receptors, proinflammatory molecules or blood pressure could not account for these anti-AAA effects of miRNA deficiency. Instead, we found significantly enhanced proliferation of intimal ECs upon AngII in young and old miRNA-34aEC-KO mice. The results were further corroborated in vitro, where we demonstrated loss of endothelial markers, with a concomitant increase in proliferation and preserved angiogenic function of miRNA-34aEC-KO. Additionally, we used multicolour EC lineage tracing to address the significance of endothelial proliferation during aneurysm formation. In stable aneurysms, we observed a polyclonal expansion of ECs in the intimal layer and, particularly, in the aneurysmal area. Of note, we did not detect any EC proliferation in the ruptured AAA.
Conclusions
miRNA-34a deficiency impairs EC function and stimulate EC proliferation, the latter presumably determined protection against Ang-II AAA in older mice. Therefore, we postulate that EC proliferation plays a more significant role than the preservation of EC function in protection against AAA. The fine-tuning of ECs proliferation may have a therapeutical role in the treatment of aneurysms.
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Affiliation(s)
- A Kopacz
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University , Cracow , Poland
| | - D Kloska
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University , Cracow , Poland
| | - A Bar
- Jagiellonian Centre for Experimental Therapeutics, Jagiellonian University , Cracow , Poland
| | - M Targosz-Korecka
- Faculty of Physics, Astronomy and Applied Computer Science, Jagiellonian University , Cracow , Poland
| | - S Chlopicki
- Jagiellonian Centre for Experimental Therapeutics, Jagiellonian University , Cracow , Poland
| | - A Jozkowicz
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University , Cracow , Poland
| | - K Szade
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University , Cracow , Poland
| | - A Grochot-Przeczek
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University , Cracow , Poland
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Muhamedrahimov R, Bar A, Laserson J, Akselrod-Ballin A, Elnekave E. Using Machine Learning to Identify Intravenous Contrast Phases on Computed Tomography. Comput Methods Programs Biomed 2022; 215:106603. [PMID: 34979295 DOI: 10.1016/j.cmpb.2021.106603] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 12/21/2021] [Accepted: 12/21/2021] [Indexed: 06/14/2023]
Abstract
PURPOSE The purpose of the present work is to demonstrate the application of machine learning (ML) techniques to automatically identify the presence and physiologic phase of intravenous (IV) contrast in Computed Tomography (CT) scans of the Chest, Abdomen and Pelvis. MATERIALS AND METHODS Training, testing and validation data were acquired from a dataset of 82,690 chest and abdomen CT examinations performed at 17 different institutions. Free text in DICOM metadata was utilized as weak labels for semi-supervised classification training. Contrast phase identification was approached as a classification task, using a 12-layer CNN and ResNet18 with four contrast-phase output. The model was reformulated to fit a regression task aimed to predict actual seconds from time of IV contrast administration to series image acquisition. Finally, transfer learning was used to optimize the model to predict contrast presence on CT Chest. RESULTS By training based on labels inferred from noisy, free text DICOM information, contrast phase was predicted with 93.3% test accuracy (95% CI: 89.3%, 96.6%) . Regression analysis resulted in delineation of early vs late arterial phases and a nephrogenic phase in between the portal venous and delayed excretory phase. Transfer learning applied to Chest CT achieved an AUROC of 0.776 (95% CI: 0.721, 0.832) directly using the model trained for abdomen CT and 0.999 (95% CI: 0.998, 1.000) by fine-tuning. CONCLUSIONS The presence and phase of contrast on CT examinations of the Abdomen-pelvis accurately and automatically be ascertained by a machine learning algorithm. Transfer learning applied to CT Chest achieves high precision with as little as 100 labeled samples.
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Affiliation(s)
| | - Amir Bar
- Zebra Medical Vision LTD, Shfayim, Israel
| | | | | | - Eldad Elnekave
- Zebra Medical Vision LTD, Shfayim, Israel; Department of Radiology, Rabin Medical Center, Petach Tikvah, Israel.
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Pearl Mizrahi S, Elbaz N, Argaman L, Altuvia Y, Katsowich N, Socol Y, Bar A, Rosenshine I, Margalit H. The impact of Hfq-mediated sRNA-mRNA interactome on the virulence of enteropathogenic Escherichia coli. Sci Adv 2021; 7:eabi8228. [PMID: 34705501 PMCID: PMC8550237 DOI: 10.1126/sciadv.abi8228] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Accepted: 09/07/2021] [Indexed: 06/13/2023]
Abstract
Small RNAs (sRNAs) exert their regulation posttranscriptionally by base pairing with their target mRNAs, often in association with the RNA chaperone protein Hfq. Here, integrating RNA-seq–based technologies and bioinformatics, we deciphered the Hfq-mediated sRNA-target interactome of enteropathogenic Escherichia coli (EPEC). The emerging network comprises hundreds of sRNA-mRNA pairs, including mRNAs of virulence-associated genes interacting with known sRNAs encoded within the core genome, as well as with newly found sRNAs encoded within pathogenicity islands. Some of the sRNAs affect multiple virulence genes, suggesting they function as hubs of virulence control. We further analyzed one such sRNA hub, MgrR, and one of its targets identified here, the major virulence-associated chaperon, cesT. We show that MgrR adjusts the level of EPEC cytotoxicity via regulation of CesT expression. Our results reveal an elaborate sRNA-mRNA interactome controlling the pathogenicity of EPEC and reinforce a role for sRNAs in the control of pathogen-host interaction.
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Affiliation(s)
- Sivan Pearl Mizrahi
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Netanel Elbaz
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Liron Argaman
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Yael Altuvia
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Naama Katsowich
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Yaakov Socol
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Amir Bar
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Ilan Rosenshine
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Hanah Margalit
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
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6
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Bar A, Argaman L, Altuvia Y, Margalit H. Prediction of Novel Bacterial Small RNAs From RIL-Seq RNA-RNA Interaction Data. Front Microbiol 2021; 12:635070. [PMID: 34093460 PMCID: PMC8175672 DOI: 10.3389/fmicb.2021.635070] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 04/06/2021] [Indexed: 12/27/2022] Open
Abstract
The genomic revolution and subsequent advances in large-scale genomic and transcriptomic technologies highlighted hidden genomic treasures. Among them stand out non-coding small RNAs (sRNAs), shown to play important roles in post-transcriptional regulation of gene expression in both pro- and eukaryotes. Bacterial sRNA-encoding genes were initially identified in intergenic regions, but recent evidence suggest that they can be encoded within other, well-defined, genomic elements. This notion was strongly supported by data generated by RIL-seq, a RNA-seq-based methodology we recently developed for deciphering chaperon-dependent sRNA-target networks in bacteria. Applying RIL-seq to Hfq-bound RNAs in Escherichia coli, we found that ∼64% of the detected RNA pairs involved known sRNAs, suggesting that yet unknown sRNAs may be included in the ∼36% remaining pairs. To determine the latter, we first tested and refined a set of quantitative features derived from RIL-seq data, which distinguish between Hfq-dependent sRNAs and “other RNAs”. We then incorporated these features in a machine learning-based algorithm that predicts novel sRNAs from RIL-seq data, and identified high-scoring candidates encoded in various genomic regions, mostly intergenic regions and 3′ untranslated regions, but also 5′ untranslated regions and coding sequences. Several candidates were further tested and verified by northern blot analysis as Hfq-dependent sRNAs. Our study reinforces the emerging concept that sRNAs are encoded within various genomic elements, and provides a computational framework for the detection of additional sRNAs in Hfq RIL-seq data of E. coli grown under different conditions and of other bacteria manifesting Hfq-mediated sRNA-target interactions.
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Affiliation(s)
- Amir Bar
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Liron Argaman
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yael Altuvia
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Hanah Margalit
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
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Dagan N, Elnekave E, Barda N, Bregman-Amitai O, Bar A, Orlovsky M, Bachmat E, Balicer RD. Automated opportunistic osteoporotic fracture risk assessment using computed tomography scans to aid in FRAX underutilization. Nat Med 2020; 26:77-82. [PMID: 31932801 DOI: 10.1038/s41591-019-0720-z] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Accepted: 11/26/2019] [Indexed: 12/20/2022]
Abstract
Methods for identifying patients at high risk for osteoporotic fractures, including dual-energy X-ray absorptiometry (DXA)1,2 and risk predictors like the Fracture Risk Assessment Tool (FRAX)3-6, are underutilized. We assessed the feasibility of automatic, opportunistic fracture risk evaluation based on routine abdomen or chest computed tomography (CT) scans. A CT-based predictor was created using three automatically generated bone imaging biomarkers (vertebral compression fractures (VCFs), simulated DXA T-scores and lumbar trabecular density) and CT metadata of age and sex. A cohort of 48,227 individuals (51.8% women) aged 50-90 with available CTs before 2012 (index date) were assessed for 5-year fracture risk using FRAX with no bone mineral density (BMD) input (FRAXnb) and the CT-based predictor. Predictions were compared to outcomes of major osteoporotic fractures and hip fractures during 2012-2017 (follow-up period). Compared with FRAXnb, the major osteoporotic fracture CT-based predictor presented better receiver operating characteristic area under curve (AUC), sensitivity and positive predictive value (PPV) (+1.9%, +2.4% and +0.7%, respectively). The AUC, sensitivity and PPV measures of the hip fracture CT-based predictor were noninferior to FRAXnb at a noninferiority margin of 1%. When FRAXnb inputs are not available, the initial evaluation of fracture risk can be done completely automatically based on a single abdomen or chest CT, which is often available for screening candidates7,8.
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Affiliation(s)
- Noa Dagan
- Clalit Research Institute, Clalit Health Services, Tel Aviv, Israel. .,Department of Computer Science, Ben-Gurion University, Beer Sheva, Israel. .,School of Public Health, Ben-Gurion University, Beer Sheva, Israel.
| | - Eldad Elnekave
- Department of Diagnostic Radiology, Rabin Medical Center, Beilinson Hospital, Petah Tikva, Israel.,Zebra Medical Vision, Ltd, Shefayim, Israel
| | - Noam Barda
- Clalit Research Institute, Clalit Health Services, Tel Aviv, Israel.,Department of Computer Science, Ben-Gurion University, Beer Sheva, Israel.,School of Public Health, Ben-Gurion University, Beer Sheva, Israel
| | | | - Amir Bar
- Zebra Medical Vision, Ltd, Shefayim, Israel
| | | | - Eitan Bachmat
- Department of Computer Science, Ben-Gurion University, Beer Sheva, Israel
| | - Ran D Balicer
- Clalit Research Institute, Clalit Health Services, Tel Aviv, Israel.,School of Public Health, Ben-Gurion University, Beer Sheva, Israel
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8
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Altuvia Y, Bar A, Reiss N, Karavani E, Argaman L, Margalit H. In vivo cleavage rules and target repertoire of RNase III in Escherichia coli. Nucleic Acids Res 2019; 46:10380-10394. [PMID: 30113670 PMCID: PMC6212723 DOI: 10.1093/nar/gky684] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 07/18/2018] [Indexed: 12/02/2022] Open
Abstract
Bacterial RNase III plays important roles in the processing and degradation of RNA transcripts. A major goal is to identify the cleavage targets of this endoribonuclease at a transcriptome-wide scale and delineate its in vivo cleavage rules. Here we applied to Escherichia coli grown to either exponential or stationary phase a tailored RNA-seq-based technology, which allows transcriptome-wide mapping of RNase III cleavage sites at a nucleotide resolution. Our analysis of the large-scale in vivo cleavage data substantiated the established cleavage pattern of a double cleavage in an intra-molecular stem structure, leaving 2-nt-long 3′ overhangs, and refined the base-pairing preferences in the cleavage site vicinity. Intriguingly, we observed that the two stem positions between the cleavage sites are highly base-paired, usually involving at least one G-C or C-G base pair. We present a clear distinction between intra-molecular stem structures that are RNase III substrates and intra-molecular stem structures randomly selected across the transcriptome, emphasizing the in vivo specificity of RNase III. Our study provides a comprehensive map of the cleavage sites in both intra-molecular and inter-molecular duplex substrates, providing novel insights into the involvement of RNase III in post-transcriptional regulation in the bacterial cell.
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Affiliation(s)
- Yael Altuvia
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Amir Bar
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Niv Reiss
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Ehud Karavani
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Liron Argaman
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Hanah Margalit
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
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9
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Krishnaraj A, Barrett S, Bregman-Amitai O, Cohen-Sfady M, Bar A, Chettrit D, Orlovsky M, Elnekave E. Simulating Dual-Energy X-Ray Absorptiometry in CT Using Deep-Learning Segmentation Cascade. J Am Coll Radiol 2019; 16:1473-1479. [PMID: 30982683 DOI: 10.1016/j.jacr.2019.02.033] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 01/28/2019] [Accepted: 02/09/2019] [Indexed: 10/27/2022]
Abstract
PURPOSE Osteoporosis is an underdiagnosed condition despite effective screening modalities. Dual-energy x-ray absorptiometry (DEXA) screening, although recommended in clinical guidelines, remains markedly underutilized. In contrast to DEXA, CT utilization is high and presents a valuable data source for opportunistic osteoporosis screening. The purpose of this study was to describe a method to simulate lumbar DEXA scores from routinely acquired CT studies using a machine-learning algorithm. METHODS Between January 2010 and September 2014, 610 CT studies of the abdomen and pelvis were used to develop spinal column and L1 to L4 multiclass segmentation. DEXA simulation training and validation used 1,843 pairs of CT studies accompanied by DEXA results obtained within a 6-month interval from the same individual. Machine learning-based regression was used to determine correlation between calculated grade (on the basis of vertebrae L1-L4) and DEXA t score. RESULTS Analysis of the t score equivalent, generated by the algorithm, revealed true positives in 1,144 patients, false positives in 92 patients, true negatives in 245 patients, and false negatives in 212 patients, resulting in an accuracy of 82%. Sensitivity for the detection of osteoporosis or osteopenia was 84.4% (95% confidence interval, 82.3%-86.2%), and specificity was 72.7% (95% confidence interval, 67.7%-77.2%). CONCLUSIONS The presented algorithm can identify osteoporosis and osteopenia with a high degree of accuracy (82%) and a small proportion of false positives. Efforts to cull greater information using machine-learning algorithms from pre-existing data have the potential to have a marked impact on population health efforts such as bone mineral density screening for osteoporosis, in which gaps in screening currently exist.
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Affiliation(s)
- Arun Krishnaraj
- Department of Radiology and Medical Imaging, University of Virginia, Charlottesville, Virginia.
| | - Spencer Barrett
- Department of Radiology and Medical Imaging, University of Virginia, Charlottesville, Virginia
| | | | | | - Amir Bar
- Zebra Medical Vision, Shfayim, Israel
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10
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Altuvia Y, Bar A, Reiss N, Karavani E, Argaman L, Margalit H. In vivo cleavage rules and target repertoire of RNase III in Escherichia coli. Nucleic Acids Res 2018; 46:10530-10531. [PMID: 30184218 PMCID: PMC6212792 DOI: 10.1093/nar/gky816] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Yael Altuvia
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Amir Bar
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Niv Reiss
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Ehud Karavani
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Liron Argaman
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Hanah Margalit
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
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11
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Melamed S, Peer A, Faigenbaum-Romm R, Gatt YE, Reiss N, Bar A, Altuvia Y, Argaman L, Margalit H. Global Mapping of Small RNA-Target Interactions in Bacteria. Mol Cell 2017; 63:884-97. [PMID: 27588604 PMCID: PMC5145812 DOI: 10.1016/j.molcel.2016.07.026] [Citation(s) in RCA: 253] [Impact Index Per Article: 36.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 04/25/2016] [Accepted: 07/27/2016] [Indexed: 02/07/2023]
Abstract
Small RNAs (sRNAs) associated with the RNA chaperon protein Hfq are key posttranscriptional regulators of gene expression in bacteria. Deciphering the sRNA-target interactome is an essential step toward understanding the roles of sRNAs in the cellular networks. We developed a broadly applicable methodology termed RIL-seq (RNA interaction by ligation and sequencing), which integrates experimental and computational tools for in vivo transcriptome-wide identification of interactions involving Hfq-associated sRNAs. By applying this methodology to Escherichia coli we discovered an extensive network of interactions involving RNA pairs showing sequence complementarity. We expand the ensemble of targets for known sRNAs, uncover additional Hfq-bound sRNAs encoded in various genomic regions along with their trans encoded targets, and provide insights into binding and possible cycling of RNAs on Hfq. Comparison of the sRNA interactome under various conditions has revealed changes in the sRNA repertoire as well as substantial re-wiring of the network between conditions. A widely applicable method for in vivo global mapping of small RNA interactome Substantial re-wiring of the network upon changes in cellular conditions Regulatory circuits involving two regulators derived from the same transcript sRNAs acting in trans are encoded within almost every possible genomic element
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Affiliation(s)
- Sahar Melamed
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Asaf Peer
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Raya Faigenbaum-Romm
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Yair E Gatt
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Niv Reiss
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Amir Bar
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Yael Altuvia
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel.
| | - Liron Argaman
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel.
| | - Hanah Margalit
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel.
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12
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Abstract
We study extreme-value statistics for spatially extended models exhibiting mixed-order phase transitions (MOT). These are phase transitions that exhibit features common to both first-order (discontinuity of the order parameter) and second-order (diverging correlation length) transitions. We consider here the truncated inverse distance squared Ising model, which is a prototypical model exhibiting MOT, and study analytically the extreme-value statistics of the domain lengths The lengths of the domains are identically distributed random variables except for the global constraint that their sum equals the total system size L. In addition, the number of such domains is also a fluctuating variable, and not fixed. In the paramagnetic phase, we show that the distribution of the largest domain length l_{max} converges, in the large L limit, to a Gumbel distribution. However, at the critical point (for a certain range of parameters) and in the ferromagnetic phase, we show that the fluctuations of l_{max} are governed by novel distributions, which we compute exactly. Our main analytical results are verified by numerical simulations.
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Affiliation(s)
- Amir Bar
- Department of Complex Systems, Weizmann Institute, Rehovot, Israel
| | - Satya N Majumdar
- Université Paris-Sud, CNRS, LPTMS, UMR 8626, Orsay F-91405, France
| | - Grégory Schehr
- Université Paris-Sud, CNRS, LPTMS, UMR 8626, Orsay F-91405, France
| | - David Mukamel
- Department of Complex Systems, Weizmann Institute, Rehovot, Israel
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13
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Paramanik UB, Bar A, Das D, Caroca-Canales N, Prasad R, Geibel C, Hossain Z. Valence fluctuation and magnetic ordering in EuNi2(P(1-x)Ge(x))2 single crystals. J Phys Condens Matter 2016; 28:166001. [PMID: 26988385 DOI: 10.1088/0953-8984/28/16/166001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Unusual phases and phase transitions are seen at the magnetic-nonmagnetic boundary in Ce-, Eu- and Yb-based compounds. EuNi2P2 is a very unusual valence fluctuating Eu system, because at low temperatures the Eu valence stays close to 2.5 instead of approaching an integer value. The Eu valence, and thus the magnetic property in this system, can be tuned by Ge substitution in the P site as EuNi2Ge2 is known to exhibit the antiferromagnetc (AFM) ordering of divalent Eu moments with T(N)=30K. We have grown EuNi2(P(1-x)Ge(x))2 (0.0≤ x ≤0.5)) single crystals and studied their magnetic, thermodynamic and transport properties. Increasing Ge doping to x > 0.4 results in a well-defined AFM ordered state with T(N)=12K for x = 0.5. Moreover, the reduced value of magnetic entropy for x = 0.5 at T(N) suggests the presence of valance fluctuation/the Kondo effect in this compound. Interestingly, the specific heat exhibits an enhanced Sommerfeld coefficient upon Ge doping. Subsequently, electronic structure calculations lead to a non-integral valence in EuNi2P2 but a stable divalent Eu state in EuNi2Ge2, which is in good agreement with the experimental results.
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Affiliation(s)
- U B Paramanik
- Department of Physics, Indian Institute of Technology, Kanpur 208016, India
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14
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Kokot F, Duława J, Bar A, Klin M, Grzeszczak W, Darocha Z. Water-immersion-induced alterations of atrial natriuretic peptide, plasma renin activity, aldosterone and vasopressin in diabetic patients. Contrib Nephrol 2015; 73:102-10; discussion 110-1. [PMID: 2532119 DOI: 10.1159/000417383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- F Kokot
- Department of Nephrology, Silesian School of Medicine, Katowice, Poland
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15
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Coignard P, Departe JP, Remy Neris O, Baillet A, Bar A, Drean D, Verier A, Leroux C, Belletante P, Le Guiet JL. ANSO study: evaluation in an indoor environment of a mobile assistance robotic grasping arm. Ann Phys Rehabil Med 2014; 56:621-33. [PMID: 24459695 DOI: 10.1016/j.rehab.2013.08.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
OBJECTIVE To evaluate the reliability and functional acceptability of the ‘‘Synthetic Autonomous Majordomo’’ (SAM) robotic aid system (a mobile Neobotix base equipped with a semi-automatic vision interface and a Manus robotic arm). MATERIALS AND METHODS An open, multicentre, controlled study. We included 29 tetraplegic patients (23 patients with spinal cord injuries, 3 with locked-in syndrome and 4 with other disorders; mean SD age: 37.83 13.3) and 34 control participants (mean SD age: 32.44 11.2). The reliability of the user interface was evaluated in three multi-step scenarios: selection of the room in which the object to be retrieved was located (in the presence or absence of visual control by the user), selection of the object to be retrieved, the grasping of the object itself and the robot’s return to the user with the object. A questionnaire was used to assess the robot’s user acceptability. RESULTS The SAM system was stable and reliable: both patients and control participants experienced few failures when completing the various stages of the scenarios. The graphic interface was effective for selecting and grasping the object – even in the absence of visual control. Users and carers were generally satisfied with SAM, although only a quarter of patients said that they would consider using the robot in their activities of daily living.
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16
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Abstract
We introduce and analyze an exactly soluble one-dimensional Ising model with long range interactions that exhibits a mixed-order transition, namely a phase transition in which the order parameter is discontinuous as in first order transitions while the correlation length diverges as in second order transitions. Such transitions are known to appear in a diverse classes of models that are seemingly unrelated. The model we present serves as a link between two classes of models that exhibit a mixed-order transition in one dimension, namely, spin models with a coupling constant that decays as the inverse distance squared and models of depinning transitions, thus making a step towards a unifying framework.
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Affiliation(s)
- Amir Bar
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - David Mukamel
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 7610001, Israel
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17
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Bar A, Kabakçıoğlu A, Mukamel D. Denaturation of circular DNA: supercoils and overtwist. Phys Rev E Stat Nonlin Soft Matter Phys 2012; 86:061904. [PMID: 23367973 DOI: 10.1103/physreve.86.061904] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Indexed: 06/01/2023]
Abstract
The denaturation transition of circular DNA is studied within a Poland-Scheraga-type approach, generalized to account for the fact that the total linking number (LK), which measures the number of windings of one strand around the other, is conserved. In the model the LK conservation is maintained by invoking both overtwisting and writhing (supercoiling) mechanisms. This generalizes previous studies, which considered each mechanism separately. The phase diagram of the model is analyzed as a function of the temperature and the elastic constant κ associated with the overtwisting energy for any given loop entropy exponent c. As in the case where the two mechanisms apply separately, the model exhibits no denaturation transition for c ≤ 2. For c > 2 and κ = 0 we find that the model exhibits a first-order transition. The transition becomes of higher order for any κ > 0. We also calculate the contribution of the two mechanisms separately in maintaining the conservation of the linking number and find that it is weakly dependent on the loop exponent c.
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Affiliation(s)
- Amir Bar
- Department of Physics of Complex Systems, The Weizmann Institute of Science, Rehovot 76100, Israel
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18
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Landan G, Cohen NM, Mukamel Z, Bar A, Molchadsky A, Brosh R, Horn-Saban S, Zalcenstein DA, Goldfinger N, Zundelevich A, Gal-Yam EN, Rotter V, Tanay A. Epigenetic polymorphism and the stochastic formation of differentially methylated regions in normal and cancerous tissues. Nat Genet 2012; 44:1207-14. [PMID: 23064413 DOI: 10.1038/ng.2442] [Citation(s) in RCA: 201] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Accepted: 09/20/2012] [Indexed: 12/13/2022]
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19
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Kabakçıoğlu A, Bar A, Mukamel D. Macroscopic loop formation in circular DNA denaturation. Phys Rev E Stat Nonlin Soft Matter Phys 2012; 85:051919. [PMID: 23004799 DOI: 10.1103/physreve.85.051919] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2012] [Indexed: 06/01/2023]
Abstract
The statistical mechanics of DNA denaturation under fixed linking number is qualitatively different from that of unconstrained DNA. Quantitatively different melting scenarios are reached from two alternative assumptions, namely, that the denatured loops are formed at the expense of (i) overtwist or (ii) supercoils. Recent work has shown that the supercoiling mechanism results in a picture similar to Bose-Einstein condensation where a macroscopic loop appears at T{c} and grows steadily with temperature, while the nature of the denatured phase for the overtwisting case has not been studied. By extending an earlier result, we show here that a macroscopic loop appears in the overtwisting scenario as well. We calculate its size as a function of temperature and show that the fraction of the total sum of microscopic loops decreases above T{c}, with a cusp at the critical point.
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Affiliation(s)
- Alkan Kabakçıoğlu
- Department of Physics, Koç University, Sarıyer 34450 İstanbul, Turkey
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20
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Ashkenazi I, Ohana A, Azaria B, Gelfer A, Nave C, Deutch Z, Gens I, Fadlon M, Dahan Y, Rapaport L, Kishkinov D, Bar A, Tal-Or E, Vaknin N, Blumenfeld A, Kessel B, Alfici R, Olsha O, Michaelson M. Assessment of hospital disaster plans for conventional mass casualty incidents following terrorist explosions using a live exercise based upon the real data of actual patients. Eur J Trauma Emerg Surg 2011; 38:113-7. [DOI: 10.1007/s00068-011-0154-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Accepted: 09/05/2011] [Indexed: 10/17/2022]
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21
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Abstract
The denaturation transition which takes place in circular DNA is analyzed by extending the Poland-Scheraga (PS) model to include the winding degrees of freedom. We consider the case of a homopolymer whereby the winding number of the double-stranded helix, released by a loop denaturation, is absorbed by supercoils. We find that as in the case of linear DNA, the order of the transition is determined by the loop exponent c. However the first-order transition displayed by the PS model for c>2 in linear DNA is replaced by a continuous transition with arbitrarily high order as c approaches 2, while the second-order transition found in the linear case in the regime 1<c≤2 disappears. In addition, our analysis reveals that melting under fixed linking number is a condensation transition, where the condensate is a macroscopic loop which appears above the critical temperature.
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Affiliation(s)
- Amir Bar
- Department of Physics of Complex Systems, The Weizmann Institute of Science, Rehovot 76100, Israel
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22
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Kenigsberg E, Bar A, Segal E, Tanay A. Widespread compensatory evolution conserves DNA-encoded nucleosome organization in yeast. PLoS Comput Biol 2010; 6:e1001039. [PMID: 21203484 PMCID: PMC3009600 DOI: 10.1371/journal.pcbi.1001039] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2010] [Accepted: 11/22/2010] [Indexed: 12/02/2022] Open
Abstract
Evolution maintains organismal fitness by preserving genomic information. This is widely assumed to involve conservation of specific genomic loci among species. Many genomic encodings are now recognized to integrate small contributions from multiple genomic positions into quantitative dispersed codes, but the evolutionary dynamics of such codes are still poorly understood. Here we show that in yeast, sequences that quantitatively affect nucleosome occupancy evolve under compensatory dynamics that maintain heterogeneous levels of A+T content through spatially coupled A/T-losing and A/T-gaining substitutions. Evolutionary modeling combined with data on yeast polymorphisms supports the idea that these substitution dynamics are a consequence of weak selection. This shows that compensatory evolution, so far believed to affect specific groups of epistatically linked loci like paired RNA bases, is a widespread phenomenon in the yeast genome, affecting the majority of intergenic sequences in it. The model thus derived suggests that compensation is inevitable when evolution conserves quantitative and dispersed genomic functions. Purifying selection is a major force in conserving genomic features. It pushes deleterious mutations to extinction while conserving the specific DNA sequence. Here we show that a large proportion of the yeast genome evolves under compensatory dynamics that conserve genomic properties while modifying the genomic sequence. Such compensatory evolution conserves the local G+C content of the genome, which influences nucleosome organization. Since purifying selection is too weak to eliminate every weakly deleterious mutation in nucleosome bound or unbound sequences, the local G+C content is frequently stabilized by compensatory G+C gaining and G+C losing mutations in proximal loci. Theoretical analysis shows that compensatory evolution is inevitable when natural selection is weak and the genomic feature is distributed over many loci. These results imply that sequence conservation may not always be equated with overall selection. They demonstrate that cycles of weakly deleterious substitutions followed by positive selection for corrective mutations, which were so far studied mostly in RNA coding genes, are observed broadly and profoundly affect genome evolution.
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Affiliation(s)
- Ephraim Kenigsberg
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Amir Bar
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
| | - Eran Segal
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Amos Tanay
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
- * E-mail:
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23
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Bar A, Dorfman SE, Fischer P, Hilfiker-Kleiner D, Cebotari S, Tudorache I, Suprunov M, Haverich A, Hilfiker A. The pro-angiogenic factor CCN1 enhances the re-endothelialization of biological vascularized matrices in vitro. Cardiovasc Res 2009; 85:806-13. [DOI: 10.1093/cvr/cvp370] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Poduval A, Antal Z, Lee T, Bar A, Dalmau J, Muzumdar R. Immune-mediated encephalitis and virilization in association with a mature cystic ovarian teratoma in an adolescent girl. Horm Res 2009; 72:252-6. [PMID: 19786797 DOI: 10.1159/000236087] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2008] [Accepted: 11/21/2008] [Indexed: 11/19/2022]
Abstract
BACKGROUND Mature cystic teratomas are the most common form of ovarian tumor in children and adolescents. These tumors are mostly benign and non-secreting. Virilization from an ovarian teratoma is exceptionally rare in pediatrics. Equally rare is the association of ovarian teratomas with auto-immune encephalitis. METHODS We describe the case of a 15-year-old girl with menstrual abnormalities and virilization, who had a past medical history of encephalitis of an unknown etiology 16 months prior to presentation. RESULTS Endocrine evaluation revealed an elevated serum testosterone and 17-hydroxy progesterone. A large left ovarian tumor was seen on a CT scan. Surgical excision revealed a mature cystic teratoma containing 6 liters of clear fluid with high androgen levels. Antibodies to the N-methyl-D-aspartate receptor of the hippocampus were detected in pre-operatively archived serum, but undetectable 6 months postoperatively. Immunohistochemistry studies on the tumor sections revealed that the antibodies in the patient's serum reacted with areas of the tumor expressing the N-methyl-D-aspartate receptor. Postoperatively, the patient's menstrual cycles became regular and her behavioral problems resolved. Her testosterone levels fell precipitously as well. CONCLUSION Both virilizing mature cystic teratomas and teratoma-associated encephalitis are extremely rare in the pediatric population. We report on the first instance of these 2 rare entities occurring in the same patient.
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Affiliation(s)
- A Poduval
- Division of Pediatric Endocrinology, Children's Hospital at Montefiore, Bronx, New York, USA.
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25
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Abstract
The dynamics of loops at the DNA denaturation transition is studied. A scaling argument is used to evaluate the asymptotic behavior of the autocorrelation function of the state of complementary bases (either open or closed). The long-time asymptotic behavior of the autocorrelation function is expressed in terms of the entropy exponent, c, of a loop. The validity of the scaling argument is tested using a microscopic model of an isolated loop and a toy model of interacting loops. This suggests a method for measuring the entropy exponent using single-molecule experiments such as fluorescence correlation spectroscopy.
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Affiliation(s)
- A Bar
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
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26
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Abstract
AIM To evaluate the effects of nasal respiratory support on physiologic parameters and comfort of premature infants, when compared to spontaneous breathing without nasal respiratory support. METHODS This was a prospective, randomized, controlled, cross-over clinical study. Infants were enrolled into the study when in 'stable' condition (when discontinuation of nasal respiratory support was considered appropriate). Infants were randomized to receive first 3 h of nasal respiratory support (nasal continuous positive airway pressure or nasal intermittent mandatory ventilation) or to spontaneous breathing, and then were crossed-over to the other assignment. Each infant served as his own control. RESULTS Fifty-four infants were included in the study (birth-weight: 1528 +/- 545 g; gestational age: 30.5 +/- 2.7 weeks). Average values of systolic, diastolic and mean blood pressure and discomfort score were significantly higher while respiratory rate was significantly slower on nasal respiratory support compared to spontaneous breathing. Heart rate was comparable on both modes. CONCLUSIONS Nasal respiratory support in 'stable' premature infants is associated with increased blood pressure and increased discomfort, despite a decreased respiratory rate. The clinical importance of these effects is modest. Medical teams should consider these effects and balance its need with its adverse effects according to the clinical condition.
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Affiliation(s)
- A Kugelman
- Department of Neonatology, Bnai Zion Medical Center, The B. Rappaport Faculty of Medicine, Technion, Haifa, Israel.
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Bar A, Srugo I, Amirav I, Tzverling C, Naftali G, Kugelman A. Inhaled furosemide in hospitalized infants with viral bronchiolitis: a randomized, double-blind, placebo-controlled pilot study. Pediatr Pulmonol 2008; 43:261-7. [PMID: 18214942 DOI: 10.1002/ppul.20765] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
OBJECTIVE To evaluate the short and long-term clinical effects and the treatment-feasibility of inhaled-furosemide (IF) as compared with placebo via hood in hospitalized infants with viral-bronchiolitis (VB). STUDY-DESIGN A randomized, double-blind, placebo-controlled pilot-study was performed in previously healthy infants (0-12 months). Enrolled infants were randomized to receive either IF (2 mg/kg), or placebo nebulized by hood three times daily throughout the hospitalization. Clinical assessment (respiratory distress assessment instrument [RDAI]) was performed before, 30 and 60 min after the 1st daily inhalation. The short-term effects were evaluated by the RDAI, respiratory assessment change score (RACS) and oxygen requirement and the long-term effects by time to be weaned off oxygen, time to full enteral feeding, length of stay, and "ready to discharge" time. RESULTS Both groups (16 infants each) had comparable characteristics at study entry. Mean (+/-SD) age was 72 +/- 43 days, and 29/32 infants were RSV positive. Oxygen requirement (FiO(2)) decreased significantly at 30 min post-inhalation (30 +/- 9.2% to 26 +/- 7.1%, P < 0.05) only in the IF group. RACSs and long-term effects of both groups were comparable. Analysis of IF particles generated by the hood-nebulizer demonstrated that 36% and 49% of the particles were <3 and 5 microm, respectively. No side effects were observed during IF treatment. CONCLUSION Based on our pilot study, IF has no significant clinical effects in hospitalized infants with VB. IF via hood seems to be feasible and safe.
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Affiliation(s)
- Amir Bar
- Department of Pediatrics, Bnai Zion Medical Center, The Bruce Rappaport Faculty of Medicine, Haifa, Israel
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28
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Bar A, Riskin A, Iancu T, Manov I, Arad A, Shaoul R. A newborn infant with protracted diarrhea and metabolic acidosis. J Pediatr 2007; 150:198-201. [PMID: 17236902 DOI: 10.1016/j.jpeds.2006.11.041] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2006] [Revised: 09/16/2006] [Accepted: 11/15/2006] [Indexed: 11/25/2022]
Affiliation(s)
- Amir Bar
- Department of Pediatrics, Bnai Zion Medical Center, Haifa, Israel
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29
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Abstract
The dynamics of a loop in DNA molecules at the denaturation transition is studied by scaling arguments and numerical simulations. The autocorrelation function of the state of complementary bases (either closed or open) is calculated. The long-time decay of the autocorrelation function is expressed in terms of the loop exponent c both for homopolymers and heteropolymers. This suggests an experimental method for measuring the exponent c using florescence correlation spectroscopy.
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Affiliation(s)
- A Bar
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel 76100
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30
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Abstract
1. The effect of age on ovarian function was studied in 245-, 350-, 500-, 700- and 800-d-old Lohmann hens. The effect of three different methods for moult induction on ovarian function and corticosterone concentration was studied in 500-d-old hens. 2. No significant reductions in ovarian weight or in number of follicles before the age of 700 d were found. The ability to produce progesterone and oestradiol-17beta was unchanged up to the age of 700 d and the circadian secretion of these two steroids was identical in young (225 d) and old hens (600 d). 3. The effects of induced moulting by feed withdrawal (FW) and a high Zn (HZn) diet on body weight and ovarian function were very similar; those of a moderate Zn with low Ca (MZn/LCa) diet were smaller. 4. The first significant effect of moulting was a decrease in oestradiol-17beta plasma concentration (d 2). Plasma progesterone decreased more gradually than oestradiol-17beta, and reached a nadir on d 6 in FW- and HZn-treated hens and on d 9 in MZn/LCa-treated ones. 5. Hens treated with either FW or the MZn/LCa, but not those with the HZn diet, showed a very sharp rise in corticosterone concentration on d 2 of treatment. Thus the MZn/LCa diet was less efficient than the other treatments in induction of ovarian involution, but had a similar effect on stress induction, as indicated by increases in plasma corticosterone.
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Affiliation(s)
- R Braw-Tal
- Institute of Animal Science, Agricultural Research Organization, The Volcani Center, Bet Dagan, Israel.
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Abstract
OBJECTIVES AND BACKGROUND Arousals from sleep are associated with increased sympathetic activation and therefore with peripheral vasoconstriction. Sleep fragmentation in the form of multiple arousals is associated with daytime somnolence and cognitive impairment; however, manual scoring of arousal is time consuming and problematic due to relatively high inter-scorer variability. We have recently shown that automated analysis of in-lab recorded peripheral arterial tone (PAT) signal and the pulse rate derived from it can accurately assess arousals from sleep as defined by the American Academy of Sleep Medicine (AASM). In the current study we sought to extend these findings to the Watch_PAT100 (WP100), an ambulatory device measuring PAT, oximetry and actigraphy. METHODS Sixty-eight subjects (61 patients referred to the sleep lab with suspected obstructive sleep apnea and seven healthy volunteers, mean age 46.3+/-14.2 years) underwent a whole night polysomnography (PSG) with simultaneous recording of PAT signal by the ambulatory WP100 device. The PSG recordings were blindly manually analyzed for arousals based on AASM criteria, while PAT was scored automatically based on the algorithm developed previously. RESULTS There was a significant correlation between AASM arousals derived from the PSG and PAT autonomic arousals derived from the WP100 (R=0.87, P<0.001), with a good agreement across a wide range of values. The sensitivity and specificity of PAT in detecting patients with at least 20 arousals per hour of sleep were 0.80 and 0.79, respectively, with a receiver operating characteristic curve having an area under the curve of 0.87. CONCLUSIONS We conclude that automatic analysis of peripheral arterial tonometry signal derived from the ambulatory device Watch_PAT100 can accurately identify arousals from sleep in a simple and time saving fashion.
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Affiliation(s)
- Giora Pillar
- Sleep Laboratory, Bruce Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel.
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Abstract
OBJECTIVE To compare the effect of adenotonsillectomy on rapid eye movement (REM)- and non-REM-related respiratory and sleep architecture characteristics in children with obstructive sleep apnea syndrome (OSAS). STUDY DESIGN This prospective study evaluated 36 children (median age, 6.9 years; range, 1.8 to 12.6 years) with OSAS using polysomnography before and a few months after adenotonsillectomy. Primary outcomes included the number of obstructive apnea and hypopnea and arousals per hour of sleep. RESULTS At 4.6 months (range, 1 to 16 months) after adenotonsillectomy, there was a significant improvement of all respiratory parameters. The median respiratory disturbance index (RDI) decreased from 4.1/h (range, 0 to 85/h) to 0.9/h (range, 0 to 13/h) after adenotonsillectomy (p < 0.0001). The median non-REM RDI decreased from 3.0/h (range, 0 to 89/h) to 0.4/h (range, 0 to 13/h) [p < 0.001] as compared with REM RDI, which decreased from 7.8/h (range, 0 to 69/h) to 2.3/h (range, 0 to 54/h) after adenotonsillectomy (p < 0.01). Median arousal index decreased following adenotonsillectomy from 17.5/h (range, 7 to 57/h) to 14.0/h (range, 6 to 47/h) [p < 0.03]. CONCLUSIONS Adenotonsillectomy resulted in a greater improvement in non-REM RDI as compared with REM-RDI, and a decrease in the number of arousals.
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Affiliation(s)
- Asher Tal
- Department of Pediatrics B, Soroka Medical Center, Ben-Gurion University of the Negev, PO Box 151, Beer-Sheva, Israel.
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33
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Abstract
1. A series of 5 trials was conducted with Cobb chickens in order to determine the effect of 25-hydroxycholecalciferol (25OHD3) on their performance and bone development under adequate Calcium (Ca) and Phosphorus (P) supplementation, and under moderate dietary restriction of Ca and P. Formulated beadlets of 25OHD3, trade name HY-D (IsoGen, Naperville, IL, USA) were used as the 25OHD3 source. 2. Five to 10 microg of cholecalciferol (vitamin D3) or 25OHD3/kg diet were sufficient to ensure normal body weight (BW) and bone ash in chickens under continuous lighting. The two materials had similar effects on BW and bone ash. 3. In one out of the three experiments, 25OHD3 increased BW and BW gain, while in the others it had a similar effect to that of vitamin D3, or even a slight negative effect in a trial conducted on the floor, in which the diets were supplemented with the D sources at 75 microg/kg. The effects of both D sources on bone ash and on the severity or frequency of tibial dischondroplasia were similar. 4. 25OHD3 restrained the effect of moderate dietary P restriction, but not of Ca restriction, on BW gain and bone ash in 22-d-old chickens. This effect could not be explained by an higher P bioavailability in the 25OHD3-fed chickens.
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Affiliation(s)
- A Bar
- Institute of Animal Science, Agricultural Research Organization, the Volcani Center, Bet Dagan, Israel.
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34
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Abstract
Shortening daylight (to 10.5 to 11 h/d) slightly reduced the rest period (the interval between last egg and first clutch), whereas feeding a low-protein diet during the 22-d period following 8 d of feed withdrawal (FW) (recovery period) markedly extended it. Feed withdrawal accompanied by a short-daylight regime and a long recovery period led to the best postmolt production. However, production per hen housed during the whole experimental period was only slightly increased. Thus, a long rest period may mask the positive effects of short daylight and recovery diet. At least 140 to 170 d were needed to enable the molted hens to compensate for the loss of eggs during the rest period. Therefore, under certain economic conditions, rearing of nonmolting hens for 640 to 700 d should be an economic consideration. Ten days of feeding of a diet containing 0.06% nicarbazin (NICR) arrested egg production and caused a 22-d rest period but not a typical molt. Few variables of production or shell quality were improved by NICR but to a lesser extent than by FW or Zn feeding. Five days of feeding on a high-Zn diet (20 g Zn/kg; HZn) improved postmolt performances similarly to FW. Ten days of feeding on a modest-Zn (2.8 g Zn/kg), low-Ca, and low-P diet (Zn-CaP) affected postmolt performances inconsistently. In one out of two trials (trial 2), the effects of Zn-CaP were similar to those of FW or HZn; in the other (trial 3), the effects were less pronounced, more time was required for egg arrest, and more eggs were laid occasionally during the rest period. In trial 2, only the Zn-CaP diet was accompanied by short daylight. In both trials, feed intake during the induction period was only slightly reduced. Zn feeding increased the yolk Zn content slightly in eggs laid during the induction period and at the onset of production. In trial 2, only Zn-CaP markedly increased yolk Zn of eggs laid during the first 5 d of production.
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Affiliation(s)
- A Bar
- Institute of Animal Science, Agricultural Research Organization, The Volcani Center, Bet Dagan 50250, Israel.
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35
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Bar A, Pillar G, Dvir I, Sheffy J, Schnall RP, Lavie P. Evaluation of a portable device based on peripheral arterial tone for unattended home sleep studies. Chest 2003; 123:695-703. [PMID: 12628865 DOI: 10.1378/chest.123.3.695] [Citation(s) in RCA: 142] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
BACKGROUND Diagnosis of obstructive sleep apnea syndrome (OSAS) by ambulatory systems is a growing practice in view of the large number of patients awaiting correct diagnosis. The Watch PAT100 (WP100) [Itamar Medical; Caesarea, Israel] is a portable device based on the peripheral arterial tone (PAT) signal, and is designed for unattended home sleep studies. OBJECTIVES To evaluate the efficacy, reliability, and reproducibility of the WP100 device for the diagnosis of OSAS as compared to in-laboratory, standard polysomnographic-based manual scoring. DESIGN AND METHODS One hundred two subjects (78 men; 69 patients with OSAS and 33 normal volunteers; mean +/- SD age, 41.4 +/- 15.2 years; body mass index, 26.8 +/- 5.5) underwent in-laboratory full polysomnography simultaneously with WP100 recording. Fourteen subjects also underwent two additional unattended home sleep studies with the WP100 alone. The polysomnography recordings were blindly scored for apnea/hypopnea according to the American Academy of Sleep Medicine criteria (1999), and the polysomnography respiratory disturbance index (RDI) [PSG-RDI] was calculated. The WP100 data were analyzed automatically for the PAT RDI (PRDI) by a proprietary algorithm that was previously developed on an independent group of subjects. RESULTS Across a wide range of RDI levels, the PRDI was highly correlated with the PSG-RDI (r = 0.88, p < 0.0001), with an area under the receiver operating characteristic curve of 0.82 and 0.87 for thresholds of 10 events per hour and 20 events per hour, respectively. The PRDI scores were also highly reproducible, showing high correlation between home and in-laboratory sleep studies (r = 0.89, p < 0.001). CONCLUSION The WP100 may offer an accurate, robust, and reliable ambulatory method for the detection of OSAS, with minimal patient discomfort.
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Affiliation(s)
- Amir Bar
- Itamar Medical Ltd., Caesarea, Israel
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36
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Pillar G, Bar A, Shlitner A, Schnall R, Shefy J, Lavie P. Autonomic Arousal Index: an Automated Detection Based on Peripheral Arterial Tonometry. Sleep 2002. [DOI: 10.1093/sleep/25.5.541] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Pillar G, Bar A, Shlitner A, Schnall R, Shefy J, Lavie P. Autonomic arousal index: an automated detection based on peripheral arterial tonometry. Sleep 2002; 25:543-9. [PMID: 12150321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/26/2023] Open
Abstract
Arousals from sleep are associated with increased sympathetic activation and are therefore associated with peripheral vasoconstriction. We hypothesized that digital vasoconstrictions as measured by peripheral arterial tonometery (PAT), combined with an increase in pulse rate, would accurately reflect arousals from sleep, and can provide an autonomic arousal index (AAI). Based on a previously studied group of 40 sleep apnea patients simultaneously recorded by both polysomnography (PSG) and PAT systems, an automated algorithm using the PAT signal (and pulse rate derived from it) was developed for detection of arousals from sleep. This was further validated in a separate group of 96 subjects (85 patients referred with suspected obstructive sleep apnea and 11 healthy volunteers mean age 46.2+/-14.4 years, BMI 28.5+/-5.4 kg/m2). All underwent a whole night PSG with simultaneous PAT recording. The PSG recordings were blindly manually analyzed for arousals based on American Academy of Sleep Medicine (AASM) criteria, while PAT was scored automatically. There was a significant correlation between PSG and PAT arousals (R=0.82, p<0.0001) with a good agreement across a wide range of values, with a ROC curve having an area under the curve (AUC) of 0.88. We conclude that automated analysis of the peripheral arterial tonometry signal can detect EEG arousals from sleep, in a relatively quick and reproducible fashion.
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Affiliation(s)
- Giora Pillar
- Sleep Laboratory, Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa
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38
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Abstract
1. A series of 5 trials was conducted with 401- to 650-d-old Lohmann, Yafa (local breed with brown eggshells) and Yarkon (local breed with white eggshells) hens fed for 56 to 84 d with diets containing 25 to 50 g/kg calcium (Ca) and 4.5 to 7.6 g/kg phosphorus (P). 2. Increasing dietary Ca from 24-25 to 36-40 g/kg improved egg production, shell weight (SW) and shell thickness (ST), and decreased mortality. 3. Increasing dietary Ca to 48 to 50 g/kg did not affect egg production but increased SW and/or ST. In one out of the 4 trials, this effect was not significant, most likely because of the high shell quality of the eggs from the Yafa hens used for this trial. 4. Dietary P content of 4.5 g/kg (1.0 g/kg added inorganic P) appears to be sufficient for maintaining egg production and shell quality in aged laying hen given 36 to 40 g/kg Ca. 5. Increasing dietary Ca above 40 g/kg may require a higher dietary P content.
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Affiliation(s)
- A Bar
- Institute of Animal Science, Agricultural Research Organization, the Volcani Center, Bet Dagan, Israel.
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39
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Abstract
Molt was induced at the 431, 501, or 571 d, in Lohmann (L) and Hy-Line W-77 (H) hens, by 8 or 14 d, respectively, of feed withdrawal followed by a rest period of 16 d. Induced molt resulted in increases in egg production, numbers of intact eggs, egg mass per housed or surviving hen, and shell quality and in decreases in egg breakage (not significant), mortality, and culling. Egg weight was only slightly affected by molt, and the EW of hens induced to molt at 431 or 501 d of age were slightly lower than those of the unmolted hens or of those induced to molt at 571 d. Both strains reacted similarly to molt, although the L hens responded better, and expressed their responses more intensively when induced to molt earlier (431 d). This finding suggests that although different breeds have some effects of molt in common, molt protocols should be finely tuned for each breed. Total intact egg production and egg mass of the molted hens became higher than those of the unmolted hens at 650 to 728 d, which suggests that no benefit would be achieved by rearing molted hens for less than 700 to 730 d.
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Affiliation(s)
- A Bar
- Institute of Animal Science, Agricultural Research Organization, the Volcani Center, Bet Dagan, Israel.
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40
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Abstract
1. The effects of relative humidity (rh=40% to 70%) at high ambient temperature (Ta) on the performance of laying hens at different ages (8 to 10 months, Trial 1; and 16 to 18 months, Trial 2) was evaluated. Laying hens were exposed to 25 degrees C (control) for 3 weeks and thereafter acclimated for 1 week to 35 degrees C and 4 different rh. 2. Body weight declined significantly in young and older hens exposed to 60% or 70% and 70% rh, respectively: Food intake declined with increasing Ta, except in the case of older hens exposed to 60% rh, for which it remained relatively constant. Water consumption, however, increased with increasing Ta but the increase was significant in young hens exposed to 70% rh only. 3. Egg production was not affected by the changes in Ta. However, a decrease in egg production was observed in older hens exposed to 60% rh. 4. Egg weight (EW), shell weight (SW) and shell thickness (ST) were significantly reduced by exposure to elevated Ta, whereas % breakage significantly increased. In young hens, a response to rh was exhibited in ST which was significantly higher in hens exposed to the low rh (40% to 45%) than in those exposed to the highest rh (70% to 75%). 5. It can be concluded that Ta is the main environmental factor affecting young and older laying hens while the effect of rh is minor.
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Affiliation(s)
- S Yahav
- Instute of Animal Science, ARO, Bet Dagan, Israel.
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41
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Bar A, Tarasiuk A, Segev Y, Phillip M, Tal A. The effect of adenotonsillectomy on serum insulin-like growth factor-I and growth in children with obstructive sleep apnea syndrome. J Pediatr 1999; 135:76-80. [PMID: 10393608 DOI: 10.1016/s0022-3476(99)70331-8] [Citation(s) in RCA: 174] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
OBJECTIVE Obstructive sleep apnea syndrome (OSAS) in children is frequently associated with growth interruption. The objective of this study was to evaluate the effect of OSAS and adenotonsillectomy on the insulin-like growth factor-I (IGF-I) axis in children. STUDY DESIGN Thirteen prepubertal children (mean age, 6.0 +/- 2.8 years) were studied before and after adenotonsillectomy (T&A). Weight, height, overnight polysomnography, and IGF-I and IGF-binding protein-3 levels were evaluated before and 3 to 12 months after T&A. The children's weights and heights were monitored for 18 months. RESULTS The respiratory disturbance index improved from 7.8 +/- 9.1 events/h to 1.0 +/- 2.1 events/h after T&A (P <.02). Slow-wave sleep increased from 29.1% +/- 7.2% to 34.6% +/- 9.8% after T&A (P <.02). The weight standard deviation score increased from 0.86 +/- 1 to 1. 24 +/- 0.9, 18 months after T&A (P <.01). Serum IGF-I levels increased from 146.3 +/- 76.2 ng/mL before T&A to 210.3 +/- 112.5 ng/mL after surgery (P <.01), but IGF-binding protein-3 levels did not change significantly. CONCLUSION The respiratory improvement after T&A in children with OSAS is associated with a significant increase in serum IGF-I levels and weight. We conclude that the IGF-I axis is affected in children with OSAS.
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Affiliation(s)
- A Bar
- Department of Pediatrics, Soroka Medical Center of Kupat Holim Klalit, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
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42
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Bar A, Vax E, Striem S. Relationships among age, eggshell thickness and vitamin D metabolism and its expression in the laying hen. Comp Biochem Physiol A Mol Integr Physiol 1999; 123:147-54. [PMID: 10425734 DOI: 10.1016/s1095-6433(99)00039-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hens forming uncalcified shells synthesized less 1,25-hydroxycholecalciferol (1,25(OH)2D3) and less duodenal and eggshell gland (ESG) calbindin than normal laying hens. Hens forming thin shells had lower intestinal and ESG calbindin and its mRNA. Reducing ESG calcium (Ca2+) transport by the carbonic anhydrase inhibitor acetazolamide, but not by dietary Ca2+ restriction, reduced ESG calbindin and its mRNA. Two sub-populations of hens characterized by shell thickness (ST) maintained this characteristic throughout the whole production period. The differences between the two sub-populations increased with age. In old laying hens, the two sub-populations responded differently to dietary Ca2+ restriction and to exogenous 1,25(OH)2D3. Those forming a thin shell responded to 1,25(OH)2D3 by a significant improvement in ST. The results suggest that: (a) the mechanism responsible for Ca2+ transport to the egg shell consists of a vitamin D-dependent absorption of Ca2+ and a multi-factor-dependent transfer of Ca2+ to the shell; (b) both steps are, most likely, calbindin-mediated; however, the induction of calbindin gene expression in the ESG is predominantly calcium-dependent; and (c) the apparent defect in vitamin D metabolism or its expression in old hens is typical of, or even exclusive, to thin-shell-forming hens.
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Affiliation(s)
- A Bar
- Institute of Animal Science, Agricultural Research Organization, Volcani Center, Bet Dagan, Israel.
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43
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Lavelin I, Yarden N, Ben-Bassat S, Bar A, Pines M. Regulation of osteopontin gene expression during egg shell formation in the laying hen by mechanical strain. Matrix Biol 1998; 17:615-23. [PMID: 9923654 DOI: 10.1016/s0945-053x(98)90112-3] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The aim of this study is to evaluate the regulation of the osteopontin (OPN) gene expression by non-hormonal stimuli, such as calcium flux and mechanical strain during the daily egg cycle in the oviduct of the laying hen. After the egg enters the eggshell gland (ESG), the OPN gene is expressed by the epithelium cells in two waves: first by the basal cells and only then by the apical cells of the epithelium. A reduction in OPN gene expression was observed 1 h prior to laying. The calbindin gene, which marks the onset of calcification, was found to be expressed in the glandular epithelium starting 2 h after OPN gene expression. In addition, the formation of soft shells was accompanied by a reduction in calbindin, but not in OPN, gene expression. The application of a mechanical strain comparable to that induced by an egg led to induction of OPN gene expression at a normally quiescent phase in the cyclical expression of this gene. The induction of the gene was time- and strain-dependent and temporally similar to that induced by the entry of the egg into the ESG. In contrast, the calbindin gene was not affected by mechanical strain. The ESG of the laying hen provides a system to study the effect of a mechanical strain on matrix protein production in vivo, in a relevant physiological setting. The finding suggests that, in contrast to calbindin, OPN gene expression is not regulated by calcium flux but rather by the mechanical strain imposed by the resident egg.
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Affiliation(s)
- I Lavelin
- Institute of Animal Science, Agricultural Research Organization, The Volcani Center, Bet Dagan, Israel
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44
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Bar A, Vax E, Striem S. Effects of age at onset of production, light regime and dietary calcium on performance, eggshell traits, duodenal calbindin and cholecalciferol metabolism. Br Poult Sci 1998; 39:282-90. [PMID: 9649885 DOI: 10.1080/00071669889268] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
1. Rate of production and shell thickness (ST) decreased, while body weight (BW), egg weight (EW) and percentage breakage increased progressively with age. Shell weight (SW) increased until 8 to 13 months of age and then decreased. 2. Early onset of production resulted in lower BW and EW at the onset of production, and lower pooled averages of BW, EW, SW and ST, as compared with late or medial onset of production. In 4 out of 5 trials, early onset did not result in the production of more eggs during the laying period. 3. Early onset of production is associated with physiological Ca deficiency as indicated by increases in kidney-1-hydroxylase and duodenal calbindin in early layers as compared with late layers. Early layers exhibited a more severe reduction in shell quality as the result of Ca deficiency as compared with late layers. 4. Feeding pullets with a prelaying diet containing 3.9% Ca did not affect unequivocally the performance or shell quality during the whole productive period, whether the birds started to lay early or late. The dietary treatment did not cause renal damage, as indicated by morphological examination and by plasma calcium and uric acid concentration.
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Affiliation(s)
- A Bar
- Institute of Animal Science, Volcani Center, Bet Dagan, Israel
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45
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Waszczuk J, Duława J, Kokot F, Bar A. [Does a relationship exist between urinary excretion of Tamm-Horsfall protein and electrolytes in patients with diabetes type I and II without diabetic nephropathy?]. Pol Arch Med Wewn 1997; 98:111-116. [PMID: 9508663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Studies were performed in 22 patients with diabetes mellitus type I, in 19 patients with diabetes type II, and in 15 healthy subjects. In all subjects the following parameters were assessed: creatinine clearance and 24 h urinary excretion of THP, albumin, sodium, potassium, and calcium. All studies were performed twice: first after 3 days on a normal sodium diet and subsequently after 3 days of sodium restriction (30-40 mmol Na/24 h). Urinary excretion of sodium was significantly lower in patients with diabetes mellitus type II than in healthy subjects. In patients with diabetes mellitus type I urinary excretion of sodium was significantly lower than in controls only after sodium restriction. No significant correlation was found between urinary excretion of THP and electrolytes. Results obtained in this study do not confirm presence of any relationship between urinary excretion THP and electrolytes.
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Affiliation(s)
- J Waszczuk
- Katedry i Kliniki Nefrologii Sl., Katowicach
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46
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Bockenek S, Duława J, Kokot F, Kokot M, Bar A. [The activity of renal glomeruli and tubules during uncomplicated pregnancy: influence of delivery on urinary excretion of albumin, beta 2-microglobulin and Tamm-Horsfall protein]. Ginekol Pol 1997; 68:226-31. [PMID: 9480237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
There were examined the influence the various types of delivery (spontaneous, oxytocin induced, cesarean section) on the value of albumin's (marker of glomerular activity), beta 2-microglobulin's (beta 2-M) (marker of activity proximal renal tubule) and Tamm-Horsfall's protein (pTH) (as a marker of activity distal's renal tubule) excretion in 50 healthy pregnant women without clinical symptoms of nephropathy. There were also estimated creating concentration in plasma and value of creating excretion in urine before and after delivery in every women. There were stated a little increase of albumin and beta 2-microglobulin but proper excretion (pTH) in urine in every group of pregnant women. There were estimated increase of albumin and pTH excretion in urine after spontaneous delivery, oxytocin inducted or cesarean section, particularly in women after cesarean section. The type of delivery had not an effect on the beta 2-microglobulin's urine excretion. The results of conducted researches suggest occurrence of functional changes in both renal glomeruli and tubules in physiologic pregnancy. The type of delivery reveals differentiated in quantity's respect the influence on albumin's and pTH excretion, but it has not an effect on beta 2-microglobulin's urine excretion.
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47
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Hurwitz S, Bar A. ABSORPTION OF CALCIUM AND PHOSPHORUS ALONG THE GASTROINTESTINAL TRACT OF THE LAYING FOWL AS INFLUENCED BY DIETARY CALCIUM AND EGG SHELL FORMATION. J Nutr 1996; 86:433-8. [PMID: 14324451 DOI: 10.1093/jn/86.4.433] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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48
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Abstract
Acute and chronic changes in calbindin (Mr 28,000) mRNA and calbindin concentrations were determined to assess the roles of steroid hormones in calbindin mRNA and calbindin synthesis in the eggshell gland (ESG). The results support an earlier suggestion that calbindin gene expression in the ESG is associated with Ca2+ flux through the ESG. The evidence includes wide oscillation of the mRNA during the diurnal egg cycle, in close temporal association with egg shell calcification. Progesterone (single im injection of 1 mg/kg body weight, BW) prolonged the period of egg formation and reduced the rate of Ca2+ transport and the concentration of calbindin mRNA in the ESG. Dexamethasone (single im injection of 5 mg/kg BW) prolonged the period of egg formation, increased shell Ca2+, and reduced calbindin mRNA in the ESG and intestine. Testosterone (single im injection of 2 mg/kg BW) did not affect calbindin mRNA synthesis in the ESG. The effects of estradiol on the synthesis of calbindin mRNA in the ESG of sexually immature or laying birds were minor, while it affected plasma Ca in the same birds. The antiestrogen Tamoxifen (60 mg/kg BW, given orally) reduced plasma Ca, but did not affect the synthesis of calbindin mRNA in the ESG. The antiprogesterone RU-38486 (20 mg/kg BW, orally) increased shell Ca2+ but had no effect on plasma Ca or the synthesis of calbindin mRNA. It appears that estrogens alone cannot account for the markedly elevated synthesis of calbindin mRNA in the ESG of the laying bird. The hypothesis that the regulatory mechanism for the synthesis of calbindin mRNA in the ESG may involve a stimulator(s), associated with the onset of production, and an oscillating depressor(s) is supported and both appear to be closely linked to the reproductive cycle. The specific in vivo effect of progesterone on calbindin mRNA in the ESG, together with its already known changes during the ovulatory cycle in birds, supports the idea that it is a depressor.
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Affiliation(s)
- A Bar
- Institute of Animal Science, Agricultural Research Organization, The Volcani Center, Bet Dagan, Israel
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49
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Abstract
Expression of the osteopontin (OPN) gene in the oviduct of the laying hen was studied. It was detected only in the egg shell gland (ESG), where massive calcification occurs. No OPN gene expression was detected in any other part of the oviduct, such as the magnum and isthmus. The OPN gene was expressed in a circadian fashion during the daily egg cycle only during the period of egg shell calcification. No OPN gene expression was detected in the ESG of a pre-laying hen before the onset of reproduction, or after forced removal of the egg close to its entrance into the ESG. OPN was found to be synthesized by the epithelial cells of the ESG lining the lumen. Upon synthesis, OPN is immediately secreted out of cells and accumulates in the egg shell. These findings demonstrate for the first time temporal and spatial association of OPN with egg shell calcification. OPN, which was found to be part of the organic matrix of the egg shell, may play an important role in egg shell calcification.
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Affiliation(s)
- M Pines
- Institute of Animal Science, Agricultural Research Organization, Volcani Center, Bet Dagan, Israel
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Franek E, Bar A, Kokot F, Duława J, Wiecek A, Kochańska-Dziurowicz A, Bar K, Szkodny A, Pawłowski W, Myrta J. Abnormal function of renal tubules in patients with simple renal cysts. Int Urol Nephrol 1995; 27:679-85. [PMID: 8725031 DOI: 10.1007/bf02552131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The present study aimed to assess the function of proximal and distal tubules in patients with simple renal cysts. Thirty-one patients with simple renal cysts and 10 healthy subjects were examined. Based on the cyst fluid/plasma sodium ratio, 25 cysts were found to be of proximal origin and 6 of undetermined origin. In all patients cyst fluid and plasma concentrations of beta-2-microglobulin (beta-2-MG), sodium, potassium, calcium, phosphorus and total protein were assessed. Urinary excretions of sodium, potassium, calcium, phosphorus, beta-2-MG and Tamm-Horsfall protein (THP) were also estimated. Fractional excretion of beta-2-MG was calculated. The concentrations of beta-2-MG in fluid obtained from cysts of proximal origin were significantly higher than in fluid from cysts of undetermined origin (2.26 +/- 0 36 vs. 0.65 +/- 0.13 mg/l, p = 0.0004). Concentrations of THP (6.85 +/- 1.21 vs. 3.14 +/- 1.06 micrograms/ml, p < 0.05), and potassium (4.39 +/- 0.07 vs. 3.13 +/- 0.44 mmol/l, p < 0.05) were also higher in fluid from proximal cysts than in fluid from cysts of undetermined origin. Plasma beta-2-MG concentration was significantly higher in patients with proximal and undetermined cysts than in the control group (4.35 +/- 0.34 and 4.11 +/- 0.74 vs. 1.89 +/- 0.1 mg/l, p < 0.001). Urinary beta-2-MG excretion was also significantly higher in both groups of patients than in healthy subjects (474.8 +/- 165.9 and 346 +/- 94 vs. 100.2 +/- 19.6 micrograms/24 h, p < 0.05). Urinary THP excretion was significantly higher in patients with proximal cysts than in healthy subjects (31.0 +/- 5.1 vs. 16.3 +/- 2.5 mg/24 h, p < 0.05). From the results obtained in this study it seems that patients with simple renal cysts of proximal origin are characterized by abnormal tubular handling of beta-2-MG, and calcium and THP excretion. Thus, in patients with proximal cysts presence of a latent renal tubulopathy seems to be likely.
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Affiliation(s)
- E Franek
- Department of Nephrology, Silesian University of Medicine, Katowice, Poland
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