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Article ; Online: rnaCrosslinkOO: An Object-Oriented R Package for the Analysis of RNA Structural Data Generated by RNA Crosslinking Experiments.

Price, Jonathan L / Ziv, Omer / Pinckert, Malte L / Lim, Andrew / Miska, Eric A

2024

Abstract: Summary: RNA (Ribonucleic Acid) molecules have secondary and tertiary structures in vivo which play a crucial role in cellular processes such as the regulation of gene expression, RNA processing and localisation. The ability to investigate these ... ...

Abstract	Summary: RNA (Ribonucleic Acid) molecules have secondary and tertiary structures in vivo which play a crucial role in cellular processes such as the regulation of gene expression, RNA processing and localisation. The ability to investigate these structures will enhance our understanding of their function and contribute to the diagnosis and treatment of diseases caused by RNA dysregulation. However, there are no mature pipelines or packages for processing and analysing complex in vivo RNA structural data. Here, we present rnaCrosslinkOO (RNA Crosslink Object-Oriented), a novel software package for the comprehensive analysis of data derived from the COMRADES (Crosslinking of Matched RNA and Deep Sequencing) method. rnaCrosslinkOO offers a comprehensive pipeline from raw sequencing reads to the identification and comparison of RNA structural features. It includes read processing and alignment, clustering of duplexes, data exploration, folding and comparisons of RNA structures. rnaCrosslinkOO also enables comparisons between conditions, the identification of inter-RNA interactions, and the incorporation of reactivity data to improve structure prediction. Availability and implementation: rnaCrosslinkOO is freely available to non-commercial users and implemented in R, with the source code and documentation accessible at [https://CRAN.R-project.org/package=rnaCrosslinkOO]. The software is supported on Linux, macOS, and Windows platforms.
Language	English
Publishing date	2024-04-10
Publishing country	England
Document type	Journal Article
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btae193
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Article: Effects of Agronomic Practices on the Severity of Sweet Basil Downy Mildew (

Omer, Chen / Nisan, Ziv / Rav-David, Dalia / Elad, Yigal

Plants (Basel, Switzerland)

2021 Volume 10, Issue 5

Abstract: Downy mildew (caused ... ...

Abstract	Downy mildew (caused by
Language	English
Publishing date	2021-04-30
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2704341-1
ISSN	2223-7747
ISSN	2223-7747
DOI	10.3390/plants10050907
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Article ; Online: Leukocytosis and C-Reactive Protein Levels as Indicators of Infection in Children With Diabetic Ketoacidosis.

Hamtzany, Omer / Weiser, Giora / Heiman, Eyal / Avnon-Ziv, Carmit / Auerbauch, Adi / Levy-Khademi, Floris

Pediatric emergency care

2023 Volume 39, Issue 11, Page(s) 828–831

Abstract: Background: Diabetic ketoacidosis (DKA) is one of the serious complications of type 1 diabetes mellitus and may be aggravated by infection. Diagnosing an infection in a patient with DKA is often complicated because of the overlap of symptoms and the ... ...

Abstract	Background: Diabetic ketoacidosis (DKA) is one of the serious complications of type 1 diabetes mellitus and may be aggravated by infection. Diagnosing an infection in a patient with DKA is often complicated because of the overlap of symptoms and the presence of leukocytosis in both conditions. Reliable indicators for the diagnosis of bacterial infection in DKA may reduce unnecessary use of antibiotics and enable closer monitoring of patients at risk. Methods: This is a retrospective study. The study cohort included 180 children and adolescents with type 1 diabetes mellitus who were admitted to the Pediatric Emergency Department at Shaare Zedek Medical Center and had blood test results. We compared white blood cell count, C-reactive protein (CRP) levels, blood glucose levels, pH, the degree of acidosis, and the incidence of infection in patients with and without DKA. Results: The incidence of probable bacterial infection in the entire cohort was 13.9%: 15.7% in the DKA group and 7.5% in the non-DKA group ( P = 0.65). The incidence of leukocytosis was significantly higher in patients with DKA ( P = 0.0003), although this was not related to bacterial infection. The CRP levels were higher in the DKA group with infection than without infection, and this was statistically significant ( P = 0.008). Conclusions: Our findings suggest that leukocytosis in DKA is not a reliable indicator of concomitant bacterial infection. In contrast, CRP levels were not related to the DKA or degree of acidosis and were significantly higher in patients with infection within the DKA group, and are therefore a more reliable indicator of concomitant infection in these patients.
MeSH term(s)	Adolescent ; Humans ; Child ; Diabetes Mellitus, Type 1/complications ; Diabetic Ketoacidosis/complications ; Diabetic Ketoacidosis/diagnosis ; C-Reactive Protein ; Retrospective Studies ; Leukocytosis ; Bacterial Infections/complications
Chemical Substances	C-Reactive Protein (9007-41-4)
Language	English
Publishing date	2023-03-29
Publishing country	United States
Document type	Journal Article
ZDB-ID	632588-9
ISSN	1535-1815 ; 0749-5161
ISSN (online)	1535-1815
ISSN	0749-5161
DOI	10.1097/PEC.0000000000002934
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Article ; Online: Making the most of potential

Omer Edhan / Ziv Hellman / Ilan Nehama

Royal Society Open Science, Vol 8, Iss

potential games and genotypic convergence

2021 Volume 8

Abstract: We consider genotypic convergence of populations and show that under fixed fitness asexual and haploid sexual populations attain monomorphic convergence (even under genetic linkage between loci) to basins of attraction with locally exponential ... ...

Abstract	We consider genotypic convergence of populations and show that under fixed fitness asexual and haploid sexual populations attain monomorphic convergence (even under genetic linkage between loci) to basins of attraction with locally exponential convergence rates; the same convergence obtains in single locus diploid sexual reproduction but to polymorphic populations. Furthermore, we show that there is a unified theory underlying these convergences: all of them can be interpreted as instantiations of players in a potential game implementing a multiplicative weights updating algorithm to converge to equilibrium, making use of the Baum–Eagon Theorem. To analyse varying environments, we introduce the concept of ‘virtual convergence’, under which, even if fixation is not attained, the population nevertheless achieves the fitness growth rate it would have had under convergence to an optimal genotype. Virtual convergence is attained by asexual, haploid sexual and multi-locus diploid reproducing populations, even if environments vary arbitrarily. We also study conditions for true monomorphic convergence in asexually reproducing populations in varying environments.
Keywords	evolutionary dynamics ; sexual reproduction ; population genetics ; potential games ; Science ; Q
Subject code	519
Language	English
Publishing date	2021-08-01T00:00:00Z
Publisher	The Royal Society
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Blockchains as a means to promote privacy protecting, access availing, incentive increasing, ELSI lessening DNA databases.

Zarchi, Gal / Sherman, Maya / Gady, Omer / Herzig, Tomer / Idan, Ziv / Greenbaum, Dov

Frontiers in digital health

2023 Volume 4, Page(s) 1028249

Abstract: Not all blockchains are created equal, and many cannot accommodate all of the primary characteristics of big data: Variety, Velocity, Volume and Veracity. Currently, public blockchains are slow and clunky, it can be expensive to keep up with the velocity ...

Abstract	Not all blockchains are created equal, and many cannot accommodate all of the primary characteristics of big data: Variety, Velocity, Volume and Veracity. Currently, public blockchains are slow and clunky, it can be expensive to keep up with the velocity of genomic data production. Further, the transparent and universally accessible nature of public blockchain doesn't necessarily accommodate all of the variety of sequence data, including very private information. Bespoke private permissioned blockchains, however, can be created to optimally accommodate all of the big data features of genomic data. Further, private permissioned chains can be implemented to both protect the privacy and security of the genetic information therein, while also providing access to researchers. An NFT marketplace associated with that private chain can provide the discretized sale of anonymous and encrypted data sets while also incentivizing individuals to share their data through payments mediated by smart contracts. Private blockchains can provide a transparent chain of custody for each use of the customers' data, and validation that this data is not corrupted. However, even with all of these benefits there remain some concerns with the implementation of this new technology including the ethical, legal and social implications typically associated with DNA databases.
Language	English
Publishing date	2023-01-10
Publishing country	Switzerland
Document type	Journal Article ; Review
ISSN	2673-253X
ISSN (online)	2673-253X
DOI	10.3389/fdgth.2022.1028249
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Article: Making the most of potential: potential games and genotypic convergence.

Edhan, Omer / Hellman, Ziv / Nehama, Ilan

Royal Society open science

2021 Volume 8, Issue 8, Page(s) 210309

Abstract	We consider genotypic convergence of populations and show that under fixed fitness asexual and haploid sexual populations attain monomorphic convergence (even under genetic linkage between loci) to basins of attraction with locally exponential convergence rates; the same convergence obtains in single locus diploid sexual reproduction but to polymorphic populations. Furthermore, we show that there is a unified theory underlying these convergences: all of them can be interpreted as instantiations of players in a potential game implementing a multiplicative weights updating algorithm to converge to equilibrium, making use of the Baum-Eagon Theorem. To analyse varying environments, we introduce the concept of 'virtual convergence', under which, even if fixation is not attained, the population nevertheless achieves the fitness growth rate it would have had under convergence to an optimal genotype. Virtual convergence is attained by asexual, haploid sexual and multi-locus diploid reproducing populations, even if environments vary arbitrarily. We also study conditions for true monomorphic convergence in asexually reproducing populations in varying environments.
Language	English
Publishing date	2021-08-25
Publishing country	England
Document type	Journal Article
ZDB-ID	2787755-3
ISSN	2054-5703
ISSN	2054-5703
DOI	10.1098/rsos.210309
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Article ; Online: Fluctuations in Pediatric Acute Otitis Media Burden During the First Two COVID-19 Years in Israel.

Zloczower, Elchanan / Pitaro, Jacob / Hazan, Itai / Warman, Meir / Ziv, Oren / Yaakov, Omer / Marom, Tal

The Pediatric infectious disease journal

2022 Volume 42, Issue 2, Page(s) 146–151

Abstract: Background: To study pediatric acute otitis media (AOM) burden fluctuations before and during the first two COVID years, which were characterized by measures to reduce the spread of airborne diseases. We used urinary tract infection (UTI) as a ... ...

Abstract	Background: To study pediatric acute otitis media (AOM) burden fluctuations before and during the first two COVID years, which were characterized by measures to reduce the spread of airborne diseases. We used urinary tract infection (UTI) as a comparison infection. Methods: This was a cross-sectional study encompassing three pre-COVID years (March 1, 2017-February 29, 2020) and the first two COVID years (March 1, 2020-February 28, 2021, and March 1, 2021-February 28, 2022). Records were retrieved from the Clalit Health Services database, Israel's largest healthcare maintenance organization. Children 0-15 years with AOM and UTI episodes were categorized according to age (1>, 1-4, 5-15 years). We collected demographics, seasonality, AOM complications, antibiotic prescriptions, and recent COVID-19 infections. The average AOM/UTI rates of the three pre-COVID years vs. two COVID years were used to calculate the incidence rate ratios (IRRs). Results: We identified 1,102,826 AOM and 121,263 UTI episodes. The median age at AOM diagnosis was 2.0 years (IQR, 1.1-4.1). Male predominance, age at presentation, and the dominant age group of 1-4 years did not change during the COVID years. While UTI episode rates decreased during the COVID years (IRR 0.76, 95% CI, 0.68-0.84, P < 0.001), the reduction in AOM episode rates was >2-fold (IRR 0.46, 95% CI, 0.34-0.63, P < 0.001). The largest decrease was observed among children 1-4 years old during the first COVID year (β=-1,938 AOM episodes/100,00 children, 95% CI, -2,038 to -1,912, P < 0.001). Recent COVID-19 infection was associated with low AOM morbidity (IRR 0.05, 95% CI 0.05-0.05, P < 0.001). Conclusions: AOM burden substantially decreased during the first COVID year but almost reached pre-pandemic levels during the second year.
MeSH term(s)	Child ; Humans ; Male ; Infant ; Child, Preschool ; Female ; Israel/epidemiology ; Cross-Sectional Studies ; COVID-19/epidemiology ; Otitis Media/epidemiology ; Incidence ; Acute Disease
Language	English
Publishing date	2022-11-08
Publishing country	United States
Document type	Journal Article
ZDB-ID	392481-6
ISSN	1532-0987 ; 0891-3668
ISSN (online)	1532-0987
ISSN	0891-3668
DOI	10.1097/INF.0000000000003767
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Article: Effects of Agronomic Practices on the Severity of Sweet Basil Downy Mildew (Peronospora belbahrii)

Omer, Chen / Nisan, Ziv / Rav-David, Dalia / Elad, Yigal

Plants. 2021 Apr. 30, v. 10, no. 5

2021

Abstract: Downy mildew (caused by Peronospora belbahrii) is a severe disease of sweet basil (Ocimum basilicum) crops around the world. We examined cultural methods for reducing the severity of sweet basil downy mildew (SBDM) under commercial conditions in ... ...

Abstract	Downy mildew (caused by Peronospora belbahrii) is a severe disease of sweet basil (Ocimum basilicum) crops around the world. We examined cultural methods for reducing the severity of sweet basil downy mildew (SBDM) under commercial conditions in greenhouses and walk-in tunnels. The effects of the orientation of walk-in tunnels, air circulation in greenhouses, plant density, and soil mulch were tested. SBDM was less severe in the tunnels that were oriented north-south than in those oriented east-west, but the yields in both types of tunnels were similar. Increased air circulation reduced SBDM severity, but did not affect yield. Gray or transparent polyethylene mulch reduced SBDM severity and, in most cases, increased yield relative to bare soil/growth medium. Yellow polyethylene mulch provided a smaller amount of control. The combination of increased air circulation and yellow polyethylene mulch provided synergistic SBDM control, whereas no synergism was observed when we combined increased air circulation with the other two types of mulch. Planting at half the usual density reduced disease severity. The reduced plant density was associated with reduced yield in the greenhouses, but not in the tunnels. All of the tested methods provided an intermediate level of SBDM control that varied among the different experiments.
Keywords	Ocimum basilicum ; Peronospora ; air ; culture media ; disease severity ; downy mildew ; plant density ; planting ; plastic film mulches ; soil ; synergism
Language	English
Dates of publication	2021-0430
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	2704341-1
ISSN	2223-7747
ISSN	2223-7747
DOI	10.3390/plants10050907
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Acetic acid treatment for toe web infection caused by Pseudomonas Aeruginosa combined with fungal infection: A case series of ten patients.

Rozenblat, Mati / Last, Omer / Fisher, Shani / Ziv, Michael

Dermatologic therapy

2019 Volume 32, Issue 3, Page(s) e12883

Abstract: Gram-negative bacterial toe web infection (GNBTWI) caused by Pseudomonas Aeruginosa combined with fungal infection has variety of treatments. However, these treatments have been poorly described in the literature. Our retrospective study describes ... ...

Abstract	Gram-negative bacterial toe web infection (GNBTWI) caused by Pseudomonas Aeruginosa combined with fungal infection has variety of treatments. However, these treatments have been poorly described in the literature. Our retrospective study describes patients that had been treated in our medical center with acetic acid combined with local antifungal treatment, to evaluate evidences for the appropriateness of this treatment. Ten patients with evidence of GNBTWI caused by Pseudomonas Aeruginosa combined with local fungal infection which have been treated with acetic acid in Emek Medical Center were identified. Eight patients (80%) had a complete response while two patients (20%) showed only a partial response. Side effects were minimal and included temporary stinging sensation. Acetic acid is a relatively cheap ingredient with minimal side effect profile and highly effective outcomes as a treatment for GNBTWI caused by Pseudomonas Aeruginosa and should be considered as an adjuvant treatment.
MeSH term(s)	Acetic Acid/therapeutic use ; Adult ; Aged ; Antifungal Agents/therapeutic use ; Foot Dermatoses/drug therapy ; Humans ; Male ; Middle Aged ; Mycoses/drug therapy ; Pseudomonas Infections/drug therapy ; Retrospective Studies ; Toes
Chemical Substances	Antifungal Agents ; Acetic Acid (Q40Q9N063P)
Language	English
Publishing date	2019-04-17
Publishing country	United States
Document type	Journal Article
ZDB-ID	1354801-3
ISSN	1529-8019 ; 1396-0296
ISSN (online)	1529-8019
ISSN	1396-0296
DOI	10.1111/dth.12883
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Article: Delivering Difficult News: Simulation-Enhanced Training Improves Psychiatry Residents' Clinical Communication Skills.

Amsalem, Doron / Martin, Andrés / Mosheva, Mariela / Soul, Omer / Korotkin, Liran / Ziv, Amitai / Gothelf, Doron / Gross, Raz

Frontiers in psychiatry

2021 Volume 12, Page(s) 649090

Abstract: Background: ...

Abstract	Background:
Language	English
Publishing date	2021-03-05
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2564218-2
ISSN	1664-0640
ISSN	1664-0640
DOI	10.3389/fpsyt.2021.649090
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