LIVIVO - Search results -

Search results

Result 1 - 10 of total 4676

Search options

Article ; Online: RCandy: an R package for visualizing homologous recombinations in bacterial genomes.

Chaguza, Chrispin / Tonkin-Hill, Gerry / Lo, Stephanie W / Hadfield, James / Croucher, Nicholas J / Harris, Simon R / Bentley, Stephen D

Bioinformatics (Oxford, England)

2021 Volume 38, Issue 5, Page(s) 1450–1451

Abstract: ... Here, we present RCandy, a platform-independent R package for rapid, simple and flexible visualization ... of recombination events in bacterial genomes.: Availability and implementation: RCandy is an R package freely ...

Abstract	Summary: Homologous recombination is an important evolutionary process in bacteria and other prokaryotes, which increases genomic sequence diversity and can facilitate adaptation. Several methods and tools have been developed to detect genomic regions recently affected by recombination. Exploration and visualization of such recombination events can reveal valuable biological insights, but it remains challenging. Here, we present RCandy, a platform-independent R package for rapid, simple and flexible visualization of recombination events in bacterial genomes. Availability and implementation: RCandy is an R package freely available for use under the MIT license. It is platform-independent and has been tested on Windows, Linux and MacOSX. The source code comes together with a detailed vignette available on GitHub at https://github.com/ChrispinChaguza/RCandy. Supplementary information: Supplementary data are available at Bioinformatics online.
MeSH term(s)	Genomics ; Software ; Genome ; Bacteria ; Biological Evolution
Language	English
Publishing date	2021-12-04
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btab814
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 2374: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (2.OG)
ab Jg. 2022: Lesesaal (EG)

Order via subito

This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

Details ▾
- See ZB MED holdings
- Order with fees

Article: RhierBAPS: An R implementation of the population clustering algorithm hierBAPS.

Tonkin-Hill, Gerry / Lees, John A / Bentley, Stephen D / Frost, Simon D W / Corander, Jukka

Wellcome open research

2018 Volume 3, Page(s) 93

Abstract: ... been available as a MATLAB binary. We provide an R implementation which is both easier to install and ...

Abstract	Identifying structure in collections of sequence data sets remains a common problem in genomics. hierBAPS, a popular algorithm for identifying population structure in haploid genomes, has previously only been available as a MATLAB binary. We provide an R implementation which is both easier to install and use, automating the entire pipeline. Additionally, we allow for the use of multiple processors, improve on the default settings of the algorithm, and provide an interface with the ggtree library to enable informative illustration of the clustering results. Our aim is that this package aids in the understanding and dissemination of the method, as well as enhancing the reproducibility of population structure analyses.
Language	English
Publishing date	2018-07-30
Publishing country	England
Document type	Journal Article
ISSN	2398-502X
ISSN	2398-502X
DOI	10.12688/wellcomeopenres.14694.1
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article ; Online: Sensitivity studies for the main r process

A. Aprahamian / I. Bentley / M. Mumpower / R. Surman

AIP Advances, Vol 4, Iss 4, Pp 041101-041101-

nuclear masses

2014 Volume 10

Abstract: The site of the rapid neutron capture process (r process) is one of the open challenges ... in all of physics today. The r process is thought to be responsible for the creation of more than half ... an r process to occur and a vast lack of knowledge about the properties of nuclei far from stability ...

Abstract	The site of the rapid neutron capture process (r process) is one of the open challenges in all of physics today. The r process is thought to be responsible for the creation of more than half of all elements beyond iron. The scientific challenges to understanding the origin of the heavy elements beyond iron lie in both the uncertainties associated with astrophysical conditions that are needed to allow an r process to occur and a vast lack of knowledge about the properties of nuclei far from stability. One way is to disentangle the nuclear and astrophysical components of the question. On the nuclear physics side, there is great global competition to access and measure the most exotic nuclei that existing facilities can reach, while simultaneously building new, more powerful accelerators to make even more exotic nuclei. On the astrophysics side, various astrophysical scenarios for the production of the heaviest elements have been proposed but open questions remain. This paper reports on a sensitivity study of the r process to determine the most crucial nuclear masses to measure using an r-process simulation code, several mass models (FRDM, Duflo-Zuker, and HFB-21), and three potential astrophysical scenarios.
Keywords	Science (General) ; Q1-390 ; Science ; Q ; Physics ; QC1-999
Language	English
Publishing date	2014-02-01T00:00:00Z
Publisher	AIP Publishing LLC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

Full text online

Full text

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article ; Online: Randomized, controlled trial comparing Rhodococcus equi and poly-N-acetyl glucosamine hyperimmune plasma to prevent R equi pneumonia in foals.

Kahn, Susanne K / Cywes-Bentley, Colette / Blodgett, Glenn P / Canaday, Nathan M / Turner-Garcia, Carly E / Flores-Ahlschwede, Patricia / Metcalfe, Laurie L / Nevill, Mark / Vinacur, Mariana / Sutter, Patrick J / Meyer, Sarah C / Bordin, Angela I / Pier, Gerald B / Cohen, Noah D

Journal of veterinary internal medicine

2021 Volume 35, Issue 6, Page(s) 2912–2919

Abstract: ... more opsonophagocytic killing of Rhodococcus equi (R equi) than does R equi hyperimmune plasma (RE HIP ... in vitro. The relative efficacy of PNAG HIP and RE HIP to protect foals against R equi pneumonia ... for protection against R equi pneumonia in a randomized, controlled, blinded clinical trial.: Animals: Four ...

Abstract	Background: Hyperimmune plasma raised against β-1→6-poly-N-acetyl glucosamine (PNAG HIP) mediates more opsonophagocytic killing of Rhodococcus equi (R equi) than does R equi hyperimmune plasma (RE HIP) in vitro. The relative efficacy of PNAG HIP and RE HIP to protect foals against R equi pneumonia, however, has not been evaluated. Hypothesis: Transfusion with PNAG HIP will be superior to RE HIP in foals for protection against R equi pneumonia in a randomized, controlled, blinded clinical trial. Animals: Four hundred sixty Quarter Horse and Thoroughbred foals at 5 large breeding farms in the United States. Methods: A randomized, controlled, blinded clinical trial was conducted in which foals were transfused within 24 hours after birth with 2 L of either RE HIP or PNAG HIP. Study foals were monitored through weaning for clinical signs of pneumonia by farm veterinarians. The primary outcome was the proportion of foals that developed pneumonia after receiving each type of plasma. Results: The proportion of foals that developed pneumonia was the same between foals transfused with RE HIP (14%; 32/228) and PNAG HIP (14%; 30/215). Conclusions and clinical importance: Results indicate that PNAG HIP was not superior to a commercially available, United States Department of Agriculture-licensed RE HIP product for protecting foals against R equi pneumonia under field conditions.
MeSH term(s)	Acetylglucosamine ; Actinomycetales Infections/prevention & control ; Actinomycetales Infections/veterinary ; Animals ; Antibodies, Bacterial ; Horse Diseases/prevention & control ; Horses ; Pneumonia, Bacterial/prevention & control ; Pneumonia, Bacterial/veterinary ; Rhodococcus equi
Chemical Substances	Antibodies, Bacterial ; poly-N-acetyl glucosamine ; Acetylglucosamine (V956696549)
Language	English
Publishing date	2021-11-05
Publishing country	United States
Document type	Journal Article ; Randomized Controlled Trial, Veterinary
ZDB-ID	92798-3
ISSN	1939-1676 ; 0891-6640
ISSN (online)	1939-1676
ISSN	0891-6640
DOI	10.1111/jvim.16294
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 4095: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (2.OG)
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: Hepatitis C Virus Indirectly Disrupts DNA Damage-Induced p53 Responses by Activating Protein Kinase R.

Mitchell, Jonathan K / Midkiff, Bentley R / Israelow, Benjamin / Evans, Matthew J / Lanford, Robert E / Walker, Christopher M / Lemon, Stanley M / McGivern, David R

mBio

2017 Volume 8, Issue 2

Abstract: ... protein kinase R (PKR) restored p53 responses while boosting HCV replication, showing that p53 inhibition results ...

Abstract	Many DNA tumor viruses promote cellular transformation by inactivating the critically important tumor suppressor protein p53. In contrast, it is not known whether p53 function is disrupted by hepatitis C virus (HCV), a unique, oncogenic RNA virus that is the leading infectious cause of liver cancer in many regions of the world. Here we show that HCV-permissive, liver-derived HepG2 cells engineered to constitutively express microRNA-122 (HepG2/miR-122 cells) have normal p53-mediated responses to DNA damage and that HCV replication in these cells potently suppresses p53 responses to etoposide, an inducer of DNA damage, or nutlin-3, an inhibitor of p53 degradation pathways. Upregulation of p53-dependent targets is consequently repressed within HCV-infected cells, with potential consequences for cell survival. Despite this, p53 function is not disrupted by overexpression of the complete HCV polyprotein, suggesting that altered p53 function may result from the host response to viral RNA replication intermediates. Clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9-mediated ablation of double-stranded RNA (dsRNA)-activated protein kinase R (PKR) restored p53 responses while boosting HCV replication, showing that p53 inhibition results directly from viral activation of PKR. The hepatocellular abundance of phosphorylated PKR is elevated in HCV-infected chimpanzees, suggesting that PKR activation and consequent p53 inhibition accompany HCV infection
MeSH term(s)	Animals ; Disease Models, Animal ; Hep G2 Cells ; Hepacivirus/pathogenicity ; Hepatitis C/pathology ; Host-Pathogen Interactions ; Humans ; Pan troglodytes ; Tumor Suppressor Protein p53/metabolism ; eIF-2 Kinase/metabolism
Chemical Substances	Tumor Suppressor Protein p53 ; eIF-2 Kinase (EC 2.7.11.1)
Language	English
Publishing date	2017-04-25
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2557172-2
ISSN	2150-7511 ; 2161-2129
ISSN (online)	2150-7511
ISSN	2161-2129
DOI	10.1128/mBio.00121-17
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Book ; Online: Sensitivity of the r-process to nuclear masses

Brett, S. / Bentley, I. / Paul, N. / Surman, R. / Aprahamian, A.

2012

Abstract: The rapid neutron capture process (r-process) is thought to be responsible for the creation of more ... to allow an r-process to occur and a vast lack of knowledge about the properties of nuclei far ... nuclei. This work is an attempt to determine the most crucial nuclear masses to measure using an r ...

Abstract	The rapid neutron capture process (r-process) is thought to be responsible for the creation of more than half of all elements beyond iron. The scientific challenges to understanding the origin of the heavy elements beyond iron lie in both the uncertainties associated with astrophysical conditions that are needed to allow an r-process to occur and a vast lack of knowledge about the properties of nuclei far from stability. There is great global competition to access and measure the most exotic nuclei that existing facilities can reach, while simultaneously building new, more powerful accelerators to make even more exotic nuclei. This work is an attempt to determine the most crucial nuclear masses to measure using an r-process simulation code and several mass models (FRDM, Duflo-Zuker, and HFB-21). The most important nuclear masses to measure are determined by the changes in the resulting r-process abundances. Nuclei around the closed shells near N=50, 82, and 126 have the largest impact on r-process abundances irrespective of the mass models used. Comment: 5 pages, 4 figures, accepted in European Physical Journal A
Keywords	Nuclear Theory ; Nuclear Experiment
Subject code	660
Publishing date	2012-11-30
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

Full text online

Full text

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article ; Online: Sensitivity studies for r-process nucleosynthesis in three astrophysical scenarios

Surman R. / Mumpower M. / Cass J. / Bentley I. / Aprahamian A. / McLaughlin G.C.

EPJ Web of Conferences, Vol 66, p

2014 Volume 07024

Abstract: In rapid neutron capture, or r-process, nucleosynthesis, heavy elements are built up via a sequence ... the basics of how the r process proceeds, its astrophysical site is still not conclusively known. The nuclear ... the most crucial for r-process calculations. We consider three types of astrophysical scenarios ...

Abstract	In rapid neutron capture, or r-process, nucleosynthesis, heavy elements are built up via a sequence of neutron captures and β decays that involves thousands of nuclei far from stability. Though we understand the basics of how the r process proceeds, its astrophysical site is still not conclusively known. The nuclear network simulations we use to test potential astrophysical scenarios require nuclear physics data (masses, β decay lifetimes, neutron capture rates, fission probabilities) for all of the nuclei on the neutron-rich side of the nuclear chart, from the valley of stability to the neutron drip line. Here we discuss recent sensitivity studies that aim to determine which individual pieces of nuclear data are the most crucial for r-process calculations. We consider three types of astrophysical scenarios: a traditional hot r process, a cold r process in which the temperature and density drop rapidly, and a neutron star merger trajectory.
Keywords	Physics ; QC1-999 ; Science ; Q
Language	English
Publishing date	2014-03-01T00:00:00Z
Publisher	EDP Sciences
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

Full text online

Full text

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article ; Online: Randomized, controlled trial comparing Rhodococcus equi and poly‐N‐acetyl glucosamine hyperimmune plasma to prevent R equi pneumonia in foals

Susanne K. Kahn / Colette Cywes‐Bentley / Glenn P. Blodgett / Nathan M. Canaday / Carly E. Turner‐Garcia / Patricia Flores‐Ahlschwede / Laurie L. Metcalfe / Mark Nevill / Mariana Vinacur / Patrick J. Sutter / Sarah C. Meyer / Angela I. Bordin / Gerald B. Pier / Noah D. Cohen

Journal of Veterinary Internal Medicine, Vol 35, Iss 6, Pp 2912-

2021 Volume 2919

Abstract: ... mediates more opsonophagocytic killing of Rhodococcus equi (R equi) than does R equi hyperimmune plasma (RE ... HIP) in vitro. The relative efficacy of PNAG HIP and RE HIP to protect foals against R equi pneumonia ... for protection against R equi pneumonia in a randomized, controlled, blinded clinical trial. Animals Four hundred ...

Abstract	Abstract Background Hyperimmune plasma raised against β‐1→6‐poly‐N‐acetyl glucosamine (PNAG HIP) mediates more opsonophagocytic killing of Rhodococcus equi (R equi) than does R equi hyperimmune plasma (RE HIP) in vitro. The relative efficacy of PNAG HIP and RE HIP to protect foals against R equi pneumonia, however, has not been evaluated. Hypothesis Transfusion with PNAG HIP will be superior to RE HIP in foals for protection against R equi pneumonia in a randomized, controlled, blinded clinical trial. Animals Four hundred sixty Quarter Horse and Thoroughbred foals at 5 large breeding farms in the United States. Methods A randomized, controlled, blinded clinical trial was conducted in which foals were transfused within 24 hours after birth with 2 L of either RE HIP or PNAG HIP. Study foals were monitored through weaning for clinical signs of pneumonia by farm veterinarians. The primary outcome was the proportion of foals that developed pneumonia after receiving each type of plasma. Results The proportion of foals that developed pneumonia was the same between foals transfused with RE HIP (14%; 32/228) and PNAG HIP (14%; 30/215). Conclusions and Clinical Importance Results indicate that PNAG HIP was not superior to a commercially available, United States Department of Agriculture‐licensed RE HIP product for protecting foals against R equi pneumonia under field conditions.
Keywords	bacterial ; clinical trials ; humoral immunity ; neonatology ; Rhodococcus ; transfusion ; Veterinary medicine ; SF600-1100
Subject code	610
Language	English
Publishing date	2021-11-01T00:00:00Z
Publisher	Wiley
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

Full text online

Full text

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article: Randomized, controlled trial comparing Rhodococcus equi and poly‐N‐acetyl glucosamine hyperimmune plasma to prevent R equi pneumonia in foals

Kahn, Susanne K. / Cywes‐Bentley, Colette / Blodgett, Glenn P. / Canaday, Nathan M. / Turner‐Garcia, Carly E. / Flores‐Ahlschwede, Patricia / Metcalfe, Laurie L. / Nevill, Mark / Vinacur, Mariana / Sutter, Patrick J. / Meyer, Sarah C. / Bordin, Angela I. / Pier, Gerald B. / Cohen, Noah D.

Journal of veterinary internal medicine. 2021 Nov., v. 35, no. 6

2021

Abstract	BACKGROUND: Hyperimmune plasma raised against β‐1→6‐poly‐N‐acetyl glucosamine (PNAG HIP) mediates more opsonophagocytic killing of Rhodococcus equi (R equi) than does R equi hyperimmune plasma (RE HIP) in vitro. The relative efficacy of PNAG HIP and RE HIP to protect foals against R equi pneumonia, however, has not been evaluated. HYPOTHESIS: Transfusion with PNAG HIP will be superior to RE HIP in foals for protection against R equi pneumonia in a randomized, controlled, blinded clinical trial. ANIMALS: Four hundred sixty Quarter Horse and Thoroughbred foals at 5 large breeding farms in the United States. METHODS: A randomized, controlled, blinded clinical trial was conducted in which foals were transfused within 24 hours after birth with 2 L of either RE HIP or PNAG HIP. Study foals were monitored through weaning for clinical signs of pneumonia by farm veterinarians. The primary outcome was the proportion of foals that developed pneumonia after receiving each type of plasma. RESULTS: The proportion of foals that developed pneumonia was the same between foals transfused with RE HIP (14%; 32/228) and PNAG HIP (14%; 30/215). CONCLUSIONS AND CLINICAL IMPORTANCE: Results indicate that PNAG HIP was not superior to a commercially available, United States Department of Agriculture‐licensed RE HIP product for protecting foals against R equi pneumonia under field conditions.
Keywords	Quarter Horse ; Rhodococcus equi ; Thoroughbred ; clinical trials ; farms ; glucosamine ; pneumonia ; veterinary medicine
Language	English
Dates of publication	2021-11
Size	p. 2912-2919.
Publishing place	John Wiley & Sons, Inc.
Document type	Article
Note	JOURNAL ARTICLE
ZDB-ID	92798-3
ISSN	1939-1676 ; 0891-6640
ISSN (online)	1939-1676
ISSN	0891-6640
DOI	10.1111/jvim.16294
Database	NAL-Catalogue (AGRICOLA)

In stock of ZB MED Cologne/Königswinter

Zs.A 4095: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (2.OG)
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: Conjugate addition of lithium N-phenyl-N-(α-methylbenzyl)amide: application to the asymmetric synthesis of (R)-(-)-angustureine.

Bentley, Scott A / Davies, Stephen G / Lee, James A / Roberts, Paul M / Thomson, James E

Organic letters

2011 Volume 13, Issue 10, Page(s) 2544–2547

Abstract: The conjugate addition of lithium (R)-N-phenyl-N-(α-methylbenzyl)amide to a range of α,β ... of the tetrahydroquinoline alkaloid (R)-(-)-angustureine in six steps and 32% overall yield from commercially available oct-2-enoic ...

Abstract	The conjugate addition of lithium (R)-N-phenyl-N-(α-methylbenzyl)amide to a range of α,β-unsaturated 4-methoxyphenyl esters proceeds with excellent levels of diastereoselectivity to give the corresponding β-amino esters in good yield and as single diastereoisomers (>99:1 dr). The synthetic utility of this methodology has been demonstrated via the short and concise asymmetric synthesis of the tetrahydroquinoline alkaloid (R)-(-)-angustureine in six steps and 32% overall yield from commercially available oct-2-enoic acid.
MeSH term(s)	Alkaloids/chemical synthesis ; Alkaloids/chemistry ; Fatty Acids, Monounsaturated/chemistry ; Lithium/chemistry ; Molecular Structure ; Organometallic Compounds/chemistry ; Quinolines/chemical synthesis ; Quinolines/chemistry ; Stereoisomerism
Chemical Substances	Alkaloids ; Fatty Acids, Monounsaturated ; Organometallic Compounds ; Quinolines ; angustureine ; Lithium (9FN79X2M3F)
Language	English
Publishing date	2011-05-20
Publishing country	United States
Document type	Journal Article
ISSN	1523-7052
ISSN (online)	1523-7052
DOI	10.1021/ol200625h
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

To top

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

Order via subito

Inter-library loan at ZB MED

Full text online

More links

Kategorien

Inter-library loan at ZB MED

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

Order via subito

Full text online

More links

Kategorien

Inter-library loan at ZB MED

Full text online

More links

Kategorien

Inter-library loan at ZB MED

Full text online

More links

Kategorien

Inter-library loan at ZB MED

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

Order via subito

Inter-library loan at ZB MED