LIVIVO - Search results -

Search results

Result 1 - 10 of total 64

Search options

Article ; Online: Shiny-SoSV: A web-based performance calculator for somatic structural variant detection.

Gong, Tingting / Hayes, Vanessa M / Chan, Eva K F

PloS one

2020 Volume 15, Issue 8, Page(s) e0238108

Abstract: Somatic structural variants are an important contributor to cancer development and evolution. Accurate detection of these complex variants from whole genome sequencing data is influenced by a multitude of parameters. However, there are currently no tools ...

Abstract	Somatic structural variants are an important contributor to cancer development and evolution. Accurate detection of these complex variants from whole genome sequencing data is influenced by a multitude of parameters. However, there are currently no tools for guiding study design nor are there applications that could predict the performance of somatic structural variant detection. To address this gap, we developed Shiny-SoSV, a user-friendly web-based calculator for determining the impact of common variables on the sensitivity, precision and F1 score of somatic structural variant detection, including choice of variant detection tool, sequencing depth of coverage, variant allele fraction, and variant breakpoint resolution. Using simulation studies, we determined singular and combinatoric effects of these variables, modelled the results using a generalised additive model, allowing structural variant detection performance to be predicted for any combination of predictors. Shiny-SoSV provides an interactive and visual platform for users to easily compare individual and combined impact of different parameters. It predicts the performance of a proposed study design, on somatic structural variant detection, prior to the commencement of benchwork. Shiny-SoSV is freely available at https://hcpcg.shinyapps.io/Shiny-SoSV with accompanying user's guide and example use-cases.
MeSH term(s)	Algorithms ; Carcinogenesis/genetics ; Computational Biology/methods ; Genetic Variation/genetics ; Genome/genetics ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Internet ; Neoplasms/genetics ; Software
Language	English
Publishing date	2020-08-27
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0238108
Database	MEDical Literature Analysis and Retrieval System OnLINE

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.

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: Detection of somatic structural variants from short-read next-generation sequencing data.

Gong, Tingting / Hayes, Vanessa M / Chan, Eva K F

Briefings in bioinformatics

2020 Volume 22, Issue 3

Abstract: Somatic structural variants (SVs), which are variants that typically impact >50 nucleotides, play a significant role in cancer development and evolution but are notoriously more difficult to detect than small variants from short-read next-generation ... ...

Abstract	Somatic structural variants (SVs), which are variants that typically impact >50 nucleotides, play a significant role in cancer development and evolution but are notoriously more difficult to detect than small variants from short-read next-generation sequencing (NGS) data. This is due to a combination of challenges attributed to the purity of tumour samples, tumour heterogeneity, limitations of short-read information from NGS and sequence alignment ambiguities. In spite of active development of SV detection tools (callers) over the past few years, each method has inherent advantages and limitations. In this review, we highlight some of the important factors affecting somatic SV detection and compared the performance of seven commonly used SV callers. In particular, we focus on the extent of change in sensitivity and precision for detecting different SV types and size ranges from samples with differing variant allele frequencies and sequencing depths of coverage. We highlight the reasons for why some SV callers perform well in some settings but not others, allowing our evaluation findings to be extended beyond the seven SV callers examined in this paper. As the importance of large SVs become increasingly recognized in cancer genomics, this paper provides a timely review on some of the most impactful factors influencing somatic SV detection that should be considered when choosing SV callers.
MeSH term(s)	Gene Frequency ; Genetic Variation ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Neoplasms/genetics ; Neoplasms/pathology ; Sequence Analysis, DNA/methods
Language	English
Publishing date	2020-05-04
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2068142-2
ISSN	1477-4054 ; 1467-5463
ISSN (online)	1477-4054
ISSN	1467-5463
DOI	10.1093/bib/bbaa056
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 6262: Show issues

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

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: Anesthetic Management for Squamous Cell Carcinoma of the Esophagus.

Chan, Eva Y F / Ip, Danny K Y / Irwin, Michael G

Methods in molecular biology (Clifton, N.J.)

2020 Volume 2129, Page(s) 359–383

Abstract: While surgery plays a major role in the treatment and potential cure of esophageal cancers, esophagectomy remains a high-risk operation with significant perioperative morbidity and mortality compared to other oncosurgical procedures. Perioperative ... ...

Abstract	While surgery plays a major role in the treatment and potential cure of esophageal cancers, esophagectomy remains a high-risk operation with significant perioperative morbidity and mortality compared to other oncosurgical procedures. Perioperative management for esophagectomy is complex, and close attention to detail in various areas of anesthetic and perioperative management is crucial to improve postoperative outcomes. Patients undergoing esophagectomy should be offered an evidence-based risk assessment for their postoperative outcomes to allow active participation and informed, shared-decision making. Novel perioperative risk scores have been developed to predict both short-term and long-term outcomes in patients with esophageal cancer, although independent validation of such scoring systems is still required. Apart from accurate preoperative risk assessment, further efforts to improve morbidity and mortality from esophagectomy is achieved through comprehensive Enhanced Recovery after Surgery (ERAS) protocols, which comprise an individualized bundle of care throughout the perioperative journey for each patient and should be implemented as a standard practice. Furthermore, anesthetic practice and perioperative anesthetic drug usage can potentially affect cancer progression and recurrence. This chapter reviews current evidence for various factors that contribute to the improvement of perioperative outcomes, including prehabilitation, preoperative optimization of anemia, thoracic epidural analgesia, intraoperative protective ventilatory strategies, goal-directed fluid therapy, as well as special attention to other perioperative issues that potentially reduce anastomotic and cardiopulmonary complications. In summary, it is difficult to show a measurable benefit from any one single intervention, and a multidisciplinary approach that encompasses multiple aspects of perioperative care is necessary to improve outcomes after esophagectomy.
MeSH term(s)	Adenocarcinoma/pathology ; Anesthesia/methods ; Anesthetics/therapeutic use ; Carcinoma, Squamous Cell/pathology ; Esophageal Neoplasms/pathology ; Esophageal Squamous Cell Carcinoma/metabolism ; Esophageal Squamous Cell Carcinoma/pathology ; Esophageal Squamous Cell Carcinoma/surgery ; Esophagectomy/adverse effects ; Esophagectomy/methods ; Esophagus/pathology ; Female ; Head and Neck Neoplasms/pathology ; Humans ; Male ; Mouth Neoplasms/pathology ; Perioperative Care/methods ; Postoperative Complications/etiology ; Risk Factors
Chemical Substances	Anesthetics
Language	English
Publishing date	2020-02-13
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-0377-2_26
Database	MEDical Literature Analysis and Retrieval System OnLINE

Full text online

Accessible to users with ZB MED library card

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.

Details ▾
- Full text online
- Order with fees

Article: Reading Picture Books With Elements of Positive Psychology for Enhancing the Learning of English as a Second Language in Young Children.

Hui, Anna N N / Chow, Bonnie Wing-Yin / Chan, Eva S M / Leung, Man-Tak

Frontiers in psychology

2020 Volume 10, Page(s) 2899

Abstract: This study aimed to investigate the learning effectiveness of reading picture books with EMPATHICS elements using dialogic reading techniques in enhancing young children's English language learning and creativity. EMPATHICS is an acronym of Emotion and ... ...

Abstract	This study aimed to investigate the learning effectiveness of reading picture books with EMPATHICS elements using dialogic reading techniques in enhancing young children's English language learning and creativity. EMPATHICS is an acronym of Emotion and Empathy, Meaning and Motivation, Perseverance, Agency and Autonomy, Time, Habits of Mind, Intelligences, Character Strengths, and Self Factors (Oxford, 2016). It adopted a quasi-experimental design, and 78 kindergarten children aged from 4 to 5 years old in a cluster group were randomly assigned to the experimental and control groups. Both groups read the same four picture books with their homeroom teachers, including two readers suggested in the curriculum and two picture books with enriched elements for 12 sessions over 8 weeks. A doubly multivariate analysis was used to measure the main time and group effects and the interaction effect on the performance of English receptive vocabulary, syntactic complexity, and verbal creativity of the two groups across three different times. There were significant differences only in the interactive effect on syntactic complexity. Children in the experimental condition gave responses with more complex syntactic structures. Significant time effects for receptive vocabulary, syntactic complexity, and verbal creativity were observed in all children. Reading enriched English texts better prepares children to creatively and effectively express themselves. This study extends previous research in two ways. First, this study is one of the few studies on the effectiveness of dialogic reading using EMPATHICS-enriched picture books among young language learners. Second, this study investigates the effects of dialogic teaching on English as a second language development in young children. The educational implications will be discussed.
Language	English
Publishing date	2020-01-23
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2563826-9
ISSN	1664-1078
ISSN	1664-1078
DOI	10.3389/fpsyg.2019.02899
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article: The Australasian dingo archetype:

Ballard, J William O / Field, Matt A / Edwards, Richard J / Wilson, Laura A B / Koungoulos, Loukas G / Rosen, Benjamin D / Chernoff, Barry / Dudchenko, Olga / Omer, Arina / Keilwagen, Jens / Skvortsova, Ksenia / Bogdanovic, Ozren / Chan, Eva / Zammit, Robert / Hayes, Vanessa / Aiden, Erez Lieberman

bioRxiv : the preprint server for biology

2023

Abstract: Background: One difficulty in testing the hypothesis that the Australasian dingo is a functional intermediate between wild wolves and domesticated breed dogs is that there is no reference specimen. Here we link a high-quality : Findings: We generated ...

Abstract	Background: One difficulty in testing the hypothesis that the Australasian dingo is a functional intermediate between wild wolves and domesticated breed dogs is that there is no reference specimen. Here we link a high-quality Findings: We generated a high-quality chromosome-level reference genome assembly (Canfam_ADS) using a combination of Pacific Bioscience, Oxford Nanopore, 10X Genomics, Bionano, and Hi-C technologies. Compared to the previously published Desert dingo assembly, there are large structural rearrangements on Chromosomes 11, 16, 25 and 26. Phylogenetic analyses of chromosomal data from Cooinda the Alpine dingo and nine previously published Conclusions: These combined data support the hypothesis that the dingo Cooinda fits the spectrum of genetic and morphological characteristics typical of the Alpine ecotype. We propose that she be considered the archetype specimen for future research investigating the evolutionary history, morphology, physiology, and ecology of dingoes. The female has been taxidermically prepared and is now at the Australian Museum, Sydney.
Language	English
Publishing date	2023-01-27
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.01.26.525801
Database	MEDical Literature Analysis and Retrieval System OnLINE

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.

Details ▾

Article ; Online: The Australasian dingo archetype: de novo chromosome-length genome assembly, DNA methylome, and cranial morphology.

GigaScience

2023 Volume 12

Abstract	Background: One difficulty in testing the hypothesis that the Australasian dingo is a functional intermediate between wild wolves and domesticated breed dogs is that there is no reference specimen. Here we link a high-quality de novo long-read chromosomal assembly with epigenetic footprints and morphology to describe the Alpine dingo female named Cooinda. It was critical to establish an Alpine dingo reference because this ecotype occurs throughout coastal eastern Australia where the first drawings and descriptions were completed. Findings: We generated a high-quality chromosome-level reference genome assembly (Canfam_ADS) using a combination of Pacific Bioscience, Oxford Nanopore, 10X Genomics, Bionano, and Hi-C technologies. Compared to the previously published Desert dingo assembly, there are large structural rearrangements on chromosomes 11, 16, 25, and 26. Phylogenetic analyses of chromosomal data from Cooinda the Alpine dingo and 9 previously published de novo canine assemblies show dingoes are monophyletic and basal to domestic dogs. Network analyses show that the mitochondrial DNA genome clusters within the southeastern lineage, as expected for an Alpine dingo. Comparison of regulatory regions identified 2 differentially methylated regions within glucagon receptor GCGR and histone deacetylase HDAC4 genes that are unmethylated in the Alpine dingo genome but hypermethylated in the Desert dingo. Morphologic data, comprising geometric morphometric assessment of cranial morphology, place dingo Cooinda within population-level variation for Alpine dingoes. Magnetic resonance imaging of brain tissue shows she had a larger cranial capacity than a similar-sized domestic dog. Conclusions: These combined data support the hypothesis that the dingo Cooinda fits the spectrum of genetic and morphologic characteristics typical of the Alpine ecotype. We propose that she be considered the archetype specimen for future research investigating the evolutionary history, morphology, physiology, and ecology of dingoes. The female has been taxidermically prepared and is now at the Australian Museum, Sydney.
MeSH term(s)	Dogs ; Animals ; Female ; Epigenome ; Phylogeny ; Australia ; Canidae/genetics ; Wolves/genetics ; Genome, Mitochondrial ; Chromosomes
Language	English
Publishing date	2023-03-22
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, Non-U.S. Gov't
ZDB-ID	2708999-X
ISSN	2047-217X ; 2047-217X
ISSN (online)	2047-217X
ISSN	2047-217X
DOI	10.1093/gigascience/giad018
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article: The effect of foreign strategic investors on the performance of PRC H-firms

Chan, Eva

The Chinese economy : translations and studies Vol. 40, No. 5 , p. 84-99

2007 Volume 40, Issue 5, Page(s) 84–99

Title variant	People's Republic of China
Author's details	Eva Chan
Keywords	Auslandsinvestition ; Börsengang ; Unternehmenserfolg ; Zweitlisting ; Hongkong ; China
Language	English
Publisher	Sharpe
Publishing place	Armonk, NY
Document type	Article
ZDB-ID	1417105-3
Database	ECONomics Information System

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: Mechanisms of Asymmetric Membrane Formation in Nonsolvent-Induced Phase Separation.

Garcia, Jan Ulric / Iwama, Tatsuhiro / Chan, Eva Y / Tree, Douglas R / Delaney, Kris T / Fredrickson, Glenn H

ACS macro letters

2020 Volume 9, Issue 11, Page(s) 1617–1624

Abstract: We report the first simulations of nonsolvent-induced phase separation (NIPS) that predict membrane microstructures with graded asymmetric pore size distribution. In NIPS, a polymer solution film is immersed in a nonsolvent bath, enriching the film in ... ...

Abstract	We report the first simulations of nonsolvent-induced phase separation (NIPS) that predict membrane microstructures with graded asymmetric pore size distribution. In NIPS, a polymer solution film is immersed in a nonsolvent bath, enriching the film in nonsolvent, and leading to phase separation that forms a solid polymer-rich membrane matrix and polymer-poor membrane pores. We demonstrate how mass-transfer-induced spinodal decomposition, thermal fluctuations, and glass-transition dynamics-implemented with mobility contrast between the polymer-rich and polymer-poor phases-are essential to the formation of asymmetric membrane microstructures. Specifically, we show that the competition between the propagation of the phase-separation and glass-transition fronts determines the degree of pore-size asymmetry. We also explore the sensitivity of these microstructures to the initial film composition, and compare their formation in 2D and 3D.
Language	English
Publishing date	2020-10-26
Publishing country	United States
Document type	Journal Article
ISSN	2161-1653
ISSN (online)	2161-1653
DOI	10.1021/acsmacrolett.0c00609
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: Genome-wide interrogation of structural variation reveals novel African-specific prostate cancer oncogenic drivers.

Gong, Tingting / Jaratlerdsiri, Weerachai / Jiang, Jue / Willet, Cali / Chew, Tracy / Patrick, Sean M / Lyons, Ruth J / Haynes, Anne-Maree / Pasqualim, Gabriela / Brum, Ilma Simoni / Stricker, Phillip D / Mutambirwa, Shingai B A / Sadsad, Rosemarie / Papenfuss, Anthony T / Bornman, Riana M S / Chan, Eva K F / Hayes, Vanessa M

Genome medicine

2022 Volume 14, Issue 1, Page(s) 100

Abstract: Background: African ancestry is a significant risk factor for advanced prostate cancer (PCa). Mortality rates in sub-Saharan Africa are 2.5-fold greater than global averages. However, the region has largely been excluded from the benefits of whole ... ...

Abstract	Background: African ancestry is a significant risk factor for advanced prostate cancer (PCa). Mortality rates in sub-Saharan Africa are 2.5-fold greater than global averages. However, the region has largely been excluded from the benefits of whole genome interrogation studies. Additionally, while structural variation (SV) is highly prevalent, PCa genomic studies are still biased towards small variant interrogation. Methods: Using whole genome sequencing and best practice workflows, we performed a comprehensive analysis of SVs for 180 (predominantly Gleason score ≥ 8) prostate tumours derived from 115 African, 61 European and four ancestrally admixed patients. We investigated the landscape and relationship of somatic SVs in driving ethnic disparity (African versus European), with a focus on African men from southern Africa. Results: Duplication events showed the greatest ethnic disparity, with a 1.6- (relative frequency) to 2.5-fold (count) increase in African-derived tumours. Furthermore, we found duplication events to be associated with CDK12 inactivation and MYC copy number gain, and deletion events associated with SPOP mutation. Overall, African-derived tumours were 2-fold more likely to present with a hyper-SV subtype. In addition to hyper-duplication and deletion subtypes, we describe a new hyper-translocation subtype. While we confirm a lower TMPRSS2-ERG fusion-positive rate in tumours from African cases (10% versus 33%), novel African-specific PCa ETS family member and TMPRSS2 fusion partners were identified, including LINC01525, FBXO7, GTF3C2, NTNG1 and YPEL5. Notably, we found 74 somatic SV hotspots impacting 18 new candidate driver genes, with CADM2, LSAMP, PTPRD, PDE4D and PACRG having therapeutic implications for African patients. Conclusions: In this first African-inclusive SV study for high-risk PCa, we demonstrate the power of SV interrogation for the identification of novel subtypes, oncogenic drivers and therapeutic targets. Identifying a novel spectrum of SVs in tumours derived from African patients provides a mechanism that may contribute, at least in part, to the observed ethnic disparity in advanced PCa presentation in men of African ancestry.
MeSH term(s)	Blacks/genetics ; Carcinogenesis/genetics ; Humans ; Male ; Mutation ; Neoplasm Grading ; Nuclear Proteins/genetics ; Prostatic Neoplasms/genetics ; Prostatic Neoplasms/pathology ; Repressor Proteins/genetics
Chemical Substances	Nuclear Proteins ; Repressor Proteins ; SPOP protein, human
Language	English
Publishing date	2022-08-31
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2484394-5
ISSN	1756-994X ; 1756-994X
ISSN (online)	1756-994X
ISSN	1756-994X
DOI	10.1186/s13073-022-01096-w
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article ; Online: Author Correction: Human origins in a southern African palaeo-wetland and first migrations.

Chan, Eva K F / Timmermann, Axel / Baldi, Benedetta F / Moore, Andy E / Lyons, Ruth J / Lee, Sun-Seon / Kalsbeek, Anton M F / Petersen, Desiree C / Rautenbach, Hannes / Förtsch, Hagen E A / Bornman, M S Riana / Hayes, Vanessa M

Nature

2021 Volume 592, Issue 7852, Page(s) E7

Language	English
Publishing date	2021-03-16
Publishing country	England
Document type	Published Erratum
ZDB-ID	120714-3
ISSN	1476-4687 ; 0028-0836
ISSN (online)	1476-4687
ISSN	0028-0836
DOI	10.1038/s41586-020-03156-w
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 26: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
Zs.MG 9: Show issues
Zs.MO 244: Show issues

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

To top

More links

Kategorien

Order via subito

Inter-library loan at ZB MED

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

Full text online

More links

Kategorien

Order via subito

Inter-library loan at ZB MED

More links

Kategorien

Order via subito

More links

Kategorien

Inter-library loan at ZB MED

More links

Kategorien

Order via subito

More links

Kategorien

Order via subito

Inter-library loan at ZB MED

More links

Kategorien

Order via subito

Inter-library loan at ZB MED

More links

Kategorien

Order via subito

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito