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Article ; Online: The genome and sex-dependent responses to temperature in the common yellow butterfly, Eurema hecabe.

Lee, Ivy H T / Nong, Wenyan / So, Wai Lok / Cheung, Chris K H / Xie, Yichun / Baril, Toby / Yip, Ho Yin / Swale, Thomas / Chan, Simon K F / Wei, Yingying / Lo, Nathan / Hayward, Alexander / Chan, Ting Fung / Lam, Hon-Ming / Hui, Jerome H L

BMC biology

2023 Volume 21, Issue 1, Page(s) 200

Abstract: Background: Lepidoptera (butterflies and moths) is one of the most geographically widespread insect orders in the world, and its species play important and diverse ecological and applied roles. Climate change is one of the biggest challenges to ... ...

Abstract	Background: Lepidoptera (butterflies and moths) is one of the most geographically widespread insect orders in the world, and its species play important and diverse ecological and applied roles. Climate change is one of the biggest challenges to biodiversity this century, and lepidopterans are vulnerable to climate change. Temperature-dependent gene expression differences are of relevance under the ongoing climate crisis. However, little is known about how climate affects gene expression in lepidopterans and the ecological consequences of this, particularly with respect to genes with biased expression in one of the sexes. The common yellow butterfly, Eurema hecabe (Family Pieridae), is one of the most geographically widespread lepidopterans that can be found in Asia, Africa, and Australia. Nevertheless, what temperature-dependent effects there may be and whether the effects differ between the sexes remain largely unexplored. Results: Here, we generated high-quality genomic resources for E. hecabe along with transcriptomes from eight developmental stages. Male and female butterflies were subjected to varying temperatures to assess sex-specific gene expression responses through mRNA and microRNA transcriptomics. We find that there are more temperature-dependent sex-biased genes in females than males, including genes that are involved in a range of biologically important functions, highlighting potential ecological impacts of increased temperatures. Further, by considering available butterfly data on sex-biased gene expression in a comparative genomic framework, we find that the pattern of sex-biased gene expression identified in E. hecabe is highly species-specific, rather than conserved across butterfly species, suggesting that sex-biased gene expression responses to climate change are complex in butterflies. Conclusions: Our study lays the foundation for further understanding of differential responses to environmental stress in a widespread lepidopteran model and demonstrates the potential complexity of sex-specific responses of lepidopterans to climate change.
MeSH term(s)	Female ; Male ; Animals ; Butterflies/genetics ; Temperature ; Genomics ; Australia ; Biodiversity
Language	English
Publishing date	2023-09-25
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2133020-7
ISSN	1741-7007 ; 1741-7007
ISSN (online)	1741-7007
ISSN	1741-7007
DOI	10.1186/s12915-023-01703-1
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Article ; Online: Stimulation of the wrist acupuncture point PC6 for preventing postoperative nausea and vomiting.

Lee, Anna / Chan, Simon K C / Fan, Lawrence T Y

The Cochrane database of systematic reviews

2015 , Issue 11, Page(s) CD003281

Abstract: Background: Postoperative nausea and vomiting (PONV) are common complications following surgery and anaesthesia. Antiemetic drugs are only partially effective in preventing PONV. An alternative approach is to stimulate the PC6 acupoint on the wrist. ... ...

Abstract	Background: Postoperative nausea and vomiting (PONV) are common complications following surgery and anaesthesia. Antiemetic drugs are only partially effective in preventing PONV. An alternative approach is to stimulate the PC6 acupoint on the wrist. This is an update of a Cochrane review first published in 2004, updated in 2009 and now in 2015. Objectives: To determine the effectiveness and safety of PC6 acupoint stimulation with or without antiemetic drug versus sham or antiemetic drug for the prevention of PONV in people undergoing surgery. Search methods: We searched the Cochrane Central Register of Controlled Trials (CENTRAL) (Cochrane Library, Issue 12, 2014), MEDLINE (January 2008 to December 2014), EMBASE (January 2008 to December 2014), ISI Web of Science (January 2008 to December 2014), World Health Organization Clinical Trials Registry, ClinicalTrials.gov, and reference lists of articles to identify additional studies. We applied no language restrictions. Selection criteria: All randomized trials of techniques that stimulated the PC6 acupoint compared with sham treatment or drug therapy, or combined PC6 acupoint and drug therapy compared to drug therapy, for the prevention of PONV. Interventions used in these trials included acupuncture, electro-acupuncture, transcutaneous electrical acupoint stimulation, transcutaneous nerve stimulation, laser stimulation, capsicum plaster, acu-stimulation device, and acupressure in people undergoing surgery. Primary outcomes were the incidences of nausea and vomiting after surgery. Secondary outcomes were the need for rescue antiemetic therapy and adverse effects. Data collection and analysis: Two review authors independently extracted the data and assessed the risk of bias domains for each trial. We used a random-effects model and reported risk ratio (RR) with associated 95% confidence interval (95% CI). We used trial sequential analyses to help provide information on when we had reached firm evidence in cumulative meta-analyses of the primary outcomes, based on a 30% risk ratio reduction in PONV. Main results: We included 59 trials involving 7667 participants. We rated two trials at low risk of bias in all domains (selection, attrition, reporting, blinding and other). We rated 25 trials at high risk in one or more risk-of-bias domains. Compared with sham treatment, PC6 acupoint stimulation significantly reduced the incidence of nausea (RR 0.68, 95% CI 0.60 to 0.77; 40 trials, 4742 participants), vomiting (RR 0.60, 95% CI 0.51 to 0.71; 45 trials, 5147 participants) and the need for rescue antiemetics (RR 0.64, 95% CI 0.55 to 0.73; 39 trials, 4622 participants). As heterogeneity among trials was substantial and there were study limitations, we rated the quality of evidence as low. Using trial sequential analysis, the required information size and boundary for benefit were reached for both primary outcomes.PC6 acupoint stimulation was compared with six different types of antiemetic drugs (metoclopramide, cyclizine, prochlorperazine, droperidol. ondansetron and dexamethasone). There was no difference between PC6 acupoint stimulation and antiemetic drugs in the incidence of nausea (RR 0.91, 95% CI 0.75 to 1.10; 14 trials, 1332 participants), vomiting (RR 0.93, 95% CI 0.74 to 1.17; 19 trials, 1708 participants), or the need for rescue antiemetics (RR 0.87, 95% CI 0.65 to 1.16; 9 trials, 895 participants). We rated the quality of evidence as moderate, due to the study limitations. Using trial sequential analyses, the futility boundary was crossed before the required information size was surpassed for both primary outcomes.Compared to antiemetic drugs, the combination of PC6 acupoint stimulation and antiemetic therapy reduced the incidence of vomiting (RR 0.56, 95% CI 0.35 to 0.91; 9 trials, 687 participants) but not nausea (RR 0.79, 95% CI 0.55 to 1.13; 8 trials, 642 participants). We rated the quality of evidence as very low, due to substantial heterogeneity among trials, study limitations and imprecision. Using trial sequential analysis, none of the boundaries for benefit, harm or futility were crossed for PONV. The need for rescue antiemetic was lower in the combination PC6 acupoint stimulation and antiemetic group than the antiemetic group (RR 0.61, 95% CI 0.44 to 0.86; 5 trials, 419 participants).The side effects associated with PC6 acupoint stimulation were minor, transient and self-limiting (e.g. skin irritation, blistering, redness and pain) in 14 trials. Publication bias was not apparent in the contour-enhanced funnel plots. Authors' conclusions: There is low-quality evidence supporting the use of PC6 acupoint stimulation over sham. Compared to the last update in 2009, no further sham comparison trials are needed. We found that there is moderate-quality evidence showing no difference between PC6 acupoint stimulation and antiemetic drugs to prevent PONV. Further PC6 acupoint stimulation versus antiemetic trials are futile in showing a significant difference, which is a new finding in this update. There is inconclusive evidence supporting the use of a combined strategy of PC6 acupoint stimulation and antiemetic drug over drug prophylaxis, and further high-quality trials are needed.
MeSH term(s)	Acupuncture Points ; Antiemetics/therapeutic use ; Humans ; Postoperative Nausea and Vomiting/prevention & control ; Randomized Controlled Trials as Topic ; Wrist
Chemical Substances	Antiemetics
Language	English
Publishing date	2015-11-02
Publishing country	England
Document type	Journal Article ; Meta-Analysis ; Research Support, N.I.H., Extramural ; Review ; Systematic Review
ISSN	1469-493X
ISSN (online)	1469-493X
DOI	10.1002/14651858.CD003281.pub4
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Article: Genomic structures and regulation patterns at HPV integration sites in cervical cancer.

bioRxiv : the preprint server for biology

2023

Abstract: Human papillomavirus (HPV) integration has been implicated in transforming HPV infection into cancer, but its genomic consequences have been difficult to study using short-read technologies. To resolve the dysregulation associated with HPV integration, ... ...

Abstract	Human papillomavirus (HPV) integration has been implicated in transforming HPV infection into cancer, but its genomic consequences have been difficult to study using short-read technologies. To resolve the dysregulation associated with HPV integration, we performed long-read sequencing on 63 cervical cancer genomes. We identified six categories of integration events based on HPV-human genomic structures. Of all HPV integrants, defined as two HPV-human breakpoints bridged by an HPV sequence, 24% contained variable copies of HPV between the breakpoints, a phenomenon we termed heterologous integration. Analysis of DNA methylation within and in proximity to the HPV genome at individual integration events revealed relationships between methylation status of the integrant and its orientation and structure. Dysregulation of the human epigenome and neighboring gene expression in
Language	English
Publishing date	2023-11-05
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.11.04.564800
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Article ; Online: Renal dysfunction and CABG.

Ho, Anthony M H / Chan, Simon K C

Current opinion in pharmacology

2012 Volume 12, Issue 2, Page(s) 181–188

Abstract: Renal dysfunction after coronary artery bypass grafting is common and is associated with increased morbidity and mortality. A number of strategies with potential renoprotective effects have been investigated, but no single one has been found to warrant ... ...

Abstract	Renal dysfunction after coronary artery bypass grafting is common and is associated with increased morbidity and mortality. A number of strategies with potential renoprotective effects have been investigated, but no single one has been found to warrant routine use in CABG except fenoldopam in which the data to date appear promising. Other measures such as avoidance of nephrotoxic agents, including recent radiocontrast for coronary angiography, may reduce the incidence of renal dysfunction after cardiac surgery and should be implemented in routine care, whenever possible. The best renal protection strategy remains the same as for other organ protection and consists of optimizing haemodynamics, oxygenation, metabolic states and hydration.
MeSH term(s)	Acute Kidney Injury/etiology ; Acute Kidney Injury/prevention & control ; Animals ; Contrast Media/adverse effects ; Coronary Artery Bypass/adverse effects ; Humans ; Protective Agents/therapeutic use
Chemical Substances	Contrast Media ; Protective Agents
Language	English
Publishing date	2012-04
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	2037057-X
ISSN	1471-4973 ; 1471-4892
ISSN (online)	1471-4973
ISSN	1471-4892
DOI	10.1016/j.coph.2012.02.014
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Article: De Novo

Berner, Daniel / Roesti, Marius / Bilobram, Steven / Chan, Simon K / Kirk, Heather / Pandoh, Pawan / Taylor, Gregory A / Zhao, Yongjun / Jones, Steven J M / DeFaveri, Jacquelin

Genes

2019 Volume 10, Issue 6

Abstract: ...

Abstract	:
MeSH term(s)	Animals ; Gene Library ; Genome/genetics ; Genomics/methods ; Microfluidics ; Molecular Sequence Annotation ; Sequence Analysis, DNA ; Smegmamorpha/genetics
Language	English
Publishing date	2019-06-03
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2527218-4
ISSN	2073-4425
ISSN	2073-4425
DOI	10.3390/genes10060426
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Article ; Online: A clinical transcriptome approach to patient stratification and therapy selection in acute myeloid leukemia.

Nature communications

2021 Volume 12, Issue 1, Page(s) 2474

Abstract: As more clinically-relevant genomic features of myeloid malignancies are revealed, it has become clear that targeted clinical genetic testing is inadequate for risk stratification. Here, we develop and validate a clinical transcriptome-based assay for ... ...

Abstract	As more clinically-relevant genomic features of myeloid malignancies are revealed, it has become clear that targeted clinical genetic testing is inadequate for risk stratification. Here, we develop and validate a clinical transcriptome-based assay for stratification of acute myeloid leukemia (AML). Comparison of ribonucleic acid sequencing (RNA-Seq) to whole genome and exome sequencing reveals that a standalone RNA-Seq assay offers the greatest diagnostic return, enabling identification of expressed gene fusions, single nucleotide and short insertion/deletion variants, and whole-transcriptome expression information. Expression data from 154 AML patients are used to develop a novel AML prognostic score, which is strongly associated with patient outcomes across 620 patients from three independent cohorts, and 42 patients from a prospective cohort. When combined with molecular risk guidelines, the risk score allows for the re-stratification of 22.1 to 25.3% of AML patients from three independent cohorts into correct risk groups. Within the adverse-risk subgroup, we identify a subset of patients characterized by dysregulated integrin signaling and RUNX1 or TP53 mutation. We show that these patients may benefit from therapy with inhibitors of focal adhesion kinase, encoded by PTK2, demonstrating additional utility of transcriptome-based testing for therapy selection in myeloid malignancy.
MeSH term(s)	Biomarkers, Tumor/genetics ; Biomarkers, Tumor/metabolism ; Cell Line, Tumor ; Cohort Studies ; Core Binding Factor Alpha 2 Subunit/genetics ; Core Binding Factor Alpha 2 Subunit/metabolism ; Female ; Gene Expression Regulation, Neoplastic/genetics ; Gene Fusion ; Humans ; INDEL Mutation ; Integrins/genetics ; Integrins/metabolism ; Leukemia, Myeloid, Acute/diagnosis ; Leukemia, Myeloid, Acute/genetics ; Leukemia, Myeloid, Acute/metabolism ; Male ; Polymorphism, Single Nucleotide ; Prognosis ; Prospective Studies ; RNA-Seq ; Risk Factors ; Signal Transduction/genetics ; Survival Analysis ; Transcriptome ; Tumor Suppressor Protein p53/genetics ; Tumor Suppressor Protein p53/metabolism ; Whole Exome Sequencing ; Whole Genome Sequencing
Chemical Substances	Biomarkers, Tumor ; Core Binding Factor Alpha 2 Subunit ; Integrins ; RUNX1 protein, human ; TP53 protein, human ; Tumor Suppressor Protein p53
Language	English
Publishing date	2021-04-30
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-021-22625-y
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Article ; Online: Relationship between insertion/deletion (indel) frequency of proteins and essentiality

Hormozdiari Fereydoun / Hsing Michael / Chan Simon K / Cherkasov Artem

BMC Bioinformatics, Vol 8, Iss 1, p

2007 Volume 227

Abstract: Abstract Background In a previous study, we demonstrated that some essential proteins from pathogenic organisms contained sizable insertions/deletions (indels) when aligned to human proteins of high sequence similarity. Such indels may provide sufficient ...

Abstract	Abstract Background In a previous study, we demonstrated that some essential proteins from pathogenic organisms contained sizable insertions/deletions (indels) when aligned to human proteins of high sequence similarity. Such indels may provide sufficient spatial differences between the pathogenic protein and human proteins to allow for selective targeting. In one example, an indel difference was targeted via large scale in-silico screening. This resulted in selective antibodies and small compounds which were capable of binding to the deletion-bearing essential pathogen protein without any cross-reactivity to the highly similar human protein. The objective of the current study was to investigate whether indels were found more frequently in essential than non-essential proteins. Results We have investigated three species, Bacillus subtilis, Escherichia coli , and Saccharomyces cerevisiae , for which high-quality protein essentiality data is available. Using these data, we demonstrated with t-test calculations that the mean indel frequencies in essential proteins were greater than that of non-essential proteins in the three proteomes. The abundance of indels in both types of proteins was also shown to be accurately modeled by the Weibull distribution. However, Receiver Operator Characteristic (ROC) curves showed that indel frequencies alone could not be used as a marker to accurately discriminate between essential and non-essential proteins in the three proteomes. Finally, we analyzed the protein interaction data available for S. cerevisiae and observed that indel-bearing proteins were involved in more interactions and had greater betweenness values within Protein Interaction Networks (PINs). Conclusion Overall, our findings demonstrated that indels were not randomly distributed across the studied proteomes and were likely to occur more often in essential proteins and those that were highly connected, indicating a possible role of sequence insertions and deletions in the regulation and modification of ...
Keywords	Computer applications to medicine. Medical informatics ; R858-859.7 ; Biology (General) ; QH301-705.5
Subject code	612
Language	English
Publishing date	2007-06-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
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Article ; Online: Prognostic significance of autocrine motility factor receptor expression by colorectal cancer and lymph node metastases.

Halwani, Yasmin / Kojic, Liliana D / Chan, Simon K / Phang, Terry P / Masoudi, Hamid / Jones, Steven J M / Nabi, Ivan R / Wiseman, Sam M

American journal of surgery

2015 Volume 209, Issue 5, Page(s) 884–9; discussion 889

Abstract: Background: Autocrine motility factor receptor (AMFR) has been linked to metastasis and tumorigenicity. The aim of this study was to evaluate expression and prognostic significance of AMFR in colorectal carcinoma.: Methods: AMFR expression was ... ...

Abstract	Background: Autocrine motility factor receptor (AMFR) has been linked to metastasis and tumorigenicity. The aim of this study was to evaluate expression and prognostic significance of AMFR in colorectal carcinoma. Methods: AMFR expression was evaluated in 127 colon cancer specimens, 131 rectal cancer specimens, and 47 colonic and 25 rectal corresponding lymph node metastases. Clinicopathological correlates of prognostic significance were established by univariate and multivariate analysis. Spearman's correlation determined the association of expression between cancers and their metastases. Results: AMFR was over-expressed by 22% of colon cancers and 18% of rectal cancers. AMFR over-expression correlated significantly with improved disease-free survival (DFS) (P < .05) in colon cancer and decreased DFS in corresponding nodal metastases. In rectal cancer, AMFR over-expression significantly correlated with decreased overall survival, DFS, and disease-specific survival (P < .001, P = .031, P = .005, respectively) and decreased overall survival in corresponding metastases. Conclusion: AMFR may serve as a molecular prognosticator for colon cancer and rectal cancer.
MeSH term(s)	Biomarkers, Tumor/biosynthesis ; Blotting, Western ; Cell Line, Tumor ; Colorectal Neoplasms/diagnosis ; Colorectal Neoplasms/metabolism ; Colorectal Neoplasms/secondary ; Flow Cytometry ; Humans ; Immunohistochemistry ; Lymph Nodes/metabolism ; Lymph Nodes/pathology ; Lymphatic Metastasis ; Neoplasm Staging ; Prognosis ; Receptors, Autocrine Motility Factor/biosynthesis ; Retrospective Studies
Chemical Substances	Biomarkers, Tumor ; AMFR protein, human (EC 2.3.2.27) ; Receptors, Autocrine Motility Factor (EC 2.3.2.27)
Language	English
Publishing date	2015-05
Publishing country	United States
Document type	Journal Article
ZDB-ID	2953-1
ISSN	1879-1883 ; 0002-9610
ISSN (online)	1879-1883
ISSN	0002-9610
DOI	10.1016/j.amjsurg.2015.01.010
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Article: Barriers to returning to work for people with spinal cord injuries: a focus group study.

Chan, Simon K K / Man, David W K

Work (Reading, Mass.)

2005 Volume 25, Issue 4, Page(s) 325–332

Abstract: The rate of employment for people with spinal cord injuries is relatively low, especially among Asians. To help individuals with spinal cord injuries return to work or retain employment, rehabilitation professionals must understand the barriers to ... ...

Abstract	The rate of employment for people with spinal cord injuries is relatively low, especially among Asians. To help individuals with spinal cord injuries return to work or retain employment, rehabilitation professionals must understand the barriers to employment and intervene to reduce or remove them. Hence, a focus group study was administered to 16 people with spinal cord injuries to explore return to work barriers. Various ideas, beliefs, responses, and values at different stages of work resettlement were elicited from both employed and unemployed participants, and then summarized. According to the results, several modifications of existing forms of rehabilitation intervention are necessary, as are further research directions.
MeSH term(s)	Adolescent ; Adult ; Employment ; Female ; Focus Groups ; Hong Kong ; Humans ; Male ; Middle Aged ; Spinal Cord Injuries
Language	English
Publishing date	2005
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1394194-x
ISSN	1051-9815
ISSN	1051-9815
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Article ; Online: Cannula malposition during antegrade cerebral perfusion for aortic surgery: role of cerebral oximetry.

Chan, Simon K C / Underwood, Malcolm J / Ho, Anthony M-H / So, Jack M / Ho, Adrienne K / Wan, Innes Y P / Wong, Randolph H L

Canadian journal of anaesthesia = Journal canadien d'anesthesie

2014 Volume 61, Issue 8, Page(s) 736–740

Abstract: Purpose: To describe the use of cerebral oximetry to detect a lack of right cerebral perfusion resulting from a malpositioned catheter used for antegrade cerebral perfusion during deep hypothermic circulatory arrest (DHCA). The simple corrective ... ...

Abstract	Purpose: To describe the use of cerebral oximetry to detect a lack of right cerebral perfusion resulting from a malpositioned catheter used for antegrade cerebral perfusion during deep hypothermic circulatory arrest (DHCA). The simple corrective surgical adjustment that followed averted a potentially serious complication. Clinical features: A 57-yr-old male with a type-A aortic dissection undergoing DHCA required antegrade cerebral perfusion for cerebral protection. Catheters were placed accordingly in the left common carotid and brachiocephalic arteries. Whereas frontal cerebral oximetry immediately improved on the left, it did not improve on the right. It was immediately suspected that the tip of the brachiocephalic cannula had advanced into the right subclavian artery, thus depriving the right common carotid artery of blood flow. The problem resolved upon slight withdrawal of the cannula. Conclusion: Vigilance in anesthesia should not stop during DHCA or cardiopulmonary bypass. Cerebral oximetry may provide important information leading to actions that improve brain protection. Vigilances proved important in this case where the cannula tip used for antegrade cerebral perfusion was advanced too far into the right subclavian artery.
MeSH term(s)	Aneurysm, Dissecting/surgery ; Aortic Aneurysm, Thoracic/surgery ; Brain/metabolism ; Catheters/adverse effects ; Circulatory Arrest, Deep Hypothermia Induced ; Humans ; Male ; Middle Aged ; Oximetry ; Subclavian Artery
Keywords	covid19
Language	English
Publishing date	2014-08
Publishing country	United States
Document type	Case Reports ; Journal Article
ZDB-ID	91002-8
ISSN	1496-8975 ; 0832-610X
ISSN (online)	1496-8975
ISSN	0832-610X
DOI	10.1007/s12630-014-0181-2
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