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Article ; Online: Data of de novo assembly and functional annotation of transcriptome of Peninsular Malaysian

Fareed, Fathmath Shaman / Yen Yen, Sam / Singaram, Nallammai

2023 Volume 50, Page(s) 109507

Abstract: ... ...

Abstract	The
Language	English
Publishing date	2023-08-21
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2786545-9
ISSN	2352-3409 ; 2352-3409
ISSN (online)	2352-3409
ISSN	2352-3409
DOI	10.1016/j.dib.2023.109507
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Article ; Online: Metagenomics: a path to understanding the gut microbiome.

Yen, Sandi / Johnson, Jethro S

Mammalian genome : official journal of the International Mammalian Genome Society

2021 Volume 32, Issue 4, Page(s) 282–296

Abstract: The gut microbiome is a major determinant of host health, yet it is only in the last 2 decades that the advent of next-generation sequencing has enabled it to be studied at a genomic level. Shotgun sequencing is beginning to provide insight into the ... ...

Abstract	The gut microbiome is a major determinant of host health, yet it is only in the last 2 decades that the advent of next-generation sequencing has enabled it to be studied at a genomic level. Shotgun sequencing is beginning to provide insight into the prokaryotic as well as eukaryotic and viral components of the gut community, revealing not just their taxonomy, but also the functions encoded by their collective metagenome. This revolution in understanding is being driven by continued development of sequencing technologies and in consequence necessitates reciprocal development of computational approaches that can adapt to the evolving nature of sequence datasets. In this review, we provide an overview of current bioinformatic strategies for handling metagenomic sequence data and discuss their strengths and limitations. We then go on to discuss key technological developments that have the potential to once again revolutionise the way we are able to view and hence understand the microbiome.
MeSH term(s)	Computational Biology/standards ; Gastrointestinal Microbiome/genetics ; High-Throughput Nucleotide Sequencing/standards ; Humans ; Metagenome/genetics ; Metagenomics ; Microbiota/genetics ; RNA, Ribosomal, 16S/genetics
Chemical Substances	RNA, Ribosomal, 16S
Language	English
Publishing date	2021-07-14
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	1058547-3
ISSN	1432-1777 ; 0938-8990
ISSN (online)	1432-1777
ISSN	0938-8990
DOI	10.1007/s00335-021-09889-x
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Article: Metagenomics: a path to understanding the gut microbiome

Yen, Sandi / Johnson, Jethro S.

Mammalian genome. 2021 Aug., v. 32, no. 4

2021

Abstract	The gut microbiome is a major determinant of host health, yet it is only in the last 2 decades that the advent of next-generation sequencing has enabled it to be studied at a genomic level. Shotgun sequencing is beginning to provide insight into the prokaryotic as well as eukaryotic and viral components of the gut community, revealing not just their taxonomy, but also the functions encoded by their collective metagenome. This revolution in understanding is being driven by continued development of sequencing technologies and in consequence necessitates reciprocal development of computational approaches that can adapt to the evolving nature of sequence datasets. In this review, we provide an overview of current bioinformatic strategies for handling metagenomic sequence data and discuss their strengths and limitations. We then go on to discuss key technological developments that have the potential to once again revolutionise the way we are able to view and hence understand the microbiome.
Keywords	bioinformatics ; data collection ; digestive system ; genome ; intestinal microorganisms ; mammals ; metagenomics ; microbiome ; taxonomy
Language	English
Dates of publication	2021-08
Size	p. 282-296.
Publishing place	Springer US
Document type	Article
Note	Review
ZDB-ID	1058547-3
ISSN	1432-1777 ; 0938-8990
ISSN (online)	1432-1777
ISSN	0938-8990
DOI	10.1007/s00335-021-09889-x
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Article ; Online: The effects of a hydrolyzed protein diet on the plasma, fecal and urine metabolome in cats with chronic enteropathy.

Kathrani, Aarti / Yen, Sandi / Hall, Edward J / Swann, Jonathan R

Scientific reports

2023 Volume 13, Issue 1, Page(s) 19979

Abstract: Hydrolyzed protein diets are extensively used to treat chronic enteropathy (CE) in cats. However, the biochemical effects of such a diet on feline CE have not been characterized. In this study an ... ...

Abstract	Hydrolyzed protein diets are extensively used to treat chronic enteropathy (CE) in cats. However, the biochemical effects of such a diet on feline CE have not been characterized. In this study an untargeted
MeSH term(s)	Cats ; Humans ; Animals ; Feces/chemistry ; Metabolome ; Metabolomics ; Diet/veterinary ; Inflammatory Bowel Diseases
Language	English
Publishing date	2023-11-15
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-023-47334-y
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Article ; Online: Suicide Risk and Psychotic Experiences: Considerations for Safety Planning with Adolescents.

Thompson, Elizabeth C / Nail, Margaret / Yen, Shirley

Rhode Island medical journal (2013)

2022 Volume 105, Issue 4, Page(s) 26–30

Abstract: Individuals with psychosis-spectrum conditions have strikingly high rates of suicidal thoughts and behaviors, especially in the early stages of illness. Given increasing rates of suicide among adolescents, and given that psychosis symptoms often emerge ... ...

Abstract	Individuals with psychosis-spectrum conditions have strikingly high rates of suicidal thoughts and behaviors, especially in the early stages of illness. Given increasing rates of suicide among adolescents, and given that psychosis symptoms often emerge during this developmental period, it is important that practitioners working with adolescents are attuned to the intersection of psychotic experiences and suicide risk. Furthermore, youth with emerging signs of psychosis often struggle with other mental health concerns that are linked to suicidal thoughts and behaviors, including depression, anxiety, mania, trauma, and substance use. Taken together, these factors indicate that identifying early signs of psychosis can be critical for addressing suicide risk, and psychosis-spectrum symptoms are important experiences to include in safety planning for youth. Herein we discuss considerations for safety planning for adolescents experiencing psychosis-spectrum symptoms, drawn from clinical observations and pilot data collected from adolescents in a psychiatric inpatient unit and their families.
MeSH term(s)	Adolescent ; Anxiety ; Humans ; Psychotic Disorders ; Substance-Related Disorders ; Suicidal Ideation ; Suicide/psychology ; Suicide Prevention
Language	English
Publishing date	2022-05-02
Publishing country	United States
Document type	Journal Article
ZDB-ID	419430-5
ISSN	2327-2228 ; 0363-7913
ISSN (online)	2327-2228
ISSN	0363-7913
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Article ; Online: The effect of a hydrolyzed protein diet on the fecal microbiota in cats with chronic enteropathy.

Kathrani, Aarti / Yen, Sandi / Swann, Jonathan R / Hall, Edward J

Scientific reports

2022 Volume 12, Issue 1, Page(s) 2746

Abstract: The effect of a hydrolyzed protein diet on the fecal microbiota has not been studied in feline chronic enteropathy (CE). Our study aimed to (1) compare the fecal microbiota of cats with CE to control cats with no gastrointestinal signs and (2) determine ... ...

Abstract	The effect of a hydrolyzed protein diet on the fecal microbiota has not been studied in feline chronic enteropathy (CE). Our study aimed to (1) compare the fecal microbiota of cats with CE to control cats with no gastrointestinal signs and (2) determine the effect of a hydrolyzed protein diet on the fecal microbiota of cats with CE and whether this differs between dietary responders and non-responders. The fecal microbiome of cats with CE (n = 36) showed decreased α-diversity in terms of genus richness (P = 0.04) and increased β-diversity in terms of Bray-Curtis Dissimilarity (P < 0.001) compared to control cats (n = 14). Clostridium was the only genera significantly over-represented in cats with CE compared to control cats (adjusted P < 0.1). After 6-weeks of feeding the diet, fifteen cats were classified as responders and 18 as non-responders, based on clinical signs. At the genus level, α-diversity was increased in non-responders versus responders at diagnosis, but decreased after dietary intervention in both groups (P < 0.05). At the family level, non-responders became increasingly dissimilar after dietary intervention (P = 0.012). In general, the abundance of bacteria decreased with feeding a hydrolyzed diet, with the genera most significantly affected being more frequently observed in non-responders. Bifidobacterium was the only genus that increased significantly in abundance post-diet and this effect was observed in both responders and non-responders. Both Oscillibacter and Desulfovibrionaceae_unclassified were most abundant in non-responders at diagnosis but were rarely observed post diet in neither responders nor non-responders. Cats with CE had similar microbiota changes to those described in human inflammatory bowel disease. Whether the presence of Oscillibacter and Desulfovibrionaceae_unclassified are indicators of non-response to the diet at diagnosis requires further investigation. Despite the hydrolyzed diet reducing α-diversity in all cats with CE, this did not resolve gastrointestinal signs in some cats. However, responders metabolized the diet in a similar manner, reflected by sustained β-diversity, while the microbiome of non-responders became increasingly dissimilar compared to diagnosis at the family level. Therefore, the microbiome may not be as tightly regulated in cats with CE that are non-responders and therefore, these cats would require additional therapy for remission of clinical signs.
MeSH term(s)	Animal Feed ; Animals ; Bacteria/classification ; Bacteria/isolation & purification ; Cats ; Feces/microbiology ; Female ; Inflammatory Bowel Diseases/microbiology ; Male ; Protein Hydrolysates/pharmacology
Chemical Substances	Protein Hydrolysates
Language	English
Publishing date	2022-02-17
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-022-06576-y
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Article ; Online: Bipolar Radiofrequency-Assisted Liposuction for Cervical Contouring in Eastern Asians.

Yen, ShihChun / Wang, JiGeng / Gao, Xiang / Zhu, QiuXuan / Song, CaiYing / Zhu, Fei

Aesthetic surgery journal. Open forum

2023 Volume 5, Page(s) ojad035

Language	English
Publishing date	2023-04-04
Publishing country	England
Document type	Journal Article
ISSN	2631-4797
ISSN (online)	2631-4797
DOI	10.1093/asjof/ojad035
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Article ; Online: A daily diary study of minority stressors, suicidal ideation, nonsuicidal self-injury ideation, and affective mechanisms among sexual and gender minority youth.

Mereish, Ethan H / Peters, Jessica R / Brick, Leslie A D / Killam, Matthew A / Yen, Shirley

Journal of psychopathology and clinical science

2023 Volume 132, Issue 4, Page(s) 372–384

Abstract: Sexual and gender minority youth (SGMY) are at greater risk than their heterosexual and cisgender counterparts for suicidal thoughts and behaviors (STB) and nonsuicidal self-injury (NSSI). Unique stressors (i.e., minority stressors) specific to SGMY's ... ...

Abstract	Sexual and gender minority youth (SGMY) are at greater risk than their heterosexual and cisgender counterparts for suicidal thoughts and behaviors (STB) and nonsuicidal self-injury (NSSI). Unique stressors (i.e., minority stressors) specific to SGMY's stigmatized identities such as discrimination or concealment of one's identity are posited to explain these disparities. However, there is limited research examining the associations among minority stressors, affective mediating processes, and STB and NSSI in SGMY's daily lives. We conducted a 28-day daily diary study to test the mediating effects of daily negative and positive affect and emotion dysregulation between minority stressors and STB and NSSI among SGMY who were recruited from clinical and community settings. Participants were 92 SGMY, aged 12-19 years old (
MeSH term(s)	Humans ; Adolescent ; Child ; Young Adult ; Adult ; Suicidal Ideation ; Self-Injurious Behavior/psychology ; Sexual and Gender Minorities ; Sexual Behavior ; Interpersonal Relations
Language	English
Publishing date	2023-03-30
Publishing country	United States
Document type	Journal Article
ZDB-ID	3121059-4
ISSN	2769-755X
ISSN (online)	2769-755X
DOI	10.1037/abn0000813
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Article ; Online: Fetal heart rate patterns and the incidence of adverse events after oral misoprostol administration for cervical ripening among low-risk pregnancies.

Kandahari, Nazineen / Tucker, Lue-Yen S / Schneider, Allison N / Raine-Bennett, Tina R / Mohta, Vanitha J

The journal of maternal-fetal & neonatal medicine : the official journal of the European Association of Perinatal Medicine, the Federation of Asia and Oceania Perinatal Societies, the International Society of Perinatal Obstetricians

2023 Volume 36, Issue 1, Page(s) 2199344

Abstract: Objective: Though misoprostol is commonly used for inpatient cervical ripening, its use in outpatient settings has been limited by safety concerns. This study was conducted to assess the association between early fetal heart tracing (FHT) and maternal ... ...

Abstract	Objective: Though misoprostol is commonly used for inpatient cervical ripening, its use in outpatient settings has been limited by safety concerns. This study was conducted to assess the association between early fetal heart tracing (FHT) and maternal tocodynamometry patterns and the incidence of adverse fetal and pregnancy outcomes after the administration of oral misoprostol for cervical ripening. Methods: We conducted a retrospective cohort study of 9908 low-risk patients at ≥37 weeks gestation who received oral misoprostol for cervical ripening prior to rupture of membranes between 01/01/2012 and 12/31/2017 at Kaiser Permanente Northern California hospitals as inpatients. We excluded patients who received a different agent for cervical ripening or had any need for additional inpatient monitoring, including hypertensive disorders of pregnancy, diabetes, or intrauterine growth restriction. Abnormal FHT, abnormal uterine activity, and adverse pregnancy or fetal-related events documented in the electronic health record in the four hours after administration of the first and second doses of misoprostol were assessed using descriptive statistics. Results: We found that 0.9% of patients experienced tachysystole after the first dose of misoprostol (0.6% without decelerations; 0.3% with decelerations). The incidence of variable decelerations only and other FHT abnormalities (i.e. bradycardia, late or prolonged decelerations, or absent or minimal variability) in the first hour after misoprostol administration were 7.1% and 6.7% respectively, and diminished over time. The need for tocolytic use was 0.2% in the first hour and declined over time to 0.03% in the fourth hour after the first dose. Urgent cesarean delivery occurred in 0.1% of patients after receiving the first dose of misoprostol. Patients who did not experience variable, prolonged, or late decelerations in the first hour after the initial misoprostol dose were less likely to have such FHT abnormalities in the subsequent three hours compared to patients who had other FHT abnormalities (11.8% among patients with no FHT abnormalities vs. 43.7% among patients with other FHT abnormalities; Conclusion: The risk of short-term adverse outcomes associated with misoprostol is low among relatively low-risk patients. FHT abnormalities occurred in up to 32% of patients in the first four hours of monitoring post-misoprostol. Patients with no FHT abnormalities in the first hour after receiving misoprostol had a low risk of developing adverse outcomes and FHT abnormalities on continued monitoring, while patients with any type of deceleration in the first hour were at higher risk of adverse outcomes and FHT abnormalities. Our data may inform the development of protocols for cervical ripening that allow reduced monitoring for a subset of low-risk patients, however, more research is needed to validate findings and develop clinical protocols.
MeSH term(s)	Pregnancy ; Female ; Humans ; Misoprostol/adverse effects ; Oxytocics/adverse effects ; Cervical Ripening ; Incidence ; Heart Rate, Fetal ; Retrospective Studies ; Labor, Induced/adverse effects ; Labor, Induced/methods ; Administration, Intravaginal ; Administration, Oral
Chemical Substances	Misoprostol (0E43V0BB57) ; Oxytocics
Language	English
Publishing date	2023-04-09
Publishing country	England
Document type	Journal Article
ZDB-ID	2077261-0
ISSN	1476-4954 ; 1057-0802 ; 1476-7058
ISSN (online)	1476-4954
ISSN	1057-0802 ; 1476-7058
DOI	10.1080/14767058.2023.2199344
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Article ; Online: Orthodontic and Surgical Principles for Distraction Osteogenesis in Children with Pierre-Robin Sequence.

Yen, Stephen / Gaal, Austin / Smith, Kevin S

Oral and maxillofacial surgery clinics of North America

2020 Volume 32, Issue 2, Page(s) 283–295

Abstract: Patients with Pierre-Robin sequence recalcitrant to nonsurgical intervention have historically required tracheostomy. Mandibular distraction provides a predictable alternative to tracheostomy. Orthodontic perioperative interventions should be considered, ...

Abstract	Patients with Pierre-Robin sequence recalcitrant to nonsurgical intervention have historically required tracheostomy. Mandibular distraction provides a predictable alternative to tracheostomy. Orthodontic perioperative interventions should be considered, including overcorrection, placement of temporary anchorage devices, elastics, and molding the regenerate. Mandibular distraction can be technically difficult and may cause complications. Performed correctly, mandibular distraction provides patients with a better quality of life than tracheostomy.
MeSH term(s)	Airway Obstruction ; Child ; Humans ; Infant ; Mandible ; Osteogenesis, Distraction ; Pierre Robin Syndrome/surgery ; Quality of Life ; Treatment Outcome
Language	English
Publishing date	2020-03-07
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	1316546-x
ISSN	1558-1365 ; 1042-3699
ISSN (online)	1558-1365
ISSN	1042-3699
DOI	10.1016/j.coms.2020.01.012
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