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Article ; Online: Concurrent invasions of European starlings in Australia and North America reveal population-specific differentiation in shared genomic regions.

Hofmeister, Natalie R / Stuart, Katarina C / Warren, Wesley C / Werner, Scott J / Bateson, Melissa / Ball, Gregory F / Buchanan, Katherine L / Burt, David W / Cardilini, Adam P A / Cassey, Phillip / De Meyer, Tim / George, Julia / Meddle, Simone L / Rowland, Hannah M / Sherman, Craig D H / Sherwin, William B / Vanden Berghe, Wim / Rollins, Lee Ann / Clayton, David F

Molecular ecology

2023

Abstract: A species' success during the invasion of new areas hinges on an interplay between the demographic processes common to invasions and the specific ecological context of the novel environment. Evolutionary genetic studies of invasive species can ... ...

Abstract	A species' success during the invasion of new areas hinges on an interplay between the demographic processes common to invasions and the specific ecological context of the novel environment. Evolutionary genetic studies of invasive species can investigate how genetic bottlenecks and ecological conditions shape genetic variation in invasions, and our study pairs two invasive populations that are hypothesized to be from the same source population to compare how each population evolved during and after introduction. Invasive European starlings (Sturnus vulgaris) established populations in both Australia and North America in the 19th century. Here, we compare whole-genome sequences among native and independently introduced European starling populations to determine how demographic processes interact with rapid evolution to generate similar genetic patterns in these recent and replicated invasions. Demographic models indicate that both invasive populations experienced genetic bottlenecks as expected based on invasion history, and we find that specific genomic regions have differentiated even on this short evolutionary timescale. Despite genetic bottlenecks, we suggest that genetic drift alone cannot explain differentiation in at least two of these regions. The demographic boom intrinsic to many invasions as well as potential inversions may have led to high population-specific differentiation, although the patterns of genetic variation are also consistent with the hypothesis that this infamous and highly mobile invader adapted to novel selection (e.g., extrinsic factors). We use targeted sampling of replicated invasions to identify and evaluate support for multiple, interacting evolutionary mechanisms that lead to differentiation during the invasion process.
Language	English
Publishing date	2023-11-07
Publishing country	England
Document type	Journal Article
ZDB-ID	1126687-9
ISSN	1365-294X ; 0962-1083
ISSN (online)	1365-294X
ISSN	0962-1083
DOI	10.1111/mec.17195
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Article ; Online: Transcript- and annotation-guided genome assembly of the European starling.

Stuart, Katarina C / Edwards, Richard J / Cheng, Yuanyuan / Warren, Wesley C / Burt, David W / Sherwin, William B / Hofmeister, Natalie R / Werner, Scott J / Ball, Gregory F / Bateson, Melissa / Brandley, Matthew C / Buchanan, Katherine L / Cassey, Phillip / Clayton, David F / De Meyer, Tim / Meddle, Simone L / Rollins, Lee A

Molecular ecology resources

2022 Volume 22, Issue 8, Page(s) 3141–3160

Abstract: The European starling, Sturnus vulgaris, is an ecologically significant, globally invasive avian species that is also suffering from a major decline in its native range. Here, we present the genome assembly and long-read transcriptome of an Australian- ... ...

Abstract	The European starling, Sturnus vulgaris, is an ecologically significant, globally invasive avian species that is also suffering from a major decline in its native range. Here, we present the genome assembly and long-read transcriptome of an Australian-sourced European starling (S. vulgaris vAU), and a second, North American, short-read genome assembly (S. vulgaris vNA), as complementary reference genomes for population genetic and evolutionary characterization. S. vulgaris vAU combined 10× genomics linked-reads, low-coverage Nanopore sequencing, and PacBio Iso-Seq full-length transcript scaffolding to generate a 1050 Mb assembly on 6222 scaffolds (7.6 Mb scaffold N50, 94.6% busco completeness). Further scaffolding against the high-quality zebra finch (Taeniopygia guttata) genome assigned 98.6% of the assembly to 32 putative nuclear chromosome scaffolds. Species-specific transcript mapping and gene annotation revealed good gene-level assembly and high functional completeness. Using S. vulgaris vAU, we demonstrate how the multifunctional use of PacBio Iso-Seq transcript data and complementary homology-based annotation of sequential assembly steps (assessed using a new tool, saaga) can be used to assess, inform, and validate assembly workflow decisions. We also highlight some counterintuitive behaviour in traditional busco metrics, and present buscomp, a complementary tool for assembly comparison designed to be robust to differences in assembly size and base-calling quality. This work expands our knowledge of avian genomes and the available toolkit for assessing and improving genome quality. The new genomic resources presented will facilitate further global genomic and transcriptomic analysis on this ecologically important species.
MeSH term(s)	Animals ; Australia ; Genome/genetics ; Genomics ; Molecular Sequence Annotation ; Starlings/genetics
Language	English
Publishing date	2022-07-18
Publishing country	England
Document type	Journal Article
ZDB-ID	2406833-0
ISSN	1755-0998 ; 1755-098X
ISSN (online)	1755-0998
ISSN	1755-098X
DOI	10.1111/1755-0998.13679
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Article ; Online: The latent structure of depressive symptoms across clinical high risk and chronic phases of psychotic illness.

Vargas, Teresa / Ahmed, Anthony O / Strauss, Gregory P / Brandes, Cassandra M / Walker, Elaine F / Buchanan, Robert W / Gold, James M / Mittal, Vijay A

Translational psychiatry

2019 Volume 9, Issue 1, Page(s) 229

Abstract: Depressive symptoms are highly prevalent in psychotic populations and result in significant functional impairment. Limited knowledge of whether depressive symptoms are invariant across stages of illness curtails our ability to understand how these relate ...

Abstract	Depressive symptoms are highly prevalent in psychotic populations and result in significant functional impairment. Limited knowledge of whether depressive symptoms are invariant across stages of illness curtails our ability to understand how these relate to illness progression. Clarifying the latent structure of depressive symptoms across stages of illness progression would aid etiological conceptualizations and preventive models. In the present study, one-factor (including all items) and two-factor (depression/hopelessness and guilt/self-depreciation) solutions were specified through confirmatory factor analysis (CFA). Measurement invariance analyses were undertaken across schizophrenia (SCZ; n = 312) and clinical high-risk (CHR; n = 175) groups to estimate whether the same construct is being measured across groups. Clinical correlates of the factors were examined. Results indicated that CHR individuals had a greater proportion of mood disorder diagnoses. Metric invariance held for the one-factor solution, and scalar invariance held for the two-factor solution. Notably, negative symptoms did not correlate with depressive symptoms in the SCZ group, though strong correlations were observed in CHR individuals. Positive symptoms were comparably associated with depressive symptoms in both groups. Results suggest depressive symptoms are more prevalent in CHR individuals. Targeting these symptoms may aid future efforts to identify risk of conversion. Further, some depressive symptoms may be systematically more endorsed in CHR individuals. Separating into depression/hopelessness and guilt/self-depreciation scores may aid comparability across stages of illness progression, though this issue deserves careful attention and future study.
MeSH term(s)	Adolescent ; Adult ; Affect ; Depression/complications ; Depression/psychology ; Female ; Humans ; Male ; Middle Aged ; Models, Psychological ; Psychiatric Status Rating Scales ; Psychometrics ; Psychotic Disorders/complications ; Psychotic Disorders/psychology ; Young Adult
Language	English
Publishing date	2019-09-16
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2609311-X
ISSN	2158-3188 ; 2158-3188
ISSN (online)	2158-3188
ISSN	2158-3188
DOI	10.1038/s41398-019-0563-x
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Article ; Online: Genetic Analysis of Pediatric Primary Adrenal Insufficiency of Unknown Etiology: 25 Years' Experience in the UK.

Buonocore, Federica / Maharaj, Avinaash / Qamar, Younus / Koehler, Katrin / Suntharalingham, Jenifer P / Chan, Li F / Ferraz-de-Souza, Bruno / Hughes, Claire R / Lin, Lin / Prasad, Rathi / Allgrove, Jeremy / Andrews, Edward T / Buchanan, Charles R / Cheetham, Tim D / Crowne, Elizabeth C / Davies, Justin H / Gregory, John W / Hindmarsh, Peter C / Hulse, Tony /

Krone, Nils P / Shah, Pratik / Shaikh, M Guftar / Roberts, Catherine / Clayton, Peter E / Dattani, Mehul T / Thomas, N Simon / Huebner, Angela / Clark, Adrian J / Metherell, Louise A / Achermann, John C

Journal of the Endocrine Society

2021 Volume 5, Issue 8, Page(s) bvab086

Abstract: Context: Although primary adrenal insufficiency (PAI) in children and young people is often due to congenital adrenal hyperplasia (CAH) or autoimmunity, other genetic causes occur. The relative prevalence of these conditions is poorly understood.: ... ...

Abstract	Context: Although primary adrenal insufficiency (PAI) in children and young people is often due to congenital adrenal hyperplasia (CAH) or autoimmunity, other genetic causes occur. The relative prevalence of these conditions is poorly understood. Objective: We investigated genetic causes of PAI in children and young people over a 25 year period. Design setting and participants: Unpublished and published data were reviewed for 155 young people in the United Kingdom who underwent genetic analysis for PAI of unknown etiology in three major research centers between 1993 and 2018. We pre-excluded those with CAH, autoimmune, or metabolic causes. We obtained additional data from NR0B1 (DAX-1) clinical testing centers. Intervention and outcome measurements: Genetic analysis involved a candidate gene approach (1993 onward) or next generation sequencing (NGS; targeted panels, exomes) (2013-2018). Results: A genetic diagnosis was reached in 103/155 (66.5%) individuals. In 5 children the adrenal insufficiency resolved and no genetic cause was found. Pathogenic variants occurred in 11 genes: Conclusions: PAI in children and young people often has a genetic basis. Establishing the specific etiology can influence management of this lifelong condition. NGS approaches improve the diagnostic yield when many potential candidate genes are involved.
Language	English
Publishing date	2021-05-11
Publishing country	United States
Document type	Journal Article
ISSN	2472-1972
ISSN (online)	2472-1972
DOI	10.1210/jendso/bvab086
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Article ; Online: A pan-cancer transcriptome analysis identifies replication fork and innate immunity genes as modifiers of response to the CHK1 inhibitor prexasertib.

Oncotarget

2020 Volume 11, Issue 3, Page(s) 216–236

Abstract: The combined influence of oncogenic drivers, genomic instability, and/or DNA damage repair deficiencies increases replication stress in cancer. Cells with high replication stress rely on the upregulation of checkpoints like those governed by CHK1 for ... ...

Abstract	The combined influence of oncogenic drivers, genomic instability, and/or DNA damage repair deficiencies increases replication stress in cancer. Cells with high replication stress rely on the upregulation of checkpoints like those governed by CHK1 for survival. Previous studies of the CHK1 inhibitor prexasertib demonstrated activity across multiple cancer types. Therefore, we sought to (1) identify markers of prexasertib sensitivity and (2) define the molecular mechanism(s) of intrinsic and acquired resistance using preclinical models representing multiple tumor types. Our findings indicate that while cyclin E dysregulation is a driving mechanism of prexasertib response, biomarkers associated with this aberration lack sufficient predictive power to render them clinically actionable for patient selection. Transcriptome analysis of a pan-cancer cell line panel and
Language	English
Publishing date	2020-01-21
Publishing country	United States
Document type	Journal Article
ZDB-ID	2560162-3
ISSN	1949-2553 ; 1949-2553
ISSN (online)	1949-2553
ISSN	1949-2553
DOI	10.18632/oncotarget.27400
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Article ; Online: Underutilization of Evidence-Based Smoking Cessation Support Strategies Despite High Smoking Addiction Burden in Peripheral Artery Disease Specialty Care: Insights from the International PORTRAIT Registry.

Patel, Krishna K / Jones, Philip G / Ellerbeck, Edward F / Buchanan, Donna M / Chan, Paul S / Pacheco, Christina M / Moneta, Gregory / Spertus, John A / Smolderen, Kim G

Journal of the American Heart Association

2018 Volume 7, Issue 20, Page(s) e010076

Abstract: Background Smoking is the most important risk factor for peripheral artery disease ( PAD ). Smoking cessation is key in PAD management. We aimed to examine smoking rates and smoking cessation interventions offered to patients with PAD consulting a ... ...

Abstract	Background Smoking is the most important risk factor for peripheral artery disease ( PAD ). Smoking cessation is key in PAD management. We aimed to examine smoking rates and smoking cessation interventions offered to patients with PAD consulting a vascular specialty clinic; and assess changes in smoking behavior over the year following initial visit. Methods and Results A total of 1272 patients with PAD and new or worsening claudication were enrolled at 16 vascular specialty clinics (2011-2015, PORTRAIT (Patient-Centered Outcomes Related to Treatment Practices in Peripheral Arterial Disease: Investigating Trajectories) registry). Interviews collected smoking status and cessation interventions at baseline, 3, 6, and 12 months. Among smokers, transition state models analyzed smoking transitions at each time point and identified factors associated with quitting and relapse. On presentation, 474 (37.3%) patients were active, 660 (51.9%) former, and 138 (10.8%) never smokers. Among active smokers, only 16% were referred to cessation counseling and 11% were prescribed pharmacologic treatment. At 3 months, the probability of quitting smoking was 21%; among those continuing to smoke at 3 months, the probability of quitting during the next 9 months varied between 11% and 12% ( P<0.001). The probability of relapse among initial quitters was 36%. At 12 months, 72% of all smokers continued to smoke. Conclusions More than one third of patients with claudication consulting a PAD provider are active smokers and few received evidence-based cessation interventions. Patients appear to be most likely to quit early in their treatment course, but many quickly relapse and 72% of all patients smoking at baseline are still smoking at 12 months. Better strategies are needed to provide continuous cessation support. Clinical Trial Registration URL : https://www.clinicaltrials.gov . Unique identifier: NCT 01419080.
MeSH term(s)	Aged ; Analysis of Variance ; Cigarette Smoking/adverse effects ; Cigarette Smoking/prevention & control ; Facilities and Services Utilization ; Female ; Health Services Accessibility/statistics & numerical data ; Humans ; Intermittent Claudication/prevention & control ; Male ; Middle Aged ; Peripheral Arterial Disease/prevention & control ; Prospective Studies ; Registries ; Risk Factors ; Smoking Cessation/statistics & numerical data ; Social Support
Language	English
Publishing date	2018-10-29
Publishing country	England
Document type	Journal Article ; Multicenter Study ; Observational Study ; Research Support, Non-U.S. Gov't
ZDB-ID	2653953-6
ISSN	2047-9980 ; 2047-9980
ISSN (online)	2047-9980
ISSN	2047-9980
DOI	10.1161/JAHA.118.010076
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Article ; Online: Clinical Practice Guideline: Ménière's Disease Executive Summary.

Basura, Gregory J / Adams, Meredith E / Monfared, Ashkan / Schwartz, Seth R / Antonelli, Patrick J / Burkard, Robert / Bush, Matthew L / Bykowski, Julie / Colandrea, Maria / Derebery, Jennifer / Kelly, Elizabeth A / Kerber, Kevin A / Koopman, Charles F / Kuch, Amy Angie / Marcolini, Evie / McKinnon, Brian J / Ruckenstein, Michael J / Valenzuela, Carla V / Vosooney, Alexis /

Walsh, Sandra A / Nnacheta, Lorraine C / Dhepyasuwan, Nui / Buchanan, Erin M

Otolaryngology--head and neck surgery : official journal of American Academy of Otolaryngology-Head and Neck Surgery

2020 Volume 162, Issue 4, Page(s) 415–434

Abstract: Objective: Ménière's disease (MD) is a clinical condition defined by spontaneous vertigo attacks (each lasting 20 minutes to 12 hours) with documented low- to midfrequency sensorineural hearing loss in the affected ear before, during, or after one of ... ...

Abstract	Objective: Ménière's disease (MD) is a clinical condition defined by spontaneous vertigo attacks (each lasting 20 minutes to 12 hours) with documented low- to midfrequency sensorineural hearing loss in the affected ear before, during, or after one of the episodes of vertigo. It also presents with fluctuating aural symptoms (hearing loss, tinnitus, or ear fullness) in the affected ear. The underlying etiology of MD is not completely clear, yet it has been associated with inner ear fluid volume increases, culminating in episodic ear symptoms (vertigo, fluctuating hearing loss, tinnitus, and aural fullness). Physical examination findings are often unremarkable, and audiometric testing may or may not show low- to midfrequency sensorineural hearing loss. Imaging, if performed, is also typically normal. The goals of MD treatment are to prevent or reduce vertigo severity and frequency; relieve or prevent hearing loss, tinnitus, and aural fullness; and improve quality of life. Treatment approaches to MD are many, and approaches typically include modifications of lifestyle factors (eg, diet) and medical, surgical, or a combination of therapies. Purpose: The primary purpose of this clinical practice guideline is to improve the quality of the diagnostic workup and treatment outcomes of MD. To achieve this purpose, the goals of this guideline are to use the best available published scientific and/or clinical evidence to enhance diagnostic accuracy and appropriate therapeutic interventions (medical and surgical) while reducing unindicated diagnostic testing and/or imaging.
MeSH term(s)	Humans ; Meniere Disease/complications ; Meniere Disease/diagnosis ; Meniere Disease/therapy
Language	English
Publishing date	2020-04-07
Publishing country	England
Document type	Journal Article ; Practice Guideline ; Research Support, Non-U.S. Gov't
ZDB-ID	392085-9
ISSN	1097-6817 ; 0161-6439 ; 0194-5998
ISSN (online)	1097-6817
ISSN	0161-6439 ; 0194-5998
DOI	10.1177/0194599820909439
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Article ; Online: Clinical Practice Guideline: Ménière's Disease.

Walsh, Sandra A / Nnacheta, Lorraine C / Dhepyasuwan, Nui / Buchanan, Erin M

Otolaryngology--head and neck surgery : official journal of American Academy of Otolaryngology-Head and Neck Surgery

2020 Volume 162, Issue 2_suppl, Page(s) S1–S55

Abstract	Objective: Ménière's disease (MD) is a clinical condition defined by spontaneous vertigo attacks (each lasting 20 minutes to 12 hours) with documented low- to midfrequency sensorineural hearing loss in the affected ear before, during, or after one of the episodes of vertigo. It also presents with fluctuating aural symptoms (hearing loss, tinnitus, or ear fullness) in the affected ear. The underlying etiology of MD is not completely clear, yet it has been associated with inner ear fluid (endolymph) volume increases, culminating in episodic ear symptoms (vertigo, fluctuating hearing loss, tinnitus, and aural fullness). Physical examination findings are often unremarkable, and audiometric testing may or may not show low- to midfrequency sensorineural hearing loss. Conventional imaging, if performed, is also typically normal. The goals of MD treatment are to prevent or reduce vertigo severity and frequency; relieve or prevent hearing loss, tinnitus, and aural fullness; and improve quality of life. Treatment approaches to MD are many and typically include modifications of lifestyle factors (eg, diet) and medical, surgical, or a combination of therapies. Purpose: The primary purpose of this clinical practice guideline is to improve the quality of the diagnostic workup and treatment outcomes of MD. To achieve this purpose, the goals of this guideline are to use the best available published scientific and/or clinical evidence to enhance diagnostic accuracy and appropriate therapeutic interventions (medical and surgical) while reducing unindicated diagnostic testing and/or imaging.
MeSH term(s)	Audiometry ; Counseling ; Diagnosis, Differential ; Diuretics/therapeutic use ; Ear, Inner/surgery ; Gentamicins/therapeutic use ; Glucocorticoids/therapeutic use ; Humans ; Meniere Disease/diagnosis ; Meniere Disease/epidemiology ; Meniere Disease/therapy ; Migraine Disorders/diagnosis ; Patient Education as Topic ; Quality of Life ; Vertigo/diagnosis ; Vestibular Diseases/diagnosis
Chemical Substances	Diuretics ; Gentamicins ; Glucocorticoids
Language	English
Publishing date	2020-04-08
Publishing country	England
Document type	Journal Article ; Practice Guideline ; Research Support, Non-U.S. Gov't
ZDB-ID	392085-9
ISSN	1097-6817 ; 0161-6439 ; 0194-5998
ISSN (online)	1097-6817
ISSN	0161-6439 ; 0194-5998
DOI	10.1177/0194599820909438
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Article ; Online: Emerging roles of beta-arrestins.

Buchanan, F Gregory / DuBois, Raymond N

Cell cycle (Georgetown, Tex.)

2006 Volume 5, Issue 18, Page(s) 2060–2063

Abstract: Arrestins were originally characterized as structural adaptor proteins which modulate the desensitization and trafficking of seven-membrane-spanning receptors. From these seminal observations a multitude of novel functions for this gene family have ... ...

Abstract	Arrestins were originally characterized as structural adaptor proteins which modulate the desensitization and trafficking of seven-membrane-spanning receptors. From these seminal observations a multitude of novel functions for this gene family have arisen. Here we review the recently identified roles for beta-arrestin including its nuclear function and roles in development, cellular migration, and metastasis.
MeSH term(s)	Animals ; Arrestins/genetics ; Arrestins/metabolism ; Cell Movement/physiology ; Cell Nucleus/metabolism ; Humans ; Neoplasm Metastasis/genetics ; Protein Kinases/metabolism ; Protein Transport/physiology ; Receptors, G-Protein-Coupled/metabolism ; Signal Transduction/physiology ; Wnt Proteins/metabolism ; beta-Arrestins
Chemical Substances	Arrestins ; Receptors, G-Protein-Coupled ; Wnt Proteins ; beta-Arrestins ; Protein Kinases (EC 2.7.-)
Language	English
Publishing date	2006-09-15
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	2146183-1
ISSN	1551-4005 ; 1538-4101 ; 1554-8627
ISSN (online)	1551-4005
ISSN	1538-4101 ; 1554-8627
DOI	10.4161/cc.5.18.3212
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Article ; Online: Combined Oxytocin and Cognitive Behavioral Social Skills Training for Social Function in People With Schizophrenia.

Buchanan, Robert W / Kelly, Deanna L / Strauss, Gregory P / Gold, James M / Weiner, Elaine / Zaranski, Jennifer / Chen, Shuo / Blatt, Frank / Holden, Jason / Granholm, Eric

Journal of clinical psychopharmacology

2021 Volume 41, Issue 3, Page(s) 236–243

Abstract: Background: A significant proportion of people with schizophrenia are characterized by impaired ability to socially engage with others. The development of effective interventions for social functioning remains a central therapeutic challenge. Cognitive- ... ...

Abstract	Background: A significant proportion of people with schizophrenia are characterized by impaired ability to socially engage with others. The development of effective interventions for social functioning remains a central therapeutic challenge. Cognitive-behavioral social skills training (CBSST) has been found to improve social functioning in schizophrenia, but with only medium effect sizes. Intranasal oxytocin also has prosocial effects, but also only with modest effect sizes. This study assessed whether the addition of intranasal oxytocin to CBSST can strengthen their impact on social function. Methods: Participants (N = 62) with schizophrenia or schizoaffective disorder entered a 24-week, double-blind, placebo-controlled, randomized clinical trial with a 3-month follow-up evaluation at 2 sites: Maryland and San Diego. Participants were randomized to either intranasal oxytocin 36 IU (3 sprays) twice a day (n = 31) or intranasal placebo-oxytocin (3 sprays) twice a day (n = 31). All participants received CBSST plus a social cognition skills training module (48 total sessions). Results: There were no significant treatment group differences in social functioning, positive symptoms, negative symptoms, defeatist beliefs, or asocial beliefs. The interpretation of treatment effects was complicated by site effects, whereby participants in San Diego began the trial with greater severity of impairments and subsequently showed greater improvements compared with participants in Maryland. Conclusions: The results did not support the utility of add-on intranasal oxytocin to psychosocial rehabilitation interventions like CBSST for improvement in social function (ClinicalTrials.gov trial number: NCT01752712).
MeSH term(s)	Administration, Intranasal ; Adult ; Cognitive Behavioral Therapy/methods ; Combined Modality Therapy ; Double-Blind Method ; Female ; Follow-Up Studies ; Humans ; Male ; Middle Aged ; Oxytocin/administration & dosage ; Psychotic Disorders/surgery ; Psychotic Disorders/therapy ; Schizophrenia/therapy ; Social Skills ; Treatment Outcome
Chemical Substances	Oxytocin (50-56-6)
Language	English
Publishing date	2021-03-31
Publishing country	United States
Document type	Journal Article ; Multicenter Study ; Randomized Controlled Trial
ZDB-ID	604631-9
ISSN	1533-712X ; 0271-0749
ISSN (online)	1533-712X
ISSN	0271-0749
DOI	10.1097/JCP.0000000000001397
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