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Article ; Online: Evidence-based consensus guidelines for ALS genetic testing and counseling.

Roggenbuck, Jennifer / Eubank, Breda H F / Wright, Joshua / Harms, Matthew B / Kolb, Stephen J

Annals of clinical and translational neurology

2023 Volume 10, Issue 11, Page(s) 2074–2091

Abstract: Objective: Advances in amyotrophic lateral sclerosis (ALS) gene discovery, ongoing gene therapy trials, and patient demand have driven increased use of ALS genetic testing. Despite this progress, the offer of genetic testing to persons with ALS is not ... ...

Abstract	Objective: Advances in amyotrophic lateral sclerosis (ALS) gene discovery, ongoing gene therapy trials, and patient demand have driven increased use of ALS genetic testing. Despite this progress, the offer of genetic testing to persons with ALS is not yet "standard of care." Our primary goal is to develop clinical ALS genetic counseling and testing guidelines to improve and standardize genetic counseling and testing practice among neurologists, genetic counselors or any provider caring for persons with ALS. Methods: Core clinical questions were identified and a rapid review performed according to Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA-P) 2015 method. Guideline recommendations were drafted and the strength of evidence for each recommendation was assessed by combining two systems: the Grading of Recommendations, Assessment, Development and Evaluation (GRADE) System and the Evaluation of Genomic Applications in Practice and Prevention (EGAPP). A modified Delphi approach was used to reach consensus among a group of content experts for each guideline statement. Results: A total of 35 guideline statements were developed. In summary, all persons with ALS should be offered single-step genetic testing, consisting of a C9orf72 assay, along with sequencing of SOD1, FUS, and TARDBP, at a minimum. The key education and genetic risk assessments that should be provided before and after testing are delineated. Specific guidance regarding testing methods and reporting for C9orf72 and other genes is provided for commercial laboratories. Interpretation: These evidence-based, consensus guidelines will support all stakeholders in the ALS community in navigating benefits and challenges of genetic testing.
MeSH term(s)	Humans ; Amyotrophic Lateral Sclerosis/diagnosis ; Amyotrophic Lateral Sclerosis/genetics ; Amyotrophic Lateral Sclerosis/therapy ; C9orf72 Protein/genetics ; Systematic Reviews as Topic ; Meta-Analysis as Topic ; Genetic Testing ; Counseling
Chemical Substances	C9orf72 Protein
Language	English
Publishing date	2023-09-10
Publishing country	United States
Document type	Journal Article
ZDB-ID	2740696-9
ISSN	2328-9503 ; 2328-9503
ISSN (online)	2328-9503
ISSN	2328-9503
DOI	10.1002/acn3.51895
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Proton and Electron Ultrahigh-Dose-Rate Isodose Irradiations Produce Differences in Reactive Oxygen Species Yields.

Thomas, William / Sunnerberg, Jacob / Reed, Matthew / Gladstone, David J / Zhang, Rongxiao / Harms, Joseph / Swartz, Harold M / Pogue, Brian W

International journal of radiation oncology, biology, physics

2023 Volume 118, Issue 1, Page(s) 262–267

MeSH term(s)	Humans ; Protons ; Reactive Oxygen Species ; Electrons ; Radiotherapy Dosage ; Proton Therapy
Chemical Substances	Protons ; Reactive Oxygen Species
Language	English
Publishing date	2023-08-07
Publishing country	United States
Document type	Journal Article
ZDB-ID	197614-x
ISSN	1879-355X ; 0360-3016
ISSN (online)	1879-355X
ISSN	0360-3016
DOI	10.1016/j.ijrobp.2023.07.042
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Article ; Online: Isolation and Culture of Human Mature Adipocytes Using Membrane Mature Adipocyte Aggregate Cultures (MAAC).

Alexandersson, Ida / Harms, Matthew J / Boucher, Jeremie

Journal of visualized experiments : JoVE

2020 , Issue 156

Abstract: White adipose tissue (WAT) dysregulation plays a central role in development of insulin resistance and type 2 diabetes (T2D). To develop new treatments for T2D, more physiologically relevant in vitro adipocyte models are required. This study describes a ... ...

Abstract	White adipose tissue (WAT) dysregulation plays a central role in development of insulin resistance and type 2 diabetes (T2D). To develop new treatments for T2D, more physiologically relevant in vitro adipocyte models are required. This study describes a new technique to isolate and culture mature human adipocytes. This method is entitled MAAC (membrane mature adipocyte aggregate culture), and compared to other adipocyte in vitro models, MAAC possesses an adipogenic gene signature that is the closest to freshly isolated mature adipocytes. Using MAAC, adipocytes can be cultured from lean and obese patients, different adipose depots, co-cultured with different cell types, and importantly, can be kept in culture for 2 weeks. Functional experiments can also be performed on MAAC including glucose uptake, lipogenesis, and lipolysis. Moreover, MAAC responds robustly to diverse pharmacological agonism and can be used to study adipocyte phenotypic changes, including the transdifferentiation of white adipocytes into brown-like fat cells.
MeSH term(s)	Adipocytes/metabolism ; Adipose Tissue, White/metabolism ; Cell Culture Techniques/methods ; Humans
Language	English
Publishing date	2020-02-13
Publishing country	United States
Document type	Journal Article ; Video-Audio Media
ZDB-ID	2259946-0
ISSN	1940-087X ; 1940-087X
ISSN (online)	1940-087X
ISSN	1940-087X
DOI	10.3791/60485
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Article ; Online: New Approaches for Targeting PCSK9: Small-Interfering Ribonucleic Acid and Genome Editing.

Oostveen, Reindert F / Khera, Amit V / Kathiresan, Sekar / Stroes, Erik S G / Fitzgerald, Kevin / Harms, Matthew J / Oakes, Benjamin L / Kastelein, John J P

Arteriosclerosis, thrombosis, and vascular biology

2023 Volume 43, Issue 7, Page(s) 1081–1092

Abstract: There is overwhelming clinical and genetic evidence supporting the concept that low-density-lipoprotein cholesterol should be as low as possible for as long as possible in patients at very high cardiovascular risk. Despite the wide availability of ... ...

Abstract	There is overwhelming clinical and genetic evidence supporting the concept that low-density-lipoprotein cholesterol should be as low as possible for as long as possible in patients at very high cardiovascular risk. Despite the wide availability of effective lipid-lowering therapies, the majority of patients still fail to reach guideline-based lipid goals. Advances in novel approaches targeting PCSK9 (proprotein convertase subtilisin/kexin type 9) through small-interfering RNA and genome editing hold the potential to bridge this gap, by offering long-acting alternatives, which may overcome adherence and other challenges in the current chronic care model. In this review, we discuss the history of targeting PCSK9 with the use of mRNA and small-interfering ribonucleic acid. We also shed light on targeting PCSK9 with genome editing, including discussion of the VERVE-101 clustered regularly interspaced short palindromic repeats-base editing medicine currently being evaluated in a clinical trial and others in development.
MeSH term(s)	Humans ; Proprotein Convertase 9/genetics ; Gene Editing ; Cholesterol, LDL ; RNA, Small Interfering/genetics
Chemical Substances	PCSK9 protein, human (EC 3.4.21.-) ; Proprotein Convertase 9 (EC 3.4.21.-) ; Cholesterol, LDL ; RNA, Small Interfering
Language	English
Publishing date	2023-06-01
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	1221433-4
ISSN	1524-4636 ; 1079-5642
ISSN (online)	1524-4636
ISSN	1079-5642
DOI	10.1161/ATVBAHA.122.317963
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Article: Adalimumab therapy used successfully for recalcitrant Hailey-Hailey disease.

Chen, Ailynna / DaCunha, Matthew / Harms, Jessica

JAAD case reports

2022 Volume 29, Page(s) 173–176

Language	English
Publishing date	2022-09-22
Publishing country	United States
Document type	Case Reports
ZDB-ID	2834220-3
ISSN	2352-5126
ISSN	2352-5126
DOI	10.1016/j.jdcr.2022.09.014
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Article ; Online: DYNATE: Localizing rare-variant association regions via multiple testing embedded in an aggregation tree.

Li, Xuechan / Pura, John / Allen, Andrew / Owzar, Kouros / Lu, Jianfeng / Harms, Matthew / Xie, Jichun

Genetic epidemiology

2023 Volume 48, Issue 1, Page(s) 42–55

Abstract: Rare-variants (RVs) genetic association studies enable researchers to uncover the variation in phenotypic traits left unexplained by common variation. Traditional single-variant analysis lacks power; thus, researchers have developed various methods to ... ...

Abstract	Rare-variants (RVs) genetic association studies enable researchers to uncover the variation in phenotypic traits left unexplained by common variation. Traditional single-variant analysis lacks power; thus, researchers have developed various methods to aggregate the effects of RVs across genomic regions to study their collective impact. Some existing methods utilize a static delineation of genomic regions, often resulting in suboptimal effect aggregation, as neutral subregions within the test region will result in an attenuation of signal. Other methods use varying windows to search for signals but often result in long regions containing many neutral RVs. To pinpoint short genomic regions enriched for disease-associated RVs, we developed a novel method, DYNamic Aggregation TEsting (DYNATE). DYNATE dynamically and hierarchically aggregates smaller genomic regions into larger ones and performs multiple testing for disease associations with a controlled weighted false discovery rate. DYNATE's main advantage lies in its strong ability to identify short genomic regions highly enriched for disease-associated RVs. Extensive numerical simulations demonstrate the superior performance of DYNATE under various scenarios compared with existing methods. We applied DYNATE to an amyotrophic lateral sclerosis study and identified a new gene, EPG5, harboring possibly pathogenic mutations.
MeSH term(s)	Humans ; Genetic Variation ; Trees ; Models, Genetic ; Genetic Association Studies ; Mutation ; Genome-Wide Association Study/methods ; Autophagy-Related Proteins ; Vesicular Transport Proteins
Chemical Substances	EPG5 protein, human ; Autophagy-Related Proteins ; Vesicular Transport Proteins
Language	English
Publishing date	2023-11-28
Publishing country	United States
Document type	Journal Article
ZDB-ID	605785-8
ISSN	1098-2272 ; 0741-0395
ISSN (online)	1098-2272
ISSN	0741-0395
DOI	10.1002/gepi.22542
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Article: Rare variant analyses validate known ALS genes in a multi-ethnic population and identifies

Pottinger, Tess D / Motelow, Joshua E / Povysil, Gundula / Moreno, Cristiane A Martins / Ren, Zhong / Phatnani, Hemali / Aitman, Timothy J / Santoyo-Lopez, Javier / Mitsumoto, Hiroshi / Goldstein, David B / Harms, Matthew B

medRxiv : the preprint server for health sciences

2023

Abstract: Background: Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease affecting over 30,000 people in the United States. It is characterized by the progressive decline of the nervous system that leads to the weakening of muscles which impacts ... ...

Abstract	Background: Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease affecting over 30,000 people in the United States. It is characterized by the progressive decline of the nervous system that leads to the weakening of muscles which impacts physical function. Approximately, 15% of individuals diagnosed with ALS have a known genetic variant that contributes to their disease. As therapies that slow or prevent symptoms, such as antisense oligonucleotides, continue to develop, it is important to discover novel genes that could be targets for treatment. Additionally, as cohorts continue to grow, performing analyses in ALS subtypes, such as primary lateral sclerosis (PLS), becomes possible due to an increase in power. These analyses could highlight novel pathways in disease manifestation. Methods: Building on our previous discoveries using rare variant association analyses, we conducted rare variant burden testing on a substantially larger cohort of 6,970 ALS patients from a large multi-ethnic cohort as well as 166 PLS patients, and 22,524 controls. We used intolerant domain percentiles based on sub-region Residual Variation Intolerance Score (subRVIS) that have been described previously in conjunction with gene based collapsing approaches to conduct burden testing to identify genes that associate with ALS and PLS. Results: A gene based collapsing model showed significant associations with Conclusions: In a large multi-ethnic cohort of 6,970 ALS patients, rare variant burden testing validated known ALS genes and identified a novel potentially protective gene,
Language	English
Publishing date	2023-10-23
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.09.30.23296353
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Article: Rare variant analyses validate known ALS genes in a multi-ethnic population and identifies

Research square

2023

Abstract	Background: Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease affecting over 30,000 people in the United States. It is characterized by the progressive decline of the nervous system that leads to the weakening of muscles which impacts physical function. Approximately, 15% of individuals diagnosed with ALS have a known genetic variant that contributes to their disease. As therapies that slow or prevent symptoms, such as antisense oligonucleotides, continue to develop, it is important to discover novel genes that could be targets for treatment. Additionally, as cohorts continue to grow, performing analyses in ALS subtypes, such as primary lateral sclerosis (PLS), becomes possible due to an increase in power. These analyses could highlight novel pathways in disease manifestation. Methods: Building on our previous discoveries using rare variant association analyses, we conducted rare variant burden testing on a substantially larger cohort of 6,970 ALS patients from a large multi-ethnic cohort as well as 166 PLS patients, and 22,524 controls. We used intolerant domain percentiles based on sub-region Residual Variation Intolerance Score (subRVIS) that have been described previously in conjunction with gene based collapsing approaches to conduct burden testing to identify genes that associate with ALS and PLS. Results: A gene based collapsing model showed significant associations with Conclusions: In a large multi-ethnic cohort of 6,970 ALS patients, rare variant burden testing validated known ALS genes and identified a novel potentially protective gene,
Language	English
Publishing date	2023-12-21
Publishing country	United States
Document type	Preprint
DOI	10.21203/rs.3.rs-3721598/v1
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Isolation and culture of human mature adipocytes using membrane mature adipocyte aggregate cultures (maac)

Alexandersson, Ida / Harms, Matthew J / Boucher, Jeremie

Journal of visualized experiments. 2020 Feb. 13, , no. 156

2020

Abstract	White adipose tissue (WAT) dysregulation plays a central role in development of insulin resistance and type 2 diabetes (T2D). To develop new treatments for T2D, more physiologically relevant in vitro adipocyte models are required. This study describes a new technique to isolate and culture mature human adipocytes. This method is entitled MAAC (membrane mature adipocyte aggregate culture), and compared to other adipocyte in vitro models, MAAC possesses an adipogenic gene signature that is the closest to freshly isolated mature adipocytes. Using MAAC, adipocytes can be cultured from lean and obese patients, different adipose depots, co-cultured with different cell types, and importantly, can be kept in culture for 2 weeks. Functional experiments can also be performed on MAAC including glucose uptake, lipogenesis, and lipolysis. Moreover, MAAC responds robustly to diverse pharmacological agonism and can be used to study adipocyte phenotypic changes, including the transdifferentiation of white adipocytes into brown-like fat cells.
Keywords	coculture ; genes ; glucose ; humans ; insulin resistance ; lipogenesis ; lipolysis ; models ; noninsulin-dependent diabetes mellitus ; patients ; phenotypic plasticity ; white adipocytes ; white adipose tissue
Language	English
Dates of publication	2020-0213
Size	p. e60485.
Publishing place	Journal of Visualized Experiments
Document type	Article
ZDB-ID	2259946-0
ISSN	1940-087X
ISSN	1940-087X
DOI	10.3791/60485
Database	NAL-Catalogue (AGRICOLA)

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Article: When Grades Are High but Self-Efficacy Is Low: Unpacking the Confidence Gap Between Girls and Boys in Mathematics.

Zander, Lysann / Höhne, Elisabeth / Harms, Sophie / Pfost, Maximilian / Hornsey, Matthew J

Frontiers in psychology

2020 Volume 11, Page(s) 552355

Abstract: Girls have much lower mathematics self-efficacy than boys, a likely contributor to the underrepresentation of women in STEM. To help explain this gender confidence gap, we examined predictors of mathematics self-efficacy in a sample of 1,007 9th graders ... ...

Abstract	Girls have much lower mathematics self-efficacy than boys, a likely contributor to the underrepresentation of women in STEM. To help explain this gender confidence gap, we examined predictors of mathematics self-efficacy in a sample of 1,007 9th graders aged 13-18 years (54.2% girls). Participants completed a standardized math test, after which they rated three indices of mastery: an affective component (state self-esteem), a meta-cognitive component (self-enhancement), and their prior math grade. Despite having similar grades, girls reported lower mathematics self-efficacy and state self-esteem, and were less likely than boys to self-enhance in terms of performance. Multilevel multiple-group regression analyses showed that the affective mastery component explained girls' self-efficacy while cognitive self-enhancement explained boys'. Yet, a chi-square test showed that both constructs were equally relevant in the prediction of girls' and boys' self-efficacy. Measures of interpersonal sources of self-efficacy were not predictive of self-efficacy after taking the other dimensions into account. Results suggest that boys are advantaged in their development of mathematics self-efficacy beliefs, partly due to more positive feelings and more cognitive self-enhancement following test situations.
Language	English
Publishing date	2020-10-07
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2563826-9
ISSN	1664-1078
ISSN	1664-1078
DOI	10.3389/fpsyg.2020.552355
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