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Article ; Online: RNA interference in the era of nucleic acid therapeutics.

Jadhav, Vasant / Vaishnaw, Akshay / Fitzgerald, Kevin / Maier, Martin A

2024 Volume 42, Issue 3, Page(s) 394–405

Abstract: Two decades of research on RNA interference (RNAi) have transformed a breakthrough discovery in biology into a robust platform for a new class of medicines that modulate mRNA expression. Here we provide an overview of the trajectory of small-interfering ... ...

Abstract	Two decades of research on RNA interference (RNAi) have transformed a breakthrough discovery in biology into a robust platform for a new class of medicines that modulate mRNA expression. Here we provide an overview of the trajectory of small-interfering RNA (siRNA) drug development, including the first approval in 2018 of a liver-targeted siRNA interference (RNAi) therapeutic in lipid nanoparticles and subsequent approvals of five more RNAi drugs, which used metabolically stable siRNAs combined with N-acetylgalactosamine ligands for conjugate-based liver delivery. We also consider the remaining challenges in the field, such as delivery to muscle, brain and other extrahepatic organs. Today's RNAi therapeutics exhibit high specificity, potency and durability, and are transitioning from applications in rare diseases to widespread, chronic conditions.
MeSH term(s)	RNA Interference ; RNA, Small Interfering/genetics ; RNA, Small Interfering/therapeutic use ; Liver ; Acetylgalactosamine
Chemical Substances	RNA, Small Interfering ; Acetylgalactosamine (KM15WK8O5T)
Language	English
Publishing date	2024-02-26
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	1311932-1
ISSN	1546-1696 ; 1087-0156
ISSN (online)	1546-1696
ISSN	1087-0156
DOI	10.1038/s41587-023-02105-y
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Article: CovidExplorer: A Multi-faceted AI-based Search and Visualization Engine for COVID-19 Information

Ambavi, H. / Vaishnaw, K. / Vyas, U. / Tiwari, A. / Singh, M.

29th ACM International Conference on Information and Knowledge Management, CIKM 2020

Abstract: The entire world is engulfed in the fight against the COVID-19 pandemic, leading to a significant surge in research experiments, government policies, and social media discussions A multi-modal information access and data visualization platform can play a ...

Abstract	The entire world is engulfed in the fight against the COVID-19 pandemic, leading to a significant surge in research experiments, government policies, and social media discussions A multi-modal information access and data visualization platform can play a critical role in supporting research aimed at understanding and developing preventive measures for the pandemic In this paper, we present a multi-faceted AI-based search and visualization engine, CovidExplorer Our system aims to help researchers understand current state-of-the-art COVID-19 research, identify research articles relevant to their domain, and visualize real-time trends and statistics of COVID-19 cases In contrast to other existing systems, CovidExplorer also brings in India-specific topical discussions on social media to study different aspects of COVID-19 The system, demo video, and the datasets are available at http://covidexplorer in © 2020 ACM
Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #927489
Database	COVID19

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Book ; Online: CovidExplorer

Ambavi, Heer / Vaishnaw, Kavita / Vyas, Udit / Tiwari, Abhisht / Singh, Mayank

A Multi-faceted AI-based Search and Visualization Engine for COVID-19 Information

2020

Abstract: The entire world is engulfed in the fight against the COVID-19 pandemic, leading to a significant surge in research experiments, government policies, and social media discussions. A multi-modal information access and data visualization platform can play ... ...

Abstract	The entire world is engulfed in the fight against the COVID-19 pandemic, leading to a significant surge in research experiments, government policies, and social media discussions. A multi-modal information access and data visualization platform can play a critical role in supporting research aimed at understanding and developing preventive measures for the pandemic. In this paper, we present a multi-faceted AI-based search and visualization engine, CovidExplorer. Our system aims to help researchers understand current state-of-the-art COVID-19 research, identify research articles relevant to their domain, and visualize real-time trends and statistics of COVID-19 cases. In contrast to other existing systems, CovidExplorer also brings in India-specific topical discussions on social media to study different aspects of COVID-19. The system, demo video, and the datasets are available at http://covidexplorer.in. Comment: 4 pages, 7 figures, The associated system can be accessed at http://covidexplorer.in, To be published in the Proceedings of the 29th ACM International Conference on Information and Knowledge Management (CIKM '20) (October 19-23, 2020)(Virtual Event, Ireland)
Keywords	Computer Science - Information Retrieval ; Computer Science - Computation and Language ; Computer Science - Social and Information Networks
Subject code	306
Publishing date	2020-11-30
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Conference proceedings ; Online: CovidExplorer ; A Multi-faceted AI-based Search and Visualization Engine for COVID-19 Information

Ambavi, Heer / Vaishnaw, Kavita / Vyas, Udit / Tiwari, Abhisht / Singh, Mayank

Proceedings of the 29th ACM International Conference on Information & Knowledge Management ; ISBN 9781450368599

2020

Keywords	covid19
Publisher	ACM
Publishing country	us
Document type	Conference proceedings ; Online
DOI	10.1145/3340531.3417428
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Article ; Online: Rare loss of function variants in the hepatokine gene INHBE protect from abdominal obesity.

Deaton, Aimee M / Dubey, Aditi / Ward, Lucas D / Dornbos, Peter / Flannick, Jason / Yee, Elaine / Ticau, Simina / Noetzli, Leila / Parker, Margaret M / Hoffing, Rachel A / Willis, Carissa / Plekan, Mollie E / Holleman, Aaron M / Hinkle, Gregory / Fitzgerald, Kevin / Vaishnaw, Akshay K / Nioi, Paul

Nature communications

2022 Volume 13, Issue 1, Page(s) 4319

Abstract: Identifying genetic variants associated with lower waist-to-hip ratio can reveal new therapeutic targets for abdominal obesity. We use exome sequences from 362,679 individuals to identify genes associated with waist-to-hip ratio adjusted for BMI ( ... ...

Abstract	Identifying genetic variants associated with lower waist-to-hip ratio can reveal new therapeutic targets for abdominal obesity. We use exome sequences from 362,679 individuals to identify genes associated with waist-to-hip ratio adjusted for BMI (WHRadjBMI), a surrogate for abdominal fat that is causally linked to type 2 diabetes and coronary heart disease. Predicted loss of function (pLOF) variants in INHBE associate with lower WHRadjBMI and this association replicates in data from AMP-T2D-GENES. INHBE encodes a secreted protein, the hepatokine activin E. In vitro characterization of the most common INHBE pLOF variant in our study, indicates an in-frame deletion resulting in a 90% reduction in secreted protein levels. We detect associations with lower WHRadjBMI for variants in ACVR1C, encoding an activin receptor, further highlighting the involvement of activins in regulating fat distribution. These findings highlight activin E as a potential therapeutic target for abdominal obesity, a phenotype linked to cardiometabolic disease.
MeSH term(s)	Activin Receptors, Type I/genetics ; Body Mass Index ; Diabetes Mellitus, Type 2/genetics ; Humans ; Inhibin-beta Subunits/genetics ; Obesity/genetics ; Obesity, Abdominal/genetics ; Waist-Hip Ratio
Chemical Substances	INHBE protein, human ; Inhibin-beta Subunits (93443-12-0) ; ACVR1C protein, human (EC 2.7.11.30) ; Activin Receptors, Type I (EC 2.7.11.30)
Language	English
Publishing date	2022-07-27
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-022-31757-8
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Article ; Online: Liver as a target for oligonucleotide therapeutics.

Sehgal, Alfica / Vaishnaw, Akshay / Fitzgerald, Kevin

Journal of hepatology

2013 Volume 59, Issue 6, Page(s) 1354–1359

Abstract: Oligonucleotide-based therapeutics are an emerging class of drugs that hold the promise for silencing "un-druggable" targets,thus creating unique opportunities for innovative medicines. As opposed to gene therapy, oligonucleotides are considered to be ... ...

Abstract	Oligonucleotide-based therapeutics are an emerging class of drugs that hold the promise for silencing "un-druggable" targets,thus creating unique opportunities for innovative medicines. As opposed to gene therapy, oligonucleotides are considered to be more akin to small molecule therapeutics because they are small,completely synthetic in origin, do not integrate into the host genome,and have a defined duration of therapeutic activity after which effects recover to baseline. They offer a high degree of specificity at the genetic level, thereby reducing off-target effects.At the same time, they provide a strategy for targeting any gene in the genome, including transcripts that produce mutated proteins.Oligonucleotide-based therapeutics include short interfering RNA (siRNA), that degrade target mRNA through RISC mediated RNAi; anti-miRs, that target miRNAs; miRNA mimics, that regulate target mRNA; antisense oligonucleotides, that may be working through RNAseH mediated mRNA decay; mRNA upregulation,by targeting long non-coding RNAs; and oligonucleotides induced alternative splicing [1]. All these approaches require some minimal degree of homology at the nucleic acid sequence level for them to be functional. The different mechanisms of action and their relevant activity are outlined in Fig. 1. Besides homology,RNA secondary structure has also been exploited in the case of ribozymes and aptamers, which act by binding to nucleic acids or proteins, respectively. While there have been many reports of gene knockdown and gene modulation in cell lines and mice with all these methods, very few have advanced to clinical stages.The main obstacle to date has been the safe and effective intracellular delivery of these compounds in higher species, including humans. Indeed, their action requires direct interaction with DNA/RNA within the target cell so even when one solves the issues of tissue and cellular access, intracellular/intranuclear location represents yet another barrier to overcome. To date,hepatic delivery of oligonucleotides has been the area with greatest progress, and thus we have focused on liver-targeted therapeutics that have shown promise at the preclinical and/or clinical level.The liver is the largest internal organ in the body, playing a central role in metabolism, detoxification, synthesis, and secretion of major plasma proteins (carrier proteins, coagulation factors,complement components, hormones, and apolipoproteins),and iron homeostasis. It is therefore not surprising that a large number of disease targets reside in the liver where they are susceptible to modulation by oligonucleotide therapies.
MeSH term(s)	Angiopoietin-like Proteins ; Angiopoietins/physiology ; Cholesterol, LDL/blood ; Humans ; Liver Diseases/drug therapy ; Oligonucleotides/therapeutic use ; Oligonucleotides, Antisense/therapeutic use
Chemical Substances	ANGPTL3 protein, human ; Angiopoietin-like Proteins ; Angiopoietins ; Cholesterol, LDL ; Oligonucleotides ; Oligonucleotides, Antisense
Language	English
Publishing date	2013-12
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	605953-3
ISSN	1600-0641 ; 0168-8278
ISSN (online)	1600-0641
ISSN	0168-8278
DOI	10.1016/j.jhep.2013.05.045
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Article ; Online: Single-Dose Pharmacokinetics and Pharmacodynamics of Transthyretin Targeting N-acetylgalactosamine-Small Interfering Ribonucleic Acid Conjugate, Vutrisiran, in Healthy Subjects.

Habtemariam, Bahru A / Karsten, Verena / Attarwala, Husain / Goel, Varun / Melch, Megan / Clausen, Valerie A / Garg, Pushkal / Vaishnaw, Akshay K / Sweetser, Marianne T / Robbie, Gabriel J / Vest, John

Clinical pharmacology and therapeutics

2020 Volume 109, Issue 2, Page(s) 372–382

Abstract: Vutrisiran (ALN-TTRsc02) is a liver-directed, investigational, small interfering ribonucleic acid drug for the treatment of transthyretin (TTR)-mediated amyloidosis. This phase I, randomized, single-blind, placebo-controlled, single ascending dose study ... ...

Abstract	Vutrisiran (ALN-TTRsc02) is a liver-directed, investigational, small interfering ribonucleic acid drug for the treatment of transthyretin (TTR)-mediated amyloidosis. This phase I, randomized, single-blind, placebo-controlled, single ascending dose study evaluated the pharmacodynamics, pharmacokinetics, and safety profile of subcutaneously administered vutrisiran (5-300 mg) in healthy subjects (n = 80). Vutrisiran treatment achieved potent and sustained TTR reduction in a dose-dependent manner, with mean maximum TTR reduction of 57-97%, maintained for ≥ 90 days post dose. Vutrisiran was rapidly absorbed (peak plasma concentration 3-5 hours post dose), had a short plasma half-life (4.2-7.5 hours), and plasma concentrations increased in a dose-proportional manner. Pharmacodynamic and pharmacokinetic results were similar in Japanese and non-Japanese subjects. Vutrisiran had an acceptable safety profile; the most common treatment-related adverse event was mild, transient injection site reactions in four (6.7%) vutrisiran-treated subjects. The favorable pharmacokinetic, pharmacodynamic, and safety results observed here support vutrisiran's continued clinical development.
MeSH term(s)	Acetylgalactosamine/metabolism ; Adult ; Amyloid Neuropathies, Familial/drug therapy ; Asian Continental Ancestry Group ; Dose-Response Relationship, Drug ; Drug Administration Schedule ; Female ; Half-Life ; Healthy Volunteers ; Humans ; Male ; Prealbumin/adverse effects ; RNA/pharmacokinetics ; RNA/therapeutic use ; Single-Blind Method
Chemical Substances	Prealbumin ; RNA (63231-63-0) ; Acetylgalactosamine (KM15WK8O5T)
Language	English
Publishing date	2020-08-13
Publishing country	United States
Document type	Clinical Trial, Phase I ; Journal Article ; Randomized Controlled Trial ; Research Support, Non-U.S. Gov't
ZDB-ID	123793-7
ISSN	1532-6535 ; 0009-9236
ISSN (online)	1532-6535
ISSN	0009-9236
DOI	10.1002/cpt.1974
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Article ; Online: Neurofilament Light Chain as a Biomarker of Hereditary Transthyretin-Mediated Amyloidosis.

Ticau, Simina / Sridharan, Gautham V / Tsour, Shira / Cantley, William L / Chan, Amy / Gilbert, Jason A / Erbe, David / Aldinc, Emre / Reilly, Mary M / Adams, David / Polydefkis, Michael / Fitzgerald, Kevin / Vaishnaw, Akshay / Nioi, Paul

Neurology

2020 Volume 96, Issue 3, Page(s) e412–e422

Abstract: Objective: To identify changes in the proteome associated with onset and progression of hereditary transthyretin-mediated (hATTR) amyloidosis, also known as ATTRv amyloidosis, we performed an observational, case-controlled study that compared proteomes ... ...

Abstract	Objective: To identify changes in the proteome associated with onset and progression of hereditary transthyretin-mediated (hATTR) amyloidosis, also known as ATTRv amyloidosis, we performed an observational, case-controlled study that compared proteomes of patients with ATTRv amyloidosis and healthy controls. Methods: Plasma levels of >1,000 proteins were measured in patients with ATTRv amyloidosis with polyneuropathy who received either placebo or patisiran in a Phase 3 study of patisiran (APOLLO), and in healthy controls. The effect of patisiran on the time profile of each protein was determined by linear mixed model at 0, 9, and 18 months. Neurofilament light chain (NfL) was further assessed with an orthogonal quantitative approach. Results: Levels of 66 proteins were significantly changed with patisiran vs placebo, with NfL change most significant ( Conclusions: Findings suggest that NfL may serve as a biomarker of nerve damage and polyneuropathy in ATTRv amyloidosis, enable earlier diagnosis of patients with ATTRv amyloidosis, and facilitate monitoring of disease progression. Classification of evidence: This study provides Class III evidence that NfL levels may enable earlier diagnosis of polyneuropathy in patients with ATTRv amyloidosis and facilitate monitoring of disease progression.
MeSH term(s)	Aged ; Amyloid Neuropathies, Familial/blood ; Amyloid Neuropathies, Familial/diagnosis ; Amyloid Neuropathies, Familial/drug therapy ; Biomarkers/blood ; Case-Control Studies ; Female ; Humans ; Male ; Middle Aged ; Neurofilament Proteins/blood ; Prognosis ; Proteome ; RNA, Small Interfering/therapeutic use
Chemical Substances	Biomarkers ; Neurofilament Proteins ; Proteome ; RNA, Small Interfering ; neurofilament protein L ; patisiran (50FKX8CB2Y)
Language	English
Publishing date	2020-10-21
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	207147-2
ISSN	1526-632X ; 0028-3878
ISSN (online)	1526-632X
ISSN	0028-3878
DOI	10.1212/WNL.0000000000011090
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Article ; Online: The Nonclinical Safety Profile of GalNAc-conjugated RNAi Therapeutics in Subacute Studies.

Janas, Maja M / Harbison, Carole E / Perry, Victoria K / Carito, Brenda / Sutherland, Jessica E / Vaishnaw, Akshay K / Keirstead, Natalie D / Warner, Garvin

Toxicologic pathology

2018 Volume 46, Issue 7, Page(s) 735–745

Abstract: Short interfering RNAs (siRNAs) and antisense oligonucleotides (ASOs) are the most clinically advanced oligonucleotide-based platforms. A number of N-acetylgalactosamine (GalNAc)-conjugated siRNAs (GalNAc-siRNAs), also referred to as RNA interference ( ... ...

Abstract	Short interfering RNAs (siRNAs) and antisense oligonucleotides (ASOs) are the most clinically advanced oligonucleotide-based platforms. A number of N-acetylgalactosamine (GalNAc)-conjugated siRNAs (GalNAc-siRNAs), also referred to as RNA interference (RNAi) therapeutics, are currently in various stages of development, though none is yet approved. While the safety of ASOs has been the subject of extensive review, the nonclinical safety profiles of GalNAc-siRNAs have not been reported. With the exception of sequence differences that confer target RNA specificity, GalNAc-siRNAs are largely chemically uniform, containing limited number of phosphorothioate linkages, and 2'-O-methyl and 2'-deoxy-2'-fluoro ribose modifications. Here, we present the outcomes of short-term (3-5 week) rat and monkey weekly repeat-dose toxicology studies of six Enhanced Stabilization Chemistry GalNAc-siRNAs currently in clinical development. In nonclinical studies at supratherapeutic doses, these molecules share similar safety signals, with histologic findings in the organ of pharmacodynamic effect (liver), the organ of elimination (kidney), and the reticuloendothelial system (lymph nodes). The majority of these changes are nonadverse, partially to completely reversible, correlate well with pharmacokinetic parameters and tissue distribution, and often reflect drug accumulation. Furthermore, all GalNAc-siRNAs tested to date have been negative in genotoxicity and safety pharmacology studies.
MeSH term(s)	Acetylgalactosamine/chemistry ; Acetylgalactosamine/pharmacology ; Acetylgalactosamine/toxicity ; Animals ; CHO Cells ; Chromosome Aberrations/chemically induced ; Cricetulus ; Dose-Response Relationship, Drug ; Drug Evaluation, Preclinical ; Liver/drug effects ; Liver/pathology ; Lymphocytes/drug effects ; Lymphocytes/pathology ; Macaca fascicularis ; Mutagenicity Tests ; RNA, Small Interfering/chemistry ; RNA, Small Interfering/genetics ; RNA, Small Interfering/pharmacology ; RNA, Small Interfering/toxicity ; Rats, Sprague-Dawley ; Species Specificity ; Toxicity Tests, Subacute
Chemical Substances	RNA, Small Interfering ; Acetylgalactosamine (KM15WK8O5T)
Language	English
Publishing date	2018-08-23
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	841009-4
ISSN	1533-1601 ; 0192-6233
ISSN (online)	1533-1601
ISSN	0192-6233
DOI	10.1177/0192623318792537
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Article ; Online: Association of the transthyretin variant V122I with polyneuropathy among individuals of African ancestry.

Scientific reports

2021 Volume 11, Issue 1, Page(s) 11645

Abstract: Hereditary transthyretin-mediated (hATTR) amyloidosis is an underdiagnosed, progressively debilitating disease caused by mutations in the transthyretin (TTR) gene. V122I, a common pathogenic TTR mutation, is found in 3-4% of individuals of African ... ...

Abstract	Hereditary transthyretin-mediated (hATTR) amyloidosis is an underdiagnosed, progressively debilitating disease caused by mutations in the transthyretin (TTR) gene. V122I, a common pathogenic TTR mutation, is found in 3-4% of individuals of African ancestry in the United States and has been associated with cardiomyopathy and heart failure. To better understand the phenotypic consequences of carrying V122I, we conducted a phenome-wide association study scanning 427 ICD diagnosis codes in UK Biobank participants of African ancestry (n = 6062). Significant associations were tested for replication in the Penn Medicine Biobank (n = 5737) and the Million Veteran Program (n = 82,382). V122I was significantly associated with polyneuropathy in the UK Biobank (odds ratio [OR] = 6.4, 95% confidence interval [CI] 2.6-15.6, p = 4.2 × 10
MeSH term(s)	Adult ; Aged ; Amino Acid Substitution ; Amyloid Neuropathies, Familial/complications ; Amyloid Neuropathies, Familial/diagnosis ; Amyloid Neuropathies, Familial/ethnology ; Amyloid Neuropathies, Familial/genetics ; Biological Specimen Banks ; Blacks ; Cardiomyopathies/complications ; Cardiomyopathies/diagnosis ; Cardiomyopathies/ethnology ; Cardiomyopathies/genetics ; Female ; Gene Expression ; Heart Failure/complications ; Heart Failure/diagnosis ; Heart Failure/ethnology ; Heart Failure/genetics ; Heterozygote ; Humans ; Male ; Middle Aged ; Mutation ; Phenotype ; Polyneuropathies/complications ; Polyneuropathies/diagnosis ; Polyneuropathies/ethnology ; Polyneuropathies/genetics ; Prealbumin/genetics ; Prevalence ; United Kingdom/epidemiology
Chemical Substances	Prealbumin ; TTR protein, human
Language	English
Publishing date	2021-06-02
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	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-021-91113-6
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