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Article ; Online: Calmodulin Mutations in Human Disease.

Hussey, John W / Limpitikul, Worawan B / Dick, Ivy E

2023 Volume 17, Issue 1, Page(s) 2165278

Abstract: Calcium ions ( ... ...

Abstract	Calcium ions (Ca
MeSH term(s)	Humans ; Calmodulin/genetics ; Calmodulin/metabolism ; Mutation ; Tachycardia, Ventricular/genetics ; Tachycardia, Ventricular/metabolism ; Long QT Syndrome/genetics ; Long QT Syndrome/metabolism ; Myocytes, Cardiac/metabolism ; Ryanodine Receptor Calcium Release Channel/genetics ; Ryanodine Receptor Calcium Release Channel/metabolism ; Calcium/metabolism
Chemical Substances	Calmodulin ; Ryanodine Receptor Calcium Release Channel ; Calcium (SY7Q814VUP)
Language	English
Publishing date	2023-01-11
Publishing country	United States
Document type	Review ; Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2262854-X
ISSN	1933-6969 ; 1933-6969
ISSN (online)	1933-6969
ISSN	1933-6969
DOI	10.1080/19336950.2023.2165278
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: CACNA1C-Related Channelopathies.

Herold, Kevin G / Hussey, John W / Dick, Ivy E

Handbook of experimental pharmacology

2022 Volume 279, Page(s) 159–181

Abstract: The CACNA1C gene encodes the pore-forming subunit of the ... ...

Abstract	The CACNA1C gene encodes the pore-forming subunit of the Ca
MeSH term(s)	Humans ; Channelopathies/genetics ; Calcium Channels, L-Type/genetics ; Long QT Syndrome/genetics ; Mutation
Chemical Substances	Calcium Channels, L-Type ; CACNA1C protein, human
Language	English
Publishing date	2022-12-21
Publishing country	Germany
Document type	Review ; Journal Article
ISSN	0171-2004
ISSN	0171-2004
DOI	10.1007/164_2022_624
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Article: Pancreatic stone protein point-of-care testing can reduce healthcare expenditure in sepsis.

Schneider, John E / Dick, Katherine / Cooper, Jacie T / Chami, Nadine

Health economics review

2022 Volume 12, Issue 1, Page(s) 39

Abstract: Background: Sepsis is a life-threatening organ dysfunction in response to infection. Early recognition and rapid treatment are critical to patient outcomes and cost savings, but sepsis is difficult to diagnose because of its non-specific symptoms. ... ...

Abstract	Background: Sepsis is a life-threatening organ dysfunction in response to infection. Early recognition and rapid treatment are critical to patient outcomes and cost savings, but sepsis is difficult to diagnose because of its non-specific symptoms. Biomarkers such as pancreatic stone protein (PSP) offer rapid results with greater sensitivity and specificity than standard laboratory tests. Methods: This study developed a decision tree model to compare a rapid PSP test to standard of care in the emergency department (ED) and intensive care unit (ICU) to diagnose patients with suspected sepsis. Key model parameters included length of hospital and ICU stay, readmission due to infection, cost of sepsis testing, length of antibiotic treatment, antibiotic resistance, and clostridium difficile infections. Model inputs were determined by review of sepsis literature. Results: The rapid PSP test was found to reduce costs by $1688 per patient in the ED and $3315 per patient in the ICU compared to standard of care. Cost reductions were primarily driven by the specificity of PSP in the ED and the sensitivity of PSP in the ICU. Conclusions: The results of the model indicate that PSP testing is cost saving compared to standard of care in diagnosis of sepsis. The abundance of sepsis cases in the ED and ICU make these findings important in the clinical field and further support the potential of sensitive and specific markers of sepsis to not only improve patient outcomes but also reduce healthcare expenditures.
Language	English
Publishing date	2022-07-22
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2634483-X
ISSN	2191-1991
ISSN	2191-1991
DOI	10.1186/s13561-022-00381-z
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Article ; Online: Tumor archaeology: tracking leukemic evolution to its origins.

Dick, John E

Science translational medicine

2014 Volume 6, Issue 238, Page(s) 238fs23

Abstract: Unearthing of the BRAF mutation in self-renewing hematopoietic stem cells reveals an unexpected origin for hairy cell leukemia-a mature B cell malignancy-and a potential new therapeutic target (Chung et al., this issue). ...

Abstract	Unearthing of the BRAF mutation in self-renewing hematopoietic stem cells reveals an unexpected origin for hairy cell leukemia-a mature B cell malignancy-and a potential new therapeutic target (Chung et al., this issue).
MeSH term(s)	Evolution, Molecular ; Humans ; Leukemia/genetics ; Leukemia/pathology ; Models, Biological ; Mutation
Language	English
Publishing date	2014-05-28
Publishing country	United States
Document type	Journal Article
ZDB-ID	2518854-9
ISSN	1946-6242 ; 1946-6234
ISSN (online)	1946-6242
ISSN	1946-6234
DOI	10.1126/scitranslmed.3009168
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Article ; Online: Reconstructing Complex Cancer Evolutionary Histories from Multiple Bulk DNA Samples Using Pairtree.

Wintersinger, Jeff A / Dobson, Stephanie M / Kulman, Ethan / Stein, Lincoln D / Dick, John E / Morris, Quaid

Blood cancer discovery

2022 Volume 3, Issue 3, Page(s) 208–219

Abstract: ... through time (e.g., between diagnosis and relapse). Pairtree uses DNA-sequencing data from many samples ...

Abstract	Cancers are composed of genetically distinct subpopulations of malignant cells. DNA-sequencing data can be used to determine the somatic point mutations specific to each population and build clone trees describing the evolutionary relationships between them. These clone trees can reveal critical points in disease development and inform treatment. Pairtree is a new method that constructs more accurate and detailed clone trees than previously possible using variant allele frequency data from one or more bulk cancer samples. It does so by first building a Pairs Tensor that captures the evolutionary relationships between pairs of subpopulations, and then it uses these relations to constrain clone trees and infer violations of the infinite sites assumption. Pairtree can accurately build clone trees using up to 100 samples per cancer that contain 30 or more subclonal populations. On 14 B-progenitor acute lymphoblastic leukemias, Pairtree replicates or improves upon expert-derived clone tree reconstructions. Significance: Clone trees illustrate the evolutionary history of a cancer and can provide insights into how the disease changed through time (e.g., between diagnosis and relapse). Pairtree uses DNA-sequencing data from many samples of the same cancer to build more detailed and accurate clone trees than previously possible. See related commentary by Miller, p. 176. This article is highlighted in the In This Issue feature, p. 171.
MeSH term(s)	Algorithms ; DNA ; Evolution, Molecular ; Humans ; Neoplasms/diagnosis ; Sequence Analysis, DNA
Chemical Substances	DNA (9007-49-2)
Language	English
Publishing date	2022-03-07
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	3028898-8
ISSN	2643-3249 ; 2643-3230
ISSN (online)	2643-3249
ISSN	2643-3230
DOI	10.1158/2643-3230.BCD-21-0092
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Book ; Online: (Table 2) Mass balance calculations for ODP Hole 176-735B, supplementary data to: Dick, Henry JB; Natland, James H; Alt, Jeffrey C; Bach, Wolfgang; Bideau, Daniel; Gee, Jeff S; Haggas, Sarah L; Hertogen, Jan GH; Hirth, James Gregory; Holm, Paul Martin; Ildefonse, Benoit; Iturrino, Gerardo J; John, Barbara E; Kelley, Deborah S; Kikawa, Eiichi; Kingdon, Andrew; LeRoux, Petrus J; Maeda, Jinichiro; Meyer, Peter S; Miller, D Jay; Naslund, H Richard; Niu, Yaoling; Robinson, Paul T; Snow, Jonathan E; Stephen, Ralph A; Trimby, Patrick W; Worm, Horst-Ulrich; Yoshinobu, Aaron (2000): A long in situ section of the lower ocean crust: results of ODP Leg 176 drilling at the Southwest Indian Ridge. Earth and Planetary Science Letters, 179(1), 31-51

Dick, Henry JB / Alt, Jeffrey C / Bach, Wolfgang / Bideau, Daniel / Gee, Jeff S / Haggas, Sarah L / Hertogen, Jan GH / Hirth, James Gregory / Natland, James H / al., et

2000

Abstract: Ocean Drilling Program Leg 176 deepened Hole 735B in gabbroic lower ocean crust by 1 km to 1.5 km. The section has the physical properties of seismic layer 3, and a total magnetization sufficient by itself to account for the overlying lineated sea- ... ...

Abstract	Ocean Drilling Program Leg 176 deepened Hole 735B in gabbroic lower ocean crust by 1 km to 1.5 km. The section has the physical properties of seismic layer 3, and a total magnetization sufficient by itself to account for the overlying lineated sea-surface magnetic anomaly. The rocks from Hole 735B are principally olivine gabbro, with evidence for two principal and many secondary intrusive events. There are innumerable late small ferrogabbro intrusions, often associated with shear zones that cross-cut the olivine gabbros. The ferrogabbros dramatically increase upward in the section. Whereas there are many small patches of ferrogabbro representing late iron- and titanium-rich melt trapped intragranularly in olivine gabbro, most late melt was redistributed prior to complete solidification by compaction and deformation. This, rather than in situ upward differentiation of a large magma body, produced the principal igneous stratigraphy. The computed bulk composition of the hole is too evolved to mass balance mid-ocean ridge basalt back to a primary magma, and there must be a significant mass of missing primitive cumulates. These could lie either below the hole or out of the section. Possibly the gabbros were emplaced by along-axis intrusion of moderately differentiated melts into the near-transform environment. Alteration occurred in three stages. High-temperature granulite- to amphibolite-facies alteration is most important, coinciding with brittle-ductile deformation beneath the ridge. Minor greenschist-facies alteration occurred under largely static conditions, likely during block uplift at the ridge transform intersection. Late post-uplift low-temperature alteration produced locally abundant smectite, often in previously unaltered areas. The most important features of the high- and low-temperature alteration are their respective associations with ductile and cataclastic deformation, and an overall decrease downhole with hydrothermal alteration generally <=5% in the bottom kilometer. Hole 735B provides evidence for a strongly heterogeneous lower ocean crust, and for the inherent interplay of deformation, alteration and igneous processes at slow-spreading ridges. It is strikingly different from gabbros sampled from fast-spreading ridges and at most well-described ophiolite complexes. We attribute this to the remarkable diversity of tectonic environments where crustal accretion occurs in the oceans and to the low probability of a section of old slow-spread crust formed near a major large-offset transform being emplaced on-land compared to sections of young crust from small ocean basins.
Language	English
Dates of publication	2000-9999
Size	Online-Ressource
Publisher	PANGAEA - Data Publisher for Earth & Environmental Science
Publishing place	Bremen/Bremerhaven
Document type	Book ; Online
Note	This dataset is supplement to doi:10.1016/S0012-821X(00)00102-3
DOI	10.1594/PANGAEA.717129
Database	Library catalogue of the German National Library of Science and Technology (TIB), Hannover

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Book ; Online: Integrate Any Omics

Ma, Shihao / Zeng, Andy G. X. / Haibe-Kains, Benjamin / Goldenberg, Anna / Dick, John E / Wang, Bo

Towards genome-wide data integration for patient stratification

2024

Abstract: High-throughput omics profiling advancements have greatly enhanced cancer patient stratification. However, incomplete data in multi-omics integration presents a significant challenge, as traditional methods like sample exclusion or imputation often ... ...

Abstract	High-throughput omics profiling advancements have greatly enhanced cancer patient stratification. However, incomplete data in multi-omics integration presents a significant challenge, as traditional methods like sample exclusion or imputation often compromise biological diversity and dependencies. Furthermore, the critical task of accurately classifying new patients with partial omics data into existing subtypes is commonly overlooked. To address these issues, we introduce IntegrAO (Integrate Any Omics), an unsupervised framework for integrating incomplete multi-omics data and classifying new samples. IntegrAO first combines partially overlapping patient graphs from diverse omics sources and utilizes graph neural networks to produce unified patient embeddings. Our systematic evaluation across five cancer cohorts involving six omics modalities demonstrates IntegrAO's robustness to missing data and its accuracy in classifying new samples with partial profiles. An acute myeloid leukemia case study further validates its capability to uncover biological and clinical heterogeneity in incomplete datasets. IntegrAO's ability to handle heterogeneous and incomplete data makes it an essential tool for precision oncology, offering a holistic approach to patient characterization.
Keywords	Quantitative Biology - Genomics ; Computer Science - Machine Learning ; Quantitative Biology - Quantitative Methods
Subject code	006 ; 004
Publishing date	2024-01-15
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Copper Modulates the Catalytic Activity of Protein Kinase CK2.

Chojnowski, John E / Li, Rongrong / Tsang, Tiffany / Alfaran, Fatimah H / Dick, Alexej / Cocklin, Simon / Brady, Donita C / Strochlic, Todd I

Frontiers in molecular biosciences

2022 Volume 9, Page(s) 878652

Abstract: Casein kinase 2 (CK2) is an evolutionarily conserved serine/threonine kinase implicated in a wide range of cellular functions and known to be dysregulated in various diseases such as cancer. Compared to most other kinases, CK2 exhibits several unusual ... ...

Abstract	Casein kinase 2 (CK2) is an evolutionarily conserved serine/threonine kinase implicated in a wide range of cellular functions and known to be dysregulated in various diseases such as cancer. Compared to most other kinases, CK2 exhibits several unusual properties, including dual co-substrate specificity and a high degree of promiscuity with hundreds of substrates described to date. Most paradoxical, however, is its apparent constitutive activity: no definitive mode of catalytic regulation has thus far been identified. Here we demonstrate that copper enhances the enzymatic activity of CK2 both
Language	English
Publishing date	2022-06-09
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2814330-9
ISSN	2296-889X
ISSN	2296-889X
DOI	10.3389/fmolb.2022.878652
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Article: Mendelian randomization: estimation of inpatient hospital costs attributable to obesity.

Dick, Katherine / Schneider, John E / Briggs, Andrew / Lecomte, Pascal / Regnier, Stephane A / Lean, Michael

Health economics review

2021 Volume 11, Issue 1, Page(s) 16

Abstract: Background: Mendelian Randomization is a type of instrumental variable (IV) analysis that uses inherited genetic variants as instruments to estimate causal effects attributable to genetic factors. This study aims to estimate the impact of obesity on ... ...

Abstract	Background: Mendelian Randomization is a type of instrumental variable (IV) analysis that uses inherited genetic variants as instruments to estimate causal effects attributable to genetic factors. This study aims to estimate the impact of obesity on annual inpatient healthcare costs in the UK using linked data from the UK Biobank and Hospital Episode Statistics (HES). Methods: UK Biobank data for 482,127 subjects was linked with HES inpatient admission records, and costs were assigned to episodes of care. A two-stage least squares (TSLS) IV model and a TSLS two-part cost model were compared to a naïve regression of inpatient healthcare costs on body mass index (BMI). Results: The naïve analysis of annual cost on continuous BMI predicted an annual cost of £21.61 [95% CI £20.33 - £22.89] greater cost per unit increase in BMI. The TSLS IV model predicted an annual cost of £14.36 [95% CI £0.31 - £28.42] greater cost per unit increase in BMI. Modelled with a binary obesity variable, the naïve analysis predicted that obese subjects incurred £205.53 [95% CI £191.45 - £219.60] greater costs than non-obese subjects. The TSLS model predicted a cost £201.58 [95% CI £4.32 - £398.84] greater for obese subjects compared to non-obese subjects. Conclusions: The IV models provide evidence for a causal relationship between obesity and higher inpatient healthcare costs. Compared to the naïve models, the binary IV model found a slightly smaller marginal effect of obesity, and the continuous IV model found a slightly smaller marginal effect of a single unit increase in BMI.
Language	English
Publishing date	2021-05-14
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2634483-X
ISSN	2191-1991
ISSN	2191-1991
DOI	10.1186/s13561-021-00314-2
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Article ; Online: SmMIP-tools: a computational toolset for processing and analysis of single-molecule molecular inversion probes-derived data.

Medeiros, Jessie J F / Capo-Chichi, Jose-Mario / Shlush, Liran I / Dick, John E / Arruda, Andrea / Minden, Mark D / Abelson, Sagi

Bioinformatics (Oxford, England)

2022 Volume 38, Issue 8, Page(s) 2088–2095

Abstract: Motivation: Single-molecule molecular inversion probes (smMIPs) provide an exceptionally cost-effective and modular approach for routine or large-cohort next-generation sequencing. However, processing the derived raw data to generate highly accurate ... ...

Abstract	Motivation: Single-molecule molecular inversion probes (smMIPs) provide an exceptionally cost-effective and modular approach for routine or large-cohort next-generation sequencing. However, processing the derived raw data to generate highly accurate variants calls remains challenging. Results: We introduce SmMIP-tools, a comprehensive computational method that promotes the detection of single nucleotide variants and short insertions and deletions from smMIP-based sequencing. Our approach delivered near-perfect performance when benchmarked against a set of known mutations in controlled experiments involving DNA dilutions and outperformed other commonly used computational methods for mutation detection. Comparison against clinically approved diagnostic testing of leukaemia patients demonstrated the ability to detect both previously reported variants and a set of pathogenic mutations that did not pass detection by clinical testing. Collectively, our results indicate that increased performance can be achieved when tailoring data processing and analysis to its related technology. The feasibility of using our method in research and clinical settings to benefit from low-cost smMIP technology is demonstrated. Availability and implementation: The source code for SmMIP-tools, its manual and additional scripts aimed to foster large-scale data processing and analysis are all available on github (https://github.com/abelson-lab/smMIP-tools). Raw sequencing data generated in this study have been submitted to the European Genome-Phenome Archive (EGA; https://ega-archive.org) and can be accessed under accession number EGAS00001005359. Supplementary information: Supplementary data are available at Bioinformatics online.
MeSH term(s)	Humans ; Mutation ; Genome ; Software ; High-Throughput Nucleotide Sequencing/methods ; Leukemia
Language	English
Publishing date	2022-02-11
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btac081
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