LIVIVO - The Search Portal for Life Sciences

zur deutschen Oberfläche wechseln
Advanced search

Search results

Result 1 - 10 of total 230

Search options

  1. Article ; Online: Current cardiovascular manuscripts: Society for Cardiovascular Pathology journal club.

    Halushka, Marc K

    Cardiovascular pathology : the official journal of the Society for Cardiovascular Pathology

    2023  Volume 66, Page(s) 107555

    MeSH term(s) Myocardium/pathology ; Heart Transplantation ; Heart ; Graft Rejection/pathology ; Biopsy ; Endocardium/pathology
    Language English
    Publishing date 2023-06-18
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1134600-0
    ISSN 1879-1336 ; 1054-8807
    ISSN (online) 1879-1336
    ISSN 1054-8807
    DOI 10.1016/j.carpath.2023.107555
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Zs.A 3572: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  2. Article ; Online: Letter by Halushka and Witwer Regarding Article, "Circulating MicroRNA-122-5p Is Associated With a Lack of Improvement in Left Ventricular Function After Transcatheter Aortic Valve Replacement and Regulates Viability of Cardiomyocytes Through Extracellular Vesicles".

    Halushka, Marc K / Witwer, Kenneth W

    Circulation

    2023  Volume 147, Issue 4, Page(s) e64–e65

    MeSH term(s) Humans ; Ventricular Function, Left/physiology ; Transcatheter Aortic Valve Replacement ; Circulating MicroRNA ; Myocytes, Cardiac ; Aortic Valve/surgery ; Aortic Valve Stenosis/surgery ; Extracellular Vesicles ; Treatment Outcome ; Severity of Illness Index ; Stroke Volume/physiology ; MicroRNAs
    Chemical Substances Circulating MicroRNA ; MIRN122 microRNA, human ; MicroRNAs
    Language English
    Publishing date 2023-01-23
    Publishing country United States
    Document type Letter ; Comment
    ZDB-ID 80099-5
    ISSN 1524-4539 ; 0009-7322 ; 0069-4193 ; 0065-8499
    ISSN (online) 1524-4539
    ISSN 0009-7322 ; 0069-4193 ; 0065-8499
    DOI 10.1161/CIRCULATIONAHA.122.061834
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Ui IV Zs.60: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
    ab Jg. 2022: Lesesaal (EG)

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  3. Article ; Online: A Comparison of Tissue Dissection Techniques for Diagnostic, Prognostic, and Theragnostic Analysis of Human Disease.

    Walsh, Elise M / Halushka, Marc K

    Pathobiology : journal of immunopathology, molecular and cellular biology

    2022  Volume 90, Issue 3, Page(s) 199–208

    Abstract: Histopathology has historically been the critical technique for the diagnosis and treatment of human disease. Today, genomics, transcriptomics, and proteomics from specific cells, rather than bulk tissue, have become key to understanding underlying ... ...

    Abstract Histopathology has historically been the critical technique for the diagnosis and treatment of human disease. Today, genomics, transcriptomics, and proteomics from specific cells, rather than bulk tissue, have become key to understanding underlying disease mechanisms and rendering useful diagnostic information. Extraction of desired analytes, i.e., nucleic acids or proteins, from easily accessible formalin-fixed paraffin-embedded tissues allows for clinically relevant activities, such as sequencing biomarker mutations or typing amyloidogenic proteins. Genetic profiling has become routine for cancers as varied as non-small cell lung cancer and prostatic carcinoma. The five main tissue dissection techniques that have been developed thus far include: bulk scraping, manual macrodissection, manual microdissection, laser-capture microdissection, and expression microdissection. In this review, we discuss the importance of tissue dissection in clinical practice and research, the basic methods, applications, as well as some advantages and disadvantages for each modality.
    MeSH term(s) Humans ; Carcinoma, Non-Small-Cell Lung ; Prognosis ; Lung Neoplasms ; Dissection/methods ; Microdissection/methods ; Tissue Fixation/methods ; Paraffin Embedding/methods
    Language English
    Publishing date 2022-08-11
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 1022703-9
    ISSN 1423-0291 ; 1015-2008
    ISSN (online) 1423-0291
    ISSN 1015-2008
    DOI 10.1159/000525979
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Ud II Zs.101: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
    ab Jg. 2022: Lesesaal (EG)

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  4. Article ; Online: Brooklyn plots to identify co-expression dysregulation in single cell sequencing.

    Patil, Arun H / McCall, Matthew N / Halushka, Marc K

    NAR genomics and bioinformatics

    2024  Volume 6, Issue 1, Page(s) lqad112

    Abstract: Altered open chromatin regions, impacting gene expression, is a feature of some human disorders. We discovered it is possible to detect global changes in genomically-related adjacent gene co-expression within single cell RNA sequencing (scRNA-seq) data. ... ...

    Abstract Altered open chromatin regions, impacting gene expression, is a feature of some human disorders. We discovered it is possible to detect global changes in genomically-related adjacent gene co-expression within single cell RNA sequencing (scRNA-seq) data. We built a software package to generate and test non-randomness using 'Brooklyn plots' to identify the percent of genes significantly co-expressed from the same chromosome in ∼10 MB intervals across the genome. These plots establish an expected low baseline of co-expression in scRNA-seq from most cell types, but, as seen in dilated cardiomyopathy cardiomyocytes, altered patterns of open chromatin appear. These may relate to larger regions of transcriptional bursting, observable in single cell, but not bulk datasets.
    Language English
    Publishing date 2024-01-11
    Publishing country England
    Document type Journal Article
    ISSN 2631-9268
    ISSN (online) 2631-9268
    DOI 10.1093/nargab/lqad112
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  5. Article: miR-21: a non-specific biomarker of all maladies.

    Jenike, Ana E / Halushka, Marc K

    Biomarker research

    2021  Volume 9, Issue 1, Page(s) 18

    Abstract: miRNA-21 is among the most abundant and highly conserved microRNAs (miRNAs) recognized. It is expressed in essentially all cells where it performs vital regulatory roles in health and disease. It is also frequently claimed to be a biomarker of diseases ... ...

    Abstract miRNA-21 is among the most abundant and highly conserved microRNAs (miRNAs) recognized. It is expressed in essentially all cells where it performs vital regulatory roles in health and disease. It is also frequently claimed to be a biomarker of diseases such as cancer and heart disease in bodily-fluid based miRNA studies. Here we dissociate its contributions to cellular physiology and pathology from its potential as a biomarker. We show how it has been claimed as a specific predictive or prognostic biomarker by at least 29 diseases. Thus, it has no specificity to any one disease. As a result, it should not be considered a viable candidate to be a biomarker, despite its continued evaluation as such. This theme of multiple assignments of a miRNA as a biomarker is shared with other common, ubiquitous miRNAs and should be concerning for them as well.
    Language English
    Publishing date 2021-03-12
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 2699926-2
    ISSN 2050-7771
    ISSN 2050-7771
    DOI 10.1186/s40364-021-00272-1
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  6. Article ; Online: miRge3.0: a comprehensive microRNA and tRF sequencing analysis pipeline.

    Patil, Arun H / Halushka, Marc K

    NAR genomics and bioinformatics

    2021  Volume 3, Issue 3, Page(s) lqab068

    Abstract: MicroRNAs and tRFs are classes of small non-coding RNAs, known for their roles in translational regulation of genes. Advances in next-generation sequencing (NGS) have enabled high-throughput small RNA-seq studies, which require robust alignment pipelines. ...

    Abstract MicroRNAs and tRFs are classes of small non-coding RNAs, known for their roles in translational regulation of genes. Advances in next-generation sequencing (NGS) have enabled high-throughput small RNA-seq studies, which require robust alignment pipelines. Our laboratory previously developed miRge and miRge2.0, as flexible tools to process sequencing data for annotation of miRNAs and other small-RNA species and further predict novel miRNAs using a support vector machine approach. Although miRge2.0 is a leading analysis tool in terms of speed with unique quantifying and annotation features, it has a few limitations. We present miRge3.0 that provides additional features along with compatibility to newer versions of Cutadapt and Python. The revisions of the tool include the ability to process Unique Molecular Identifiers (UMIs) to account for PCR duplicates while quantifying miRNAs in the datasets, correct erroneous single base substitutions in miRNAs with miREC and an accurate mirGFF3 formatted isomiR tool. miRge3.0 also has speed improvements benchmarked to miRge2.0, Chimira and sRNAbench. Finally, miRge3.0 output integrates into other packages for a streamlined analysis process and provides a cross-platform Graphical User Interface (GUI). In conclusion miRge3.0 is our third generation small RNA-seq aligner with improvements in speed, versatility and functionality over earlier iterations.
    Language English
    Publishing date 2021-07-21
    Publishing country England
    Document type Journal Article
    ISSN 2631-9268
    ISSN (online) 2631-9268
    DOI 10.1093/nargab/lqab068
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  7. Article ; Online: A Novel Circulating MicroRNA for the Detection of Acute Myocarditis.

    Fromm, Bastian / Patil, Arun H / Halushka, Marc K

    The New England journal of medicine

    2022  Volume 387, Issue 13, Page(s) 1240

    MeSH term(s) Circulating MicroRNA ; Humans ; Myocarditis/diagnosis ; Myocarditis/genetics ; Myocardium
    Chemical Substances Circulating MicroRNA
    Language English
    Publishing date 2022-09-28
    Publishing country United States
    Document type Letter ; Comment
    ZDB-ID 207154-x
    ISSN 1533-4406 ; 0028-4793
    ISSN (online) 1533-4406
    ISSN 0028-4793
    DOI 10.1056/NEJMc2115639
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Ua VI Zs.34: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
    ab Jg. 2022: Lesesaal (EG)

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  8. Article ; Online: HPAStainR: a Bioconductor and Shiny app to query protein expression patterns in the Human Protein Atlas.

    Nieuwenhuis, Tim O / Halushka, Marc K

    F1000Research

    2020  Volume 9, Page(s) 1210

    Abstract: The Human Protein Atlas is a website of protein expression in human tissues. It is an excellent resource of tissue and cell type protein localization, but only allows the query of a single protein at a time. We introduce HPAStainR as a new Shiny app and ... ...

    Abstract The Human Protein Atlas is a website of protein expression in human tissues. It is an excellent resource of tissue and cell type protein localization, but only allows the query of a single protein at a time. We introduce HPAStainR as a new Shiny app and Bioconductor/R package used to query the scored staining patterns in the Human Protein Atlas with multiple proteins/genes of interest. This allows the user to determine if an experimentally-generated protein/gene list associates with a particular cell type. We validated the tool using the Panglao Database cell type specific marker genes and a Genotype Expression (GTEx) tissue deconvolution dataset.  HPAStainR identified 92% of the Panglao cell types in the top quartile of confidence scores limited to tissue type of origin results. It also appropriately identified the correct cell types from the GTEx dataset. HPAStainR fills a gap in available bioinformatics tools to identify cell type protein expression patterns and can assist in establishing ground truths and exploratory analysis. HPAStainR is available from: https://32tim32.shinyapps.io/HPAStainR/.
    MeSH term(s) Computational Biology ; Humans ; Mobile Applications ; Proteins
    Chemical Substances Proteins
    Language English
    Publishing date 2020-10-08
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 2699932-8
    ISSN 2046-1402 ; 2046-1402
    ISSN (online) 2046-1402
    ISSN 2046-1402
    DOI 10.12688/f1000research.26771.2
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  9. Article ; Online: MicroRNA-144 is unlikely to play a role in bronchiolitis obliterans syndrome.

    Halushka, Marc K

    The Journal of heart and lung transplantation : the official publication of the International Society for Heart Transplantation

    2016  Volume 35, Issue 4, Page(s) 543

    MeSH term(s) Bronchiolitis Obliterans/prevention & control ; Female ; Humans ; Lung Transplantation ; Male ; MicroRNAs/physiology ; Transforming Growth Factor beta/physiology
    Chemical Substances MicroRNAs ; Transforming Growth Factor beta
    Language English
    Publishing date 2016-04
    Publishing country United States
    Document type Comment ; Letter
    ZDB-ID 1062522-7
    ISSN 1557-3117 ; 1053-2498
    ISSN (online) 1557-3117
    ISSN 1053-2498
    DOI 10.1016/j.healun.2016.01.008
    Database MEDical Literature Analysis and Retrieval System OnLINE

    Full text online

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Zs.A 2056: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  10. Article ; Online: Patterns of unwanted biological and technical expression variation among 49 human tissues.

    Nieuwenhuis, Tim O / Giles, Hunter H / Arking, Jeremy V A / Patil, Arun H / Shi, Wen / McCall, Matthew N / Halushka, Marc K

    Laboratory investigation; a journal of technical methods and pathology

    2024  , Page(s) 102069

    Abstract: Tissue gene expression studies are impacted by biological and technical sources of variation, which can be broadly classified into wanted and unwanted variation. The latter, if not addressed, results in misleading biological conclusions. Methods have ... ...

    Abstract Tissue gene expression studies are impacted by biological and technical sources of variation, which can be broadly classified into wanted and unwanted variation. The latter, if not addressed, results in misleading biological conclusions. Methods have been proposed to reduce unwanted variation, such as normalization and batch correction. A more accurate understanding of all causes of variation could significantly improve the ability of these methods to remove unwanted variation while retaining variation corresponding to the biological question of interest. We used 17,282 samples from 49 human tissues in the Genotype Tissue Expression (GTEx) dataset (v8) to investigate patterns and causes of expression variation. Transcript expression was transformed to z-scores and only the most variable 2% of transcripts were evaluated and clustered based on co-expression patterns. Clustered gene sets were assigned to different biological or technical causes based on histologic appearances and metadata elements. We identified 522 variable transcript clusters (median 11 per tissue) among the samples. Of these, 63% were confidently explained, 16% were likely explained, 7% were low confidence explanations and 14% had no clear cause. Histologic analysis annotated 46 clusters. Other common causes of variability included sex, sequencing contamination, immunoglobulin diversity, and compositional tissue differences. Less common biological causes included death interval (Hardy score), disease status, and age. Technical causes included blood draw timing and harvesting differences. Many of the causes of variation in bulk tissue expression were identifiable in the Tabula Sapiens dataset of single cell expression. This is among the largest explorations of the underlying sources of tissue expression variation. It uncovered expected and unexpected causes of variable gene expression and demonstrated the utility of matched histologic specimens. It further demonstrated the value of acquiring meaningful tissue harvesting metadata elements to use for improved normalization, batch correction, and analysis of both bulk and single cell RNA-seq data.
    Language English
    Publishing date 2024-04-24
    Publishing country United States
    Document type Journal Article
    ZDB-ID 80178-1
    ISSN 1530-0307 ; 0023-6837
    ISSN (online) 1530-0307
    ISSN 0023-6837
    DOI 10.1016/j.labinv.2024.102069
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Ud II Zs.164: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
    ab Jg. 2022: Lesesaal (EG)

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

To top