JavaCyte, a novel open-source tool for automated quantification of key hallmarks of cardiac structural remodeling.

Abstract:

:Many cardiac pathologies involve changes in tissue structure. Conventional analysis of structural features is extremely time-consuming and subject to observer bias. The possibility to determine spatial interrelations between these features is often not fully exploited. We developed a staining protocol and an ImageJ-based tool (JavaCyte) for automated histological analysis of cardiac structure, including quantification of cardiomyocyte size, overall and endomysial fibrosis, spatial patterns of endomysial fibrosis, fibroblast density, capillary density and capillary size. This automated analysis was compared to manual quantification in several well-characterized goat models of atrial fibrillation (AF). In addition, we tested inter-observer variability in atrial biopsies from the CATCH-ME consortium atrial tissue bank, with patients stratified by their cardiovascular risk profile for structural remodeling. We were able to reproduce previous manually derived histological findings in goat models for AF and AV block (AVB) using JavaCyte. Furthermore, strong correlation was found between manual and automated observations for myocyte count (r = 0.94, p < 0.001), myocyte diameter (r = 0.97, p < 0.001), endomysial fibrosis (r = 0.98, p < 0.001) and capillary count (r = 0.95, p < 0.001) in human biopsies. No significant variation between observers was observed (ICC = 0.89, p < 0.001). We developed and validated an open-source tool for high-throughput, automated histological analysis of cardiac tissue properties. JavaCyte was as accurate as manual measurements, with less inter-observer variability and faster throughput.

journal_name

Sci Rep

journal_title

Scientific reports

authors

Winters J,von Braunmuhl ME,Zeemering S,Gilbers M,Brink TT,Scaf B,Guasch E,Mont L,Batlle M,Sinner M,Hatem S,Mansour MK,Fabritz L,Sommerfeld LC,Kirchhof P,Isaacs A,Stoll M,Schotten U,Verheule S

doi

10.1038/s41598-020-76932-3

subject

Has Abstract

pub_date

2020-11-18 00:00:00

pages

20074

issue

1

issn

2045-2322

pii

10.1038/s41598-020-76932-3

journal_volume

10

pub_type

杂志文章
  • Lifetime Reduction and Enhanced Emission of Single Photon Color Centers in Nanodiamond via Surrounding Refractive Index Modification.

    abstract::The negatively-charged nitrogen vacancy (NV(-)) center in diamond is of great interest for quantum information processing and quantum key distribution applications due to its highly desirable long coherence times at room temperature. One of the challenges for their use in these applications involves the requirement to...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep11179

    authors: Khalid A,Chung K,Rajasekharan R,Lau DW,Karle TJ,Gibson BC,Tomljenovic-Hanic S

    更新日期:2015-06-25 00:00:00

  • The biogeochemical fate of nickel during microbial ISA degradation; implications for nuclear waste disposal.

    abstract::Intermediate level radioactive waste (ILW) generally contains a heterogeneous range of organic and inorganic materials, of which some are encapsulated in cement. Of particular concern are cellulosic waste items, which will chemically degrade under the conditions predicted during waste disposal, forming significant qua...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-018-26963-8

    authors: Kuippers G,Boothman C,Bagshaw H,Ward M,Beard R,Bryan N,Lloyd JR

    更新日期:2018-06-08 00:00:00

  • Early functional network alterations in asymptomatic elders at risk for Alzheimer's disease.

    abstract::Amyloid-β (Aβ) deposition is known to starts decades before the onset of clinical symptoms of Alzheimer's disease (AD), however, the detailed pathophysiological processes underlying this preclinical period are not well understood. This study aimed to investigate functional network alterations in cognitively intact eld...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-06876-8

    authors: Nakamura A,Cuesta P,Kato T,Arahata Y,Iwata K,Yamagishi M,Kuratsubo I,Kato K,Bundo M,Diers K,Fernández A,Maestú F,Ito K

    更新日期:2017-07-26 00:00:00

  • Individual differences predict endorsement of water resilience.

    abstract::In the epoch of the Anthropocene change, complexity, and uncertainty create a demand for new systems of water management and governance. One such management model that is rapidly gaining traction amongst both scholars and practitioners is the concept of water resilience. Although increasing attention has been paid to ...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-62896-x

    authors: Baird J,Dale G,Farhad S

    更新日期:2020-04-06 00:00:00

  • Establishment and application of a loop-mediated isothermal amplification (LAMP) system for detection of cry1Ac transgenic sugarcane.

    abstract::To meet the demand for detection of foreign genes in genetically modified (GM) sugarcane necessary for regulation of gene technology, an efficient method with high specificity and rapidity was developed for the cry1Ac gene, based on loop-mediated isothermal amplification (LAMP). A set of four primers was designed usin...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep04912

    authors: Zhou D,Guo J,Xu L,Gao S,Lin Q,Wu Q,Wu L,Que Y

    更新日期:2014-05-09 00:00:00

  • Platelet activation and prothrombotic properties in a mouse model of peritoneal sepsis.

    abstract::Sepsis is associated with thrombocytopenia and microvascular thrombosis. Studies have described platelets implication in this pathology but their kinetics of activation and behavior remain poorly known. We show in a mouse model of peritonitis, the appearance of platelet-rich thrombi in organ microvessels and organ dam...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-018-31910-8

    authors: Vardon Bounes F,Mémier V,Marcaud M,Jacquemin A,Hamzeh-Cognasse H,Garcia C,Series J,Sié P,Minville V,Gratacap MP,Payrastre B

    更新日期:2018-09-10 00:00:00

  • Overlapping motifs on the herpes viral proteins ICP27 and ORF57 mediate interactions with the mRNA export adaptors ALYREF and UIF.

    abstract::The TREX complex mediates the passage of bulk cellular mRNA export to the nuclear export factor TAP/NXF1 via the export adaptors ALYREF or UIF, which appear to act in a redundant manner. TREX complex recruitment to nascent RNA is coupled with 5' capping, splicing and polyadenylation. Therefore to facilitate expression...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-018-33379-x

    authors: Tunnicliffe RB,Tian X,Storer J,Sandri-Goldin RM,Golovanov AP

    更新日期:2018-10-09 00:00:00

  • Observation of strongly enhanced photoluminescence from inverted cone-shaped silicon nanostructures. [corrected].

    abstract::Silicon nanowires (SiNWs) attached to a wafer substrate are converted to inversely tapered silicon nanocones (SiNCs). After excitation with visible light, individual SiNCs show a 200-fold enhanced integral band-to-band luminescence as compared to a straight SiNW reference. Furthermore, the reverse taper is responsible...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep17089

    authors: Schmitt SW,Sarau G,Christiansen S

    更新日期:2015-11-26 00:00:00

  • An In Vivo Mouse Model of Pelvic Recurrence of Human Colorectal Cancer.

    abstract::Pelvic recurrence of colorectal cancer is a crucial problem because radical surgery can lead to excessive invasion. Novel therapeutic strategies are required instead of surgery. However, there are few suitable models because of the difficulty in transplanting and observing tumors in the pelvis. We have established an ...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-56152-0

    authors: Yamamoto M,Taniguchi K,Masubuchi S,Tominaga T,Inomata Y,Miyamoto A,Ishizuka TA,Murakami T,Osumi W,Hamamoto H,Tanaka K,Okuda J,Uchiyama K

    更新日期:2019-12-23 00:00:00

  • The influence of emotional facial expressions on gaze-following in grouped and solitary pedestrians.

    abstract::The mechanisms contributing to collective attention in humans remain unclear. Research indicates that pedestrians utilise the gaze direction of others nearby to acquire environmentally relevant information, but it is not known which, if any, additional social cues influence this transmission. Extending upon previous f...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep05794

    authors: Gallup AC,Chong A,Kacelnik A,Krebs JR,Couzin ID

    更新日期:2014-07-23 00:00:00

  • Genome-wide mapping of DNase I hypersensitive sites reveals chromatin accessibility changes in Arabidopsis euchromatin and heterochromatin regions under extended darkness.

    abstract::Light, as the energy source in photosynthesis, is essential for plant growth and development. Extended darkness causes dramatic gene expression changes. In this study, we applied DNase-seq (DNase I hypersensitive site sequencing) to study changes of chromatin accessibility in euchromatic and heterochromatic regions un...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-04524-9

    authors: Liu Y,Zhang W,Zhang K,You Q,Yan H,Jiao Y,Jiang J,Xu W,Su Z

    更新日期:2017-06-22 00:00:00

  • Integration of neurogenesis and angiogenesis models for constructing a neurovascular tissue.

    abstract::Neurovascular unit (NVU) is a basic unit in the brain, including neurons, glial cells, blood vessels and extracellular matrix. This concept implies the importance of a three-dimensional (3D) culture model including these cell types for investigating brain functions. However, little is known about the construction of a...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-17411-0

    authors: Uwamori H,Higuchi T,Arai K,Sudo R

    更新日期:2017-12-11 00:00:00

  • Neuro-inflammatory effects of photodegradative products of bilirubin.

    abstract::Phototherapy was introduced in the early 1950's, and is the primary treatment of severe neonatal jaundice or Crigler-Najjar syndrome. Nevertheless, the potential biological effects of the products generated from the photodegradation of bilirubin during phototherapy remain unknown. This is very relevant in light of rec...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-018-25684-2

    authors: Jašprová J,Dal Ben M,Hurný D,Hwang S,Žížalová K,Kotek J,Wong RJ,Stevenson DK,Gazzin S,Tiribelli C,Vítek L

    更新日期:2018-05-10 00:00:00

  • ANKRD22 promotes progression of non-small cell lung cancer through transcriptional up-regulation of E2F1.

    abstract::Lung cancer is the leading cause of death among all malignancies due to rapid tumor progression and relapse; however, the underlying molecular mechanisms of tumor progression are unclear. In the present study, we identified ANKRD22 as a novel tumor-associated gene in non-small cell lung cancer (NSCLC). According to th...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-04818-y

    authors: Yin J,Fu W,Dai L,Jiang Z,Liao H,Chen W,Pan L,Zhao J

    更新日期:2017-06-30 00:00:00

  • Functional association of cellular microtubules with viral capsid assembly supports efficient hepatitis B virus replication.

    abstract::Viruses exploit host factors and environment for their efficient replication. The virus-host interaction mechanisms for achieving an optimal hepatitis B virus (HBV) replication have been largely unknown. Here, a single cell cloning revealed that HepAD38 cells, a widely-used HBV-inducible cell line, contain cell clones...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-11015-4

    authors: Iwamoto M,Cai D,Sugiyama M,Suzuki R,Aizaki H,Ryo A,Ohtani N,Tanaka Y,Mizokami M,Wakita T,Guo H,Watashi K

    更新日期:2017-09-06 00:00:00

  • Chiral magnetoresistance in the Weyl semimetal NbP.

    abstract::NbP is a recently realized Weyl semimetal (WSM), hosting Weyl points through which conduction and valence bands cross linearly in the bulk and exotic Fermi arcs appear. The most intriguing transport phenomenon of a WSM is the chiral anomaly-induced negative magnetoresistance (NMR) in parallel electric and magnetic fie...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep43394

    authors: Niemann AC,Gooth J,Wu SC,Bäßler S,Sergelius P,Hühne R,Rellinghaus B,Shekhar C,Süß V,Schmidt M,Felser C,Yan B,Nielsch K

    更新日期:2017-03-06 00:00:00

  • Impacts of manure application on soil environment, rainfall use efficiency and crop biomass under dryland farming.

    abstract::Because of inadequate nutrient and water supply, soils are often unproductive in Northwest China. We studied the effects of manure application at low (LM 7.5  t ha(-1)), medium (MM 15 t ha(-1)), and high (HM 22.5 t ha(-1)) rates combined with fixed levels of chemical fertilizers on maize growth and rainfall use effici...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep20994

    authors: Wang X,Jia Z,Liang L,Yang B,Ding R,Nie J,Wang J

    更新日期:2016-02-12 00:00:00

  • A New Strategy of Lithography Based on Phase Separation of Polymer Blends.

    abstract::Herein, we propose a new strategy of maskless lithographic approach to fabricate micro/nano-porous structures by phase separation of polystyrene (PS)/Polyethylene glycol (PEG) immiscible polymer blend. Its simple process only involves a spin coating of polymer blend followed by a development with deionized water rinse...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep15947

    authors: Guo X,Liu L,Zhuang Z,Chen X,Ni M,Li Y,Cui Y,Zhan P,Yuan C,Ge H,Wang Z,Chen Y

    更新日期:2015-10-30 00:00:00

  • Chemosensory signalling pathways involved in sensing of amino acids by the ghrelin cell.

    abstract::Taste receptors on enteroendocrine cells sense nutrients and transmit signals that control gut hormone release. This study aimed to investigate the amino acid (AA) sensing mechanisms of the ghrelin cell in a gastric ghrelinoma cell line, tissue segments and mice. Peptone and specific classes of amino acids stimulate g...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep15725

    authors: Vancleef L,Van Den Broeck T,Thijs T,Steensels S,Briand L,Tack J,Depoortere I

    更新日期:2015-10-29 00:00:00

  • Low temperature solution process-based defect-induced orange-red light emitting diode.

    abstract::We report low-temperature solution-processed p-CuO nanorods (NRs)/n-ZnO NRs heterojunction light emitting diode (LED), exploiting the native point defects of ZnO NRs. ZnO NRs were synthesized at 90 °C by using hydrothermal method while CuO NRs were synthesized at 100 °C by using microwave reaction system. The electric...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep17961

    authors: Biswas P,Baek SD,Lee SH,Park JH,Lee SJ,Lee TI,Myoung JM

    更新日期:2015-12-09 00:00:00

  • Side-effects of pesticides on the generalist endoparasitoid Palmistichus elaeisis (Hymenoptera: Eulophidae).

    abstract::New plant protection strategies focus on minimizing chemical pesticide use and increasing their compatibility with biological control agents. The objective was to evaluate the side-effects of glyphosate, diflubenzuron, malathion, tebuconazole and triflumuron (at 720, 45, 400, 150 and 20 g ai ha-1, respectively), pesti...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-10462-3

    authors: Cruz RA,Zanuncio JC,Lacerda MC,Wilcken CF,Fernandes FL,Tavares WS,Soares MA,Sediyama CS

    更新日期:2017-08-30 00:00:00

  • Sentinel nurseries to assess the phytosanitary risks from insect pests on importations of live plants.

    abstract::Ornamental plants represent a major pathway of invasion for alien pests worldwide. Commodity risk analyses are carried out to assess the risk posed by a new trade in a commodity, but they are restricted by our limited knowledge of the pests carried by traded plants. We used the sentinel nursery technique to identify i...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-018-29551-y

    authors: Kenis M,Li H,Fan JT,Courtial B,Auger-Rozenberg MA,Yart A,Eschen R,Roques A

    更新日期:2018-07-25 00:00:00

  • Kinase inhibitor screening using artificial neural networks and engineered cardiac biowires.

    abstract::Kinase inhibitors are often used as cancer targeting agents for their ability to prevent the activation of cell growth and proliferation signals. Cardiotoxic effects have been identified for some marketed kinase inhibitors that were not detected during clinical trials. We hypothesize that more predictive cardiac funct...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-12048-5

    authors: Conant G,Ahadian S,Zhao Y,Radisic M

    更新日期:2017-09-18 00:00:00

  • Comprehensive analysis of the T-cell receptor beta chain gene in rhesus monkey by high throughput sequencing.

    abstract::Profiling immune repertoires by high throughput sequencing enhances our understanding of immune system complexity and immune-related diseases in humans. Previously, cloning and Sanger sequencing identified limited numbers of T cell receptor (TCR) nucleotide sequences in rhesus monkeys, thus their full immune repertoir...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep10092

    authors: Li Z,Liu G,Tong Y,Zhang M,Xu Y,Qin L,Wang Z,Chen X,He J

    更新日期:2015-05-11 00:00:00

  • A Cosine Similarity Algorithm Method for Fast and Accurate Monitoring of Dynamic Droplet Generation Processes.

    abstract::Droplet microfluidics has attracted significant interests in functional microcapsule synthesis, pharmaceuticals, fine chemicals, cosmetics and biomedical research. The low variability of performing chemical reactions inside droplets could benefit from improved homogeneity and reproducibility. Therefore, accurate and c...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-018-28270-8

    authors: Zhu X,Su S,Fu M,Liu J,Zhu L,Yang W,Jing G,Guo Y

    更新日期:2018-07-02 00:00:00

  • RNAi-based bioinsecticide for Aedes mosquito control.

    abstract::Zika virus infection and dengue and chikungunya fevers are emerging viral diseases that have become public health threats. Their aetiologic agents are transmitted by the bite of genus Aedes mosquitoes. Without effective therapies or vaccines, vector control is the main strategy for preventing the spread of these disea...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-39666-5

    authors: Lopez SBG,Guimarães-Ribeiro V,Rodriguez JVG,Dorand FAPS,Salles TS,Sá-Guimarães TE,Alvarenga ESL,Melo ACA,Almeida RV,Moreira MF

    更新日期:2019-03-11 00:00:00

  • The diagnostic value of human epididymis protein 4 for endometrial cancer is moderate.

    abstract::Human epididymis protein 4 (HE4) has been used as a biomarker of endometrial cancer (EC) in clinical practice. However, there remains a lack of systemic research on the critical values of HE4 for diagnosing different clinical stages and pathological types of EC. This study investigated the accuracy of human epididymis...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-79960-1

    authors: Liu J,Han L,Jiao Z

    更新日期:2021-01-12 00:00:00

  • Early evening light mitigates sleep compromising physiological and alerting responses to subsequent late evening light.

    abstract::The widespread use of electric light and electronic devices has resulted in an excessive exposure to light during the late-evening and at night. This late light exposure acutely suppresses melatonin and sleepiness and delays the circadian clock. Here we investigate whether the acute effects of late-evening light expos...

    journal_title:Scientific reports

    pub_type: 杂志文章,随机对照试验

    doi:10.1038/s41598-019-52352-w

    authors: Te Kulve M,Schlangen LJM,van Marken Lichtenbelt WD

    更新日期:2019-11-05 00:00:00

  • The human HOXA9 protein uses paralog-specific residues of the homeodomain to interact with TALE-class cofactors.

    abstract::HOX proteins interact with PBX and MEIS cofactors, which belong to the TALE-class of homeodomain (HD)-containing transcription factors. Although the formation of HOX-PBX complexes depends on a unique conserved HOX motif called hexapeptide (HX), the additional presence of MEIS induces a remodeling of the interaction, l...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-42096-y

    authors: Dard A,Jia Y,Reboulet J,Bleicher F,Lavau C,Merabet S

    更新日期:2019-04-05 00:00:00

  • Population-scale organization of cerebellar granule neuron signaling during a visuomotor behavior.

    abstract::Granule cells at the input layer of the cerebellum comprise over half the neurons in the human brain and are thought to be critical for learning. However, little is known about granule neuron signaling at the population scale during behavior. We used calcium imaging in awake zebrafish during optokinetic behavior to re...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-15938-w

    authors: Sylvester SJG,Lee MM,Ramirez AD,Lim S,Goldman MS,Aksay ERF

    更新日期:2017-11-24 00:00:00