Abstract：
:Whole-slide imaging of histologic sections captures tissue microenvironments and cytologic details in expansive high-resolution images. These images can be mined to extract quantitative features that describe tissues, yielding measurements for hundreds of millions of histologic objects. A central challenge in utilizing this data is enabling investigators to train and evaluate classification rules for identifying objects related to processes like angiogenesis or immune response. In this paper we describe HistomicsML, an interactive machine-learning system for digital pathology imaging datasets. This framework uses active learning to direct user feedback, making classifier training efficient and scalable in datasets containing 108+ histologic objects. We demonstrate how this system can be used to phenotype microvascular structures in gliomas to predict survival, and to explore the molecular pathways associated with these phenotypes. Our approach enables researchers to unlock phenotypic information from digital pathology datasets to investigate prognostic image biomarkers and genotype-phenotype associations.
journal_name
Sci Repjournal_title
Scientific reportsauthors
Nalisnik M,Amgad M,Lee S,Halani SH,Velazquez Vega JE,Brat DJ,Gutman DA,Cooper LADdoi
10.1038/s41598-017-15092-3subject
Has Abstractpub_date
2017-11-06 00:00:00pages
14588issue
1issn
2045-2322pii
10.1038/s41598-017-15092-3journal_volume
7pub_type
杂志文章abstract：:Abnormal cardiac fibrosis indicates cardiac dysfunction and poor prognosis in myocardial infarction (MI) patients. Many studies have demonstrated that the ubiquitin proteasome system (UPS) plays a significant role in the pathogenesis of fibrosis. Ubiquitin C-terminal hydrolase L1 (UCHL1), a member of the UPS, is relat...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-020-67746-4
更新日期：2020-06-30 00:00:00
abstract：:This paper presents the results of the experiments which were performed using the optical biopsy system specially developed for in vivo tissue classification during the percutaneous needle biopsy (PNB) of the liver. The proposed system includes an optical probe of small diameter acceptable for use in the PNB of the li...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-020-71089-5
更新日期：2020-08-26 00:00:00
abstract：:Studies on the transcriptional control of gene expression play an important role in many areas of biology. Reference genes, which are often referred to as housekeeping genes, such as GAPDH, G3PDH, EF2, RpL7A, RpL10, TUBα and Actin, have traditionally been assumed to be stably expressed in all conditions, and they are ...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-017-08630-6
更新日期：2017-08-21 00:00:00
abstract：:The changes of balance control mechanism caused by lumbar disc herniation (LDH) has not been well understood. This study aimed to investigate the effects of LDH on the balance control during standing on sloped surfaces. Ten patients with LDH and 10 gender- and age-matched healthy subjects were instructed to stand quie...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-020-58455-z
更新日期：2020-02-03 00:00:00
abstract：:Excessive retention of neutral lipids in cardiac lipid droplets (LDs) is a common observation in cardiomyopathy. Thus, the systematic investigation of the cardiac LD proteome will help to dissect the underlying mechanisms linking cardiac steatosis and myocardial dysfunction. Here, after isolation of LDs from normal an...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep19782
更新日期：2016-01-22 00:00:00
abstract：:Our mind's eye and the role of internal attention in mental life and suffering has intrigued scholars for centuries. Yet, experimental study of internal attention has been elusive due to our limited capacity to control the timing and content of internal stimuli. We thus developed the Simulated Thoughts Paradigm (STP) ...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-021-81756-w
更新日期：2021-01-26 00:00:00
abstract：:Recombinant Mycobacterium strains such as recombinant BCG (rBCG) have received considerable attention for the HIV-1 vaccine development. Recently, we described a temperature-sensitive Mycobacterium paragordonae (Mpg) strain as a novel live tuberculosis vaccine that is safer and showed an enhanced protective effect aga...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-019-51875-6
更新日期：2019-10-29 00:00:00
abstract：:Acute kidney injury (AKI) in patients with septic shock is associated with high mortality, but the appropriate timing for initiating continuous renal replacement therapy (CRRT) is controversial. We retrospectively enrolled 158 septic shock patients with AKI in the medical intensive care unit (ICU) from July 2016 to Ap...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-019-48418-4
更新日期：2019-08-19 00:00:00
abstract：:Detecting and analysing motion is a key feature of Smart Homes and the connected sensor vision they embrace. At present, most motion sensors operate in line-of-sight Doppler shift schemes. Here, we propose an alternative approach suitable for indoor environments, which effectively constitute disordered cavities for ra...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-018-24681-9
更新日期：2018-04-25 00:00:00
abstract：:A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper. ...
journal_title：Scientific reports
pub_type： 已发布勘误
doi：10.1038/s41598-018-28707-0
更新日期：2018-08-07 00:00:00
abstract：:In utero and upon delivery, neonates are exposed to a wide array of microorganisms from various sources, including maternal bacteria. Prior studies have proposed that the mode of feeding shapes the gut microbiota and, subsequently the child's health. However, the effect of the mode of feeding and its influence on the ...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep38309
更新日期：2016-12-06 00:00:00
abstract：:Current control of insect pests relies on chemical insecticides, however, insecticide resistance development by pests is a growing concern in pest management. The main mechanisms for insecticide resistance typically involve elevated activity of detoxifying enzymes and xenobiotic transporters that break-down and excret...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-017-01961-4
更新日期：2017-05-11 00:00:00
abstract：:A functional genetic switch from the lactococcal bacteriophage TP901-1, deciding which of two divergently transcribing promoters becomes most active and allows this bi-stable decision to be inherited in future generations requires a DNA region of less than 1 kb. The fragment encodes two repressors, CI and MOR, transcr...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-020-65493-0
更新日期：2020-05-26 00:00:00
abstract：:Crosstalk between phytohormone pathways is essential in plant growth, development and stress responses. Brassinosteroids (BRs) and ethylene are both pivotal plant growth regulators, and the interaction between these two phytohormones in the tomato response to salt stress is still unclear. Here, we explored the mechani...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep35392
更新日期：2016-10-14 00:00:00
abstract：:Coccolithophores are single-celled photosynthesizing marine algae, responsible for half of the calcification in the surface ocean, and exert a strong influence on the distribution of carbon among global reservoirs, and thus Earth's climate. Calcification in the surface ocean decreases the buffering capacity of seawate...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep34263
更新日期：2016-09-28 00:00:00
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journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-019-48298-8
更新日期：2019-08-12 00:00:00
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journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-020-58783-0
更新日期：2020-02-04 00:00:00
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journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep38649
更新日期：2016-12-07 00:00:00
abstract：:Tyrosinase efficiently catalyzes the ortho-hydroxylation of monophenols and the oxidation of diphenols without any additional cofactors. Although it is of significant interest for the biosynthesis of catechol derivatives, the rapid catechol oxidase activity and inactivation of tyrosinase have hampered its practical ut...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-017-17635-0
更新日期：2017-12-08 00:00:00
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journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-018-24733-0
更新日期：2018-04-23 00:00:00
abstract：:Ruminococcus albus 8 is a specialist plant cell wall degrading ruminal bacterium capable of utilizing hemicellulose and cellulose. Cellulose degradation requires a suite of enzymes including endoglucanases, exoglucanases, and β-glucosidases. The enzymes employed by R. albus 8 in degrading cellulose are yet to be compl...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep29979
更新日期：2016-07-21 00:00:00
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journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep40061
更新日期：2017-01-06 00:00:00
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journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-017-18097-0
更新日期：2018-01-12 00:00:00
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journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-020-68958-4
更新日期：2020-07-27 00:00:00
abstract：:The nuclear factor κB (NF-κB) pathway plays a key role in innate and adaptive immunity, cell proliferation and survival, inflammation and tumors development. MiR-146a is an immune system regulator that has anti-inflammatory function in multiple cell types and conditions. Here we demonstrate activation of canonical NF-...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-019-41530-5
更新日期：2019-03-26 00:00:00
abstract：:Intravitreal anti-vascular endothelial growth factor (VEGF) agents can treat macular edema (ME) in branch retinal vein occlusion (BRVO). However, refractory ME, the mechanism of which is not well elucidated, occurs frequently. Sixty-six eyes with ME secondary to BRVO were enrolled in this retrospective observational c...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep29445
更新日期：2016-07-08 00:00:00
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journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep37042
更新日期：2016-11-22 00:00:00
abstract：:Carbon coated TiO2 (TiO2@C) is fabricated by a convenient and green one-pot solvothermal method, in which ethylene glycol serve as both the reaction medium and carbon source without the addition of any other carbon additives. During the solvothermal process, ethylene glycol polymerize and coordinate with Ti4+ to form ...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep43895
更新日期：2017-03-03 00:00:00
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journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/srep05105
更新日期：2014-05-29 00:00:00
abstract：:Multidrug-resistant organisms are increasing in healthcare settings, and there are few antimicrobials available to treat infections from these bacteria. Pseudomonas aeruginosa is an opportunistic pathogen in burn patients and individuals with cystic fibrosis (CF), and a leading cause of nosocomial infections. P. aerug...
journal_title：Scientific reports
pub_type： 杂志文章
doi：10.1038/s41598-019-43060-6
更新日期：2019-04-30 00:00:00
