The INoVA uses entity recognition models to extract models and associated readouts (outcomes) from sentences in PubMed abstracts. The following definitions are used for these entities:
Model
The experimental setup (e.g. wound healing assay, Irwin test) used to measure an outcome, or the system in which an outcome is being measured (e.g. CACO-2 cells, the liver, ob/ob mice). The following model types are included: In vitro, in vivo, ex vivo, in silico and in chemico.
Readout
What is being measured in the model. Both quantitative measures and qualitative outcomes are being retrieved.
Searching and filtering
The INoVA hub uses free text searches as well as pre-defined filtering options to guide the user in retrieving relevant publications. The various options are described below. Multiple filters and/or free text searches can be used to define your search.
Free text search
Free text searches are available for the model name, readout and species.
By typing in the name and clicking on "apply", a substring search is performed on all models and readouts in our platform.
For species, a generative AI mapping has been performed on the sentence level.
Therefore, the species has been inferred from the model and/or sentence.
To correctly handle abbreviations, an attempt is made to map a search term on its full name if an abbreviation is being used, and vice versa, abbreviations of a full name are included when possible.
Boolean queries are currently not supported in search.
Predefined filters
The models recognized have been mapped to model parameters whenever possible.
This mapping has been performed by a generative AI model on a contextual level.
This means that the whole sentence has been used to classify the models to the predefined parameters.
The model parameters can be used either to query the INoVA hub data, or to filter results.
To use the filters, select a parameter from the pulldown menu and click the apply button.
When multiple model parameters are used, the AND logic is being performed.
The following model parameters are available:
System type, e.g. in vitro, in vivo, in silico
System format, e.g. bioengineered system, organism
Inducer type, e.g. chemical, diet, genetic engineering
Health domain, e.g. cardiovascular disease
Organ system, e.g. heart, liver
For the organ system parameter, two levels of granularity are offered.
The second level offers a more detailed.
Please note that the model parameters are set independent from each other.
The user is responsible for making meaningful intersections of the parameter values.
Dynamic data
The information available in the INoVA hub interface is updated daily and contains all PubMed abstract data from the year 2015 onwards.
Selection and Download
To select and download PMIDs for further analysis, tick the box of the publication and click the download button.
The number of downloads is limited to a maximum of 100 records.
This retrospective study reviewed data from patients undergoing ARM-P/V for proton pump inhibitor (PPI) -refractory or PPI-dependent GERD at Showa University Koto Toyosu Hospital, Tokyo, from April to August 2024.
Eighteen patients (mean age 55.4 years) underwent ARM-P/V.
Prognostic factors and long-term outcomes with endoscopic submucosal dissection for colorectal tumors in patients aged 75 years or older.
Studies regarding the long-term outcomes of endoscopic submucosal dissection (ESD) performed in older patients with colorectal tumors are limited.
CCI and NLR may be useful parameters for decision-making in older patients undergoing colorectal ESD.
Therefore, in this study, we aimed to analyze the long-term outcomes of older patients with colorectal tumors who underwent ESD and identify prognostic factors.
Of the 156 patients included, 51 patients died during the follow-up period, among whom two deaths were due to colorectal cancer.
Prognostic factors and long-term outcomes with endoscopic submucosal dissection for colorectal tumors in patients aged 75 years or older.
The data of patients aged ≥ 75 years who underwent ESD for colorectal tumors (adenoma and Tis/T1 colorectal cancer) at a single center were retrospectively analyzed.
Updated evidence on epidemiology, diagnosis, and treatment for colonic diverticular bleeding.
The novel slim gastroscope is feasible for endoscopic submucosal dissection in many locations including the pharynx and duodenum and in certain complex lesions (large gastric lesions, rectal lesions with deep submucosal invasion, and circumferential esophageal lesions).
This warrants further investigation through larger comparative studies to validate its efficacy and safety in a broader patient population.
Optimal timing of precut sphincterotomy to prevent post-endoscopic retrograde cholangiopancreatography pancreatitis in difficult biliary cannulation: A retrospective study.
Patients were divided into an optimized precut group (≤12 min, n = 198) and a delayed group (> 12 min, n = 122).
The incidence of PEP was significantly lower in the optimized precut group than in the delayed precut group (5.1 % vs. 13.1 %, p = 0.02).
This retrospective study analyzed 320 patients who underwent precut sphincterotomy during their first endoscopic retrograde cholangiopancreatography at a single center.
Endoscopic management of acute cholecystitis in high-risk surgical patients: A comprehensive review article.
This review aimed to summarize the characteristics of each drainage method and compare the clinical outcomes of the three procedures for acute cholecystitis in high-risk surgical patients.
Endoscopic management of acute cholecystitis in high-risk surgical patients: A comprehensive review article.
In high-risk surgical patients, such as those with advanced age, deteriorated performance status, or underlying diseases, conservative treatment is typically preferred to manage acute cholecystitis.
However, in patients with a disease that is refractory to conservative treatment, drainage procedures are necessary to control the infection.
Clinical backgrounds and outcomes of patients with Barrett's esophageal adenocarcinoma treated via endoscopic submucosal dissection in Kyushu, Japan: A retrospective multicenter cohort study.
Clinical backgrounds and outcomes of patients with Barrett 's esophageal adenocarcinoma treated via endoscopic submucosal dissection in Kyushu, Japan: A retrospective multicenter cohort study.
Data from patients who underwent ESD for BEA or esophageal squamous cell carcinoma between January 2010 and December 2023 were extracted from the pathology database and reviewed.
We analyzed data from 283 patients (287 lesions).
Pathological axonal enlargement in connection with amyloidosis, lysosome destabilization, and bleeding is a major defect in Alzheimer's disease.
We used immunohistochemistry and immunofluorescence staining to analyze the forebrain tissue slices of Alzheimer 's disease patients.
On average, amyloid-β-positive axon diameters in Alzheimer 's disease brains were 1.72 times those of control brain axons.
Lysosome destabilization in Alzheimer 's disease was also clearly identified in the neuronal soma, where it was associated with the co-expression of amyloid-β, Cathepsin D, alpha-hemoglobin, actin alpha 2, and collagen type IV.
Additionally, the data showed that amyloid-β-containing lysosomes were 2.23 times larger than control lysosomes.
Widespread axonal amyloidosis with distinctive axonal enlargement was observed in patients with Alzheimer 's disease.
In summary, axonal enlargement associated with amyloidosis, micro-bleeding, and lysosome destabilization is a major defect in patients with Alzheimer 's disease.
A single-cell landscape of the regenerating spinal cord of zebrafish.
In this study, we used single-cell RNA sequencing to profile distinct cell populations at different stages of spinal cord injury in zebrafish.
Furthermore, oligodendrocytes lost maturity markers while exhibiting increased proliferation following injury.
Radial glial cells exhibited significant proliferation and differentiation potential post injury, indicating their intrinsic roles in promoting neurogenesis and axonal regeneration, respectively.
A single-cell landscape of the regenerating spinal cord of zebrafish.
JOURNAL/nrgr/04.03/01300535-202602000-00046/figure1/v/2025-05-05T160104Z/r/image-tiff Unlike mammals, zebrafish possess a remarkable ability to regenerate their spinal cord after injury, making them an ideal vertebrate model for studying regeneration.
These findings demonstrated that the rapid and orderly regulation of inflammation, as well as the efficient proliferation and redifferentiation of new neurons and glial cells, enabled zebrafish to reconstruct the spinal cord.
Our analysis revealed that multiple subpopulations of neurons showed persistent activation of genes associated with axonal regeneration post injury, while molecular signals promoting growth cone collapse were inhibited.
While previous research has identified key cell types involved in this process, the underlying molecular and cellular mechanisms remain largely unexplored.
Sox2-overexpressing neural stem cells alleviate ventricular enlargement and neurological dysfunction in posthemorrhagic hydrocephalus.
However, only 1 % -10 % of transplanted NSCs survive in the ischemic and hypoxic microenvironment of posthemorrhagic hydrocephalus.
Therefore, Sox2-overexpressing NSCs (NSCSox2) may be more successful in improving neurological dysfunction after posthemorrhagic hydrocephalus.
NSCSox2 also promoted nerve regeneration, inhibited neuroinflammation and promoted M2 polarization (anti-inflammatory phenotype), thereby reducing cerebrospinal fluid secretion in choroid plexus.
In this study, human NSCSox2 was transplanted into a posthemorrhagic hydrocephalus mouse model, and retinoic acid was administered to further promote NSC differentiation.
Sox2 is an important factor for NSCs to maintain proliferation.
JOURNAL/nrgr/04.03/01300535-202602000-00045/figure1/v/2025-05-05T160104Z/r/image-tiff Neural stem cells (NSCs) have the potential for self-renewal and multidirectional differentiation, and their transplantation has achieved good efficacy in a variety of diseases.
In addition to their well-known role in action potential propagation, oligodendrocytes also provide intercellular metabolic support to axons by transferring energy metabolites and delivering exosomes.
However, the entire oligodendrocyte lineage is susceptible to changes in the biological microenvironment and other risk factors that arise as the brain ages.
Interventions that mitigate age-related myelin degeneration can improve neurological function in aging individuals.
In the central nervous system, compact myelin sheaths are formed by fully mature oligodendrocytes.
We also discuss recent advances in understanding how myelin degeneration in the aging brain contributes to neurodegenerative diseases and explore the factors that can prevent, slow down, or even reverse age-related myelin degeneration.
Therefore, myelin degeneration in the aging central nervous system is a significant contributor to the development of neurodegenerative diseases.
Myelin also provides intercellular metabolic support to axons.
Exosomes in neurodegenerative diseases: Therapeutic potential and modification methods.
This limitation can lead to side effects and toxicity when they interact with non-specific cells.
Our findings indicate that exosomes can efficiently cross the blood-brain barrier to facilitate drug delivery and can also serve as early diagnostic markers for neurodegenerative diseases.
Exosomes are small and can effectively cross the blood-brain barrier, allowing them to target deep brain lesions.
Effects of artificial intelligence assistance on endoscopist performance: Comparison of diagnostic performance in superficial esophageal squamous cell carcinoma detection using video-based models.
Therefore, this study aimed to develop and validate an AI model for ESCC detection using endoscopic video analysis and evaluate diagnostic improvements.
Effects of artificial intelligence assistance on endoscopist performance: Comparison of diagnostic performance in superficial esophageal squamous cell carcinoma detection using video-based models.
The AI model trained on annotated videos and 18 endoscopists (eight experts, 10 non-experts) evaluated their diagnostic performance.
The model 's sensitivity, specificity, and accuracy were 76.0 %, 79.4 %, and 77.2 %, respectively.
Endoscopic findings of gallbladder lesions evaluated with image-enhanced endoscopy: A preliminary study using resected gallbladders.
A colonoscopy revealed a submucosal tumor-like protrusion in the Rb lesion of the rectum without neoplastic epithelial changes.
Forceps biopsies of the overlying mucosa were non-diagnostic; however, endoscopic ultrasound-guided fine needle biopsy revealed that the specimen was poorly differentiated non-small cell invasive carcinoma.
Then, we performed a chest computed tomography and a newly detected mass lesion in the upper lobe of the right lung.
Subsequently, sputum cytology confirmed the diagnosis of lung adenocarcinoma.
A 73-year-old man visited our hospital due to hyperintestinal peristalsis and diarrhea.
Olmesartan-induced gastritis with no lower gastrointestinal symptoms: A case report.
A gastric biopsy revealed inflammatory cell infiltration.
A case of hemobilia caused by a pseudoaneurysm resulting in obstructive cholangitis in a patient who underwent plastic stent placement for pancreatic cancer (with video).
A case of hemobilia caused by a pseudoaneurysm resulting in obstructive cholangitis in a patient who underwent plastic stent placement for pancreatic cancer (with video).
We present a rare case of hemobilia caused by a pseudoaneurysm that resulted in obstructive cholangitis in a patient who underwent plastic stent placement for bile duct invasion caused by pancreatic cancer.
A 78-year-old man with a history of stroke who was using antiplatelet therapy presented with obstructive jaundice caused by locally advanced pancreatic cancer and underwent endoscopic plastic stent placement in the bile duct followed by concurrent chemoradiotherapy.
A UK single-center pilot experience using a novel robotic inchworm colonoscopy system.
However, 75 % of patients can experience pain with moderate sedation.
With no sedation it allows procedures to be conducted outside the traditional endoscopy unit such as outpatients.
Ninety-three patients were recruited (41 men:52 women), mean age of 53.8 years over 20 months.
The application of robotic technology aims to overcome difficulties faced including better utilization of rooms for advanced procedures and to achieve a complete colonoscopy in patients restricted by pain and technical challenges.
Procedures were performed outside the endoscopy unit similar to an outpatient clinical room.
RC provides a significantly more comfortable colonoscopy and has great potential to improve safety in colonoscopy from this early cohort of patients.
"Cat scratch colon" causing cecal perforation as a rare complication due to barotrauma during colonoscopy: A case report and literature review.
The resected specimen showed cecal mucosal tears with necrosis, which were pathologically consistent with cecal rupture resulting from mucosal laceration.
During surgery, a necrotic area was found in the cecal wall, requiring ileocecal resection.
CSC occurs in the colon with submucosal stiffening disease, such as collagenous colitis; however, in cases unrelated to these diseases, CSC appears in the cecum or ascending colon for anatomical reasons.
When CSC is encountered along with endoscopic findings of deep mucosal tears in the colon, the possibility of perforation after colonoscopy should be considered.
Computed tomography revealed inflammation around the cecum, with free air.
Mental Healthcare Quality Across the COVID-19 Pandemic in Rural versus Urban Patients.
This study reports on the quality of mental healthcare delivered to rural and urban Department of Veterans Affairs (VA) patients across COVID-19 pandemic.
Mental Healthcare Quality Across the COVID-19 Pandemic in Rural versus Urban Patients.
There was a dramatic increase in remote video encounters during the Early COVID Era, but urban patients experienced a much larger increase versus rural counterparts (Rural PC = 0.9 %, Urban PC = 2.0 %; Rural MH = 1.3 %, Urban MH = 2.8 %).
Across all Eras, rural patients and patients receiving remote care only received substantially lower quality mental health care compared to urban patients and patients who received a combination of remote and on-site care.
Quality of mental health care remained persistently lower among rural patients.
The study calculated the percentage of patients, by rural and urban strata, who met each quality metric throughout defined COVID Eras.
Association of Functional, Academic, Motor, and Cognitive Deficits in Graft Failure in Pediatric Liver Transplantation.
In 8062 pediatric LT recipients median age 3 (IQR: 1, 10), 28.0 %, 29.5 %, 35.0 %, and 79.8 % of recipients had pre-LT deficits in cognition, motor, academic activity, and functional status respectively.
Predicting graft failure risk in pediatric liver transplantation (LT) recipients could identify areas for improving management.
Pediatric LT recipients with pre- or post-LT motor, academic, and functional deficits are at higher risk for ACGF.
Using SRTR data 2008-2023, we evaluated the cognitive, motor, academic, and functional deficits of LT recipients at time of transplant to 14 years post-LT. We compared all cause graft failure (ACGF) among patients with versus without pre-LT and 1-year post-LT deficits using Cox regression, adjusting for recipient characteristics.
Persistent cognitive, motor, academic, and functional deficits are common in recipients and their impact on graft survival following LT helps inform risk prediction.
Care should be taken to assess deficits to identify patients who may benefit from functional intervention to potentially reduce ACGF risk.
Increased hazard of ACGF was noted in recipients with pre-LT decreased functional status (aHR = 1.13 (per 10 % decrease), 95 % CI: 1.10-1.15, p < 0.001), definite motor delay (aHR = 1.60, 95 % CI: 1.21-2.10, p < 0.001), and inability to participate in academics (aHR = 1.49, 95 % CI: 1.08-1.89, p = 0.01), but not delays in cognition (aHR = 0.91, 95 % CI: 0.69-1.21, p = 0.19).