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.
Despite the constitutive localization of centromere proteins in proliferating cells, cells rapidly disassemble most centromere proteins during quiescence entry while preserving those required to maintain centromere identity.
Here, we analyze how cells regulate their centromeres during quiescence entry and exit.
Spatial inhibition of RhoA by RhoGAP15B promotes protrusive activity during collective migration.
Using GFP knock-in lines, we systematically characterized the localization patterns of all Drosophila RhoGEFs (activators) and RhoGAPs (inhibitors) in border cells, an in vivo model of collective migration.
We have further combined RNAi screening with GFP-based validation of depletion efficiency to assess the functional significance of those RhoGEFs/GAPs expressed in border cells.
This identified RhoGAP15B as a localized inhibitor of RhoA activity at the border cell cortex.
RhoGAP15B regulates cluster morphology and is enriched at the leading cell front, where it restrains actomyosin contractility to promote protrusive behavior.
Edge-vertex flow enables rapid adhesion reinforcement under tension.
PROMIS well-being measures demonstrate acceptable construct validity in AIS patients while capturing unique variance not assessed by the SRS-22, identifying vulnerable patients with suboptimal positive functioning despite low psychopathology risk.
To evaluate the construct validity of PROMIS Positive Affect (PA), Life Satisfaction (LS), and Meaning & Purpose (MP) measures compared to the SRS-22 in AIS patients and determine whether these measures capture distinct aspects of mental health not adequately assessed by traditional instruments.
Among bracing patients, those with curves ≤30° had MP scores 10.9 (95 % CI: 2.2-19.7) points higher than those with curves > 50° (P=0.039).
PROMIS PA, LS, and MP measures need validation in AIS populations and may capture patients who can benefit from interventions prior to AIS treatment to optimize outcomes.
Patients completed PROMIS PA, LS, MP, Anxiety, and Depression measures alongside the SRS-22 questionnaire at baseline.
Between 14-40 % of patients with suboptimal PROMIS well-being scores had SRS-22 Mental Health scores indicating low depression risk.
This prospective cohort study enrolled 93 AIS patients (mean age 13.8±1.8 years, 78.5 % female) at a single institution.
From Small Parsimony to Horizontal Gene Transfer: Inferring Horizontal Transfer and Gene Loss for Single-Origin Characters.
Character-based models such as perfect transfer networks and its galled variant aim to leverage this information to predict horizontal gene transfers.
We also explore the utility of our model for tracing possible highways of gene transfers by presenting a real case study on a dataset of bacterial species and Kyoto Encyclopedia of Genes and Genome functions as characters.
Identifying patient and provider determinants of primary care experiences and outcomes for persons with chronic conditions: a multilevel analysis of a nation-wide survey in Norway.
The ICC for four of six PREMs varied from 0.035 to 0.091, while the ICCs for the PROMs varied from 0.014 to 0.022.
We aimed to: (i) examine to what extent care experiences and perceived outcomes among persons with chronic conditions depend on the GPs they are registered with and (ii) map the associations between patient and GP-level determinants of patient-reported experience and outcome measures.
Cross-sectional general practice nested survey of patients (n = 6691).
Identifying patient and provider determinants of primary care experiences and outcomes for persons with chronic conditions: a multilevel analysis of a nation-wide survey in Norway.
Performance of the Dutch Triage standard in managing fever in children in out-of-hours primary care: a secondary analysis of the chili study.
This study examines the agreement between pre-consultation NTS urgency classifications (U-scores) and post-consultation management decisions in febrile children, and whether the NTS reduces between-center variation in decision-making.
Performance of the Dutch Triage standard in managing fever in children in out-of-hours primary care: a secondary analysis of the chili study.
We performed a secondary analysis of the CHILI study, including 22 089 consultations for children under 12 with fever, across 18 out-of-hours GP centers (2015- 2016).
Measuring the relationship between outpatient family physician visit regularity and acute care utilization during the end of life: a population-level retrospective cohort study.
Adults with cardiorespiratory conditions who died in Ontario, Canada, between 2017 & 2019.
Patients ' (N = 151 030) median age at 2-years before death was 80, 55 % were male, & had a median of 9 FP outpatient visits in the last two years of life.
Efficacy and safety of PD-1/ PD-L1 inhibitors as adjuvants in the treatment of patients with solid cancers: A systematic review and meta-analysis of randomized controlled trials.
This systematic review and meta-analysis evaluated the efficacy and safety of PD-1 and PD-L1 inhibitors as adjuvant treatment in patients with solid tumors.
Adjuvant PD-1 and PD-L1 inhibitors improve disease-free and distant metastasis-free survival in selected patients with high-risk solid tumors.
Efficacy and safety of PD-1/ PD-L1 inhibitors as adjuvants in the treatment of patients with solid cancers: A systematic review and meta-analysis of randomized controlled trials.
Epigenetic dysregulation and biological function of PDX1 in prostate cancer.
In PCa cell lines (PC-3 and LNCaP) engineered to stably overexpress or knockdown PDX1, the ectopic PDX1 expression significantly enhanced cell proliferation and migration, whereas PDX1 knockdown suppressed these phenotypic processes.
Overall, our findings suggest that PDX1 plays a tumor-promoting role in human PCa cells by influencing expression of metabolites in insulin, inflammatory, and epithelial-mesenchymal transition (EMT) signaling pathways.
Inquiry of genome-wide DNA methylation dataset, we identified the homeodomain pancreatic and duodenal homeobox 1 (PDX1) gene as differentially hypermethylated in PCa compared to normal prostate tissues.
Given its potential role in metabolic regulation, full insights into the function of PDX1 in PCa could contribute to improved treatment and prevention strategies, particularly for men with PCa and comorbidities such as obesity and diabetes.
Immunohistochemical analysis of matched PCa and normal prostate tissues using tissue microarray showed a significant 2.33-fold (p = 0.0001) higher PDX1 protein expression in the PCa compared to the normal prostate tissues.
Bibliometric mapping of glioma classification research through main path, key route, and K-core analyses.
The network comprised 46,204 nodes and 231,432 arcs, highlighting DNA methylation profiling & # x2019; s role in advancing molecular biomarker-based classification models.
Retraction: Efficacy and safety of traditional chemotherapies for patients with ovarian neoplasm: a network meta-analysis.
Health Information Technology-Related Loss of Central Surveillance Data in a Heart Intensive Care Unit: Multi-Framework Case Report.
This study aimed to classify and analyze an HIT-related incident that involved loss of central surveillance data in a heart intensive care unit using multiple complementary patient safety and human factors frameworks.
The SEIPS 2.0 and sociotechnical models highlighted disruptions to monitoring tasks and the organization 's reliance on IT intervention.
Centralized electronic surveillance systems are widely used in intensive care settings to support continuous physiological monitoring and patient safety.
HIT-related monitoring failures in high-acuity settings are best understood as sociotechnical system events rather than isolated technical faults or individual errors.
Comparative Performance of 3 Analytical Models in Identifying Associated Factors of Pulmonary Dysfunction-Depression Comorbidity: China Health and Retirement Longitudinal Study-Based Nationwide Cross-Sectional Study.
The analytical sample comprised 1146 adults with confirmed pulmonary dysfunction, of whom 514 (44.9 %) exhibited clinically significant depressive symptoms (10-item Center for Epidemiologic Studies Depression Scale [ CESD-10 ] score of ≥10).
With 20 shared predictors, AUROCs converged (0.658-0.665), BN calibrated best, LR or BN remained sensitivity-forward, and XGBoost remained specificity-forward.
Clinically usable models for identifying pulmonary dysfunction-depression comorbidity remain limited by suboptimal interpretability, inconsistent validation, and uncertain generalizability.
This study developed and compared logistic regression (LR), Bayesian network (BN), and Extreme Gradient Boosting (XGBoost) models for identifying factors associated with pulmonary dysfunction-depression comorbidity and evaluated their clinical usefulness across different decision thresholds.
Performance was assessed via discrimination (area under the receiver operating characteristic curve [ AUROC ]), calibration (Hosmer-Lemeshow test), and decision curve analysis.
Correction: Bisphenol A induces cell cycle arrest in primary and prostate cancer cells through EGFR/ERK/p53 signaling pathway activation.
Vulnerable groups - women, children, and the elderly - experience the greatest inequities.
Cancer is an escalating yet neglected health crisis among refugees, migrants, and populations affected by conflict.
Integrating oncology into emergency response protocols and global health governance is essential to ensure continuity, dignity, and justice in care for displaced and conflict-affected populations.
In AR-positive cells, CREB5 overexpression promoted cell colony growth with tumorigenic properties and increased tumor sizein vivo.
Prostate gland cells can be transcriptionally and morphologically characterized as basal and luminal.
SCL tumors have reduced AR activity and increased stem-cell activity that promotes tumor formation, which contributes to poor clinical outcomes.
These findings implicate CREB5 as a driver of the transcriptional programs underlying AR-independent basal and SCL CRPC subtypes, and this activity is detectable in primary PC.
Through in silico modeling of PC transcriptomes and several pre-defined PC signaling programs, CREB5 expression was best associated with basal-like gene signatures and SCL-associated genes in primary PC and CRPCs (n = 493 and 208).
Challenges in replay detection by TDLM in post-encoding resting state.
Despite successful decoding of brain activity during a localizer task, and contrary to predictions, we found no evidence for replay during a post-learning resting state.
We infer that even if replay was present at plausible rates in our resting state dataset, we would lack statistical power to detect it with TDLM.
Fecal DPP4 concentration reflects colonic injury in the TNBS-induced rat model of colitis.
This study investigated DPP4 concentrations in feces, colonic tissue, and serum in a TNBS-induced rat model of colitis, and assessed host and/or microbiota contribution to fecal DPP4 in knockout and germ-free mice.
Fecal DPP4 concentration reflects colonic injury in the TNBS-induced rat model of colitis.
DPP4 concentrations were quantified by ELISA in serum, proximal and distal colonic tissue, luminal content, and cage-collected feces.
Fecal DPP4 concentrations were significantly increased in TNBS-treated animals, exhibited a proximal-to-distal increase, and reached highest levels in cage fecal pellets.
Fecal DPP4 levels were reduced in DPP4 knockout and germ-free mice, suggesting a modulation of fecal DPP4 by a host-microbiota crosstalk.
Methods: Colitis was induced in male Wistar rats by intrarectal administration of an ethanolic solution of TNBS.
To explore host and microbiota contributions, fecal DPP4 concentration was also measured in DPP4 knockout and germ-free mice.
In healthy rats, colonic DPP4 showed a proximal-to-distal gradient that was lost during inflammation.
However, its distribution across biological matrices during intestinal inflammation remains poorly characterized.
Results: TNBS-induced colitis resulted in regionally heterogeneous inflammation, predominantly affecting the distal colon.
Host-anellovirus interactions in an island ecosystem: non-human primates and rodents in Madagascar harbour diverse, rich anellovirus populations.
We observed distinct anellovirus lineages in the endemic lemurs and tufted-tailed rats, which we infer to be the result of their long-term geographic isolation in Madagascar.
From oral swab samples taken from natural populations of lemurs, rodents and shrews in the Manombo Special Reserve and surrounding area in southeastern Madagascar, we determined the complete genomes of anelloviruses from black rats (n=647 genomes), Webb 's tufted-tailed rats (n=2), mouse lemurs (n=4), a woolly lemur (n=1) and a house shrew (n=3).
Host-anellovirus interactions in an island ecosystem: non-human primates and rodents in Madagascar harbour diverse, rich anellovirus populations.
In contrast, anellovirus diversity in widespread, non-native rodents (i.e.
Adult relative to juvenile/subadult black rats harboured richer anellovirus populations and were more connected within the co-occurrence network.
These endemic animals frequently interact with more recently introduced populations of non-native small mammals.
Black rat anellovirus populations showed high intra-individual variation, but the overall pool of circulating anelloviruses was consistent across age classes and sexes.
black rats) was similar to that of closely related, globally dispersed rodent species, concordant with their later introduction to Madagascar.
Proximity between individuals and greater intra-individual viral diversity were also linked to more virus-sharing between black rats.
Madagascar offers a unique opportunity to study anellovirus diversity, with speciose, endemic mammalian lineages that have evolved in geographic isolation for millions of years.
With our large anellovirus dataset from black rats, we examined anellovirus alpha- and beta-diversity and viral co-occurrence networks.
The SCD1 inhibitor aramchol interacts with regorafenib and metformin to kill tumor cells.
Aramchol and metformin interacted to modestly enhance cell death in PDX UM cells, though this was less than that caused by the combination of aramchol and the multi-kinase inhibitor regorafenib.
Knock down of SCD1 enhanced the percentage of dead cells in vehicle control treated cells but did not alter the abilities of drugs to kill tumor cells.
The primary site of metastatic spread of uveal melanoma (UM) is the liver and aramchol concentrates in the liver compared to plasma and other tissues.
Mechanisms by which the Stearoyl-CoA desaturase (SCD1) inhibitor aramchol kills tumor cells have recently been described, demonstrating that enhanced signaling through the AMPK played a key role in the processes regulating cell death.
Our data demonstrates that UM cells are killed by treatment with aramchol plus regorafenib plus metformin via enhanced autophagic flux and that this combination may have the potential to control UM tumors that have metastasized to the liver.
Correction: The effectiveness of nano chemotherapeutic particles combined with mifepristone depends on the PR isoform ratio in preclinical models of breast cancer.
Correction: The effectiveness of nano chemotherapeutic particles combined with mifepristone depends on the PR isoform ratio in preclinical models of breast cancer.
Alexidine, identified as a Z-DNA inducer by the NanoZ screening platform, acts as a transcriptional regulator.
The first step, a DNA condensation assay, detects ligand-induced DNA condensation using gold nanoparticles functionalized with Z-DNA-forming sequences, providing a rapid optical readout through localized surface plasmon resonance.
Using this workflow, we screened 2000 compounds from the Natural Product and Prestwick Chemical Libraries, identifying 18 positive hits in the condensation assay and selecting Alexidine dihydrochloride as a Z-DNA inducer.
Collectively, our findings highlight Alexidine as the first small-molecule Z-DNA inducer that modulates transcription in cells and establish NanoZ as a versatile platform for discovering Z-DNA modulators.
Alexidine efficiently promoted the B-to-Z transition and DNA condensationin vitro, and markedly increased Z-DNA formation in cells, as confirmed by immunofluorescence and ChIP-seq.
Z-DNA is a left-handed DNA helix implicated in gene regulation, genome stability, and immune responses, yet effective small-molecule modulators in cells remain scarce.
Live-cell decoding of labile post-translational modifications in APE1 with a rationally engineered nano-catcher.
Here, we report a biotin-regulated avidin-based nano-catcher (bMIPAPE1) capable of capturing active APE1 in living cells.
Live-cell decoding of labile post-translational modifications in APE1 with a rationally engineered nano-catcher.
Our findings demonstrate the utility of artificial nanocomposites as tools for live-cell PTM profiling and functional modulation of target proteins, offering a powerful approach to decode protein regulation in living systems and identify potential therapeutic targets in cancer.
The trypanosome mRNA decapping enzyme ALPH1 prefers caps without m7G methylation and produces diphosphate RNA.
While the presence of the ALPH1 C-terminal domain is essential for cell viability and increases enzyme activityin vitro, substrate preferences are determined solely by the catalytic domain.
Uniquely among eukaryotes, Kinetoplastida lack DCP2 and instead employ the ApaH-like phosphatase ALPH1 for mRNA decapping.
Here, we have analysed Trypanosoma brucei ALPH1 in greater detail.
LacI strikes a balance between stability and inducibility.
We measured the binding kinetics of the mutants both in vitro on DNA microarrays with 2479 different Lac operators and in vivo via single-molecule experiments.
Systematic discovery of bacterial anti-phage systems through a protein domain-centric strategy.