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.
A sample of 103 heterosexual cisgender women aged 18 to 45 years completed an online survey.
Results: Competitive altruism was strongly and positively related to Machiavellianism and negatively related to Agreeableness and was more used when directed at other women than at men.
Our results offer preliminary self-report evidence, in a predominantly Western online sample, that women may use competitive altruism and generosity as strategies to gain a reputation in competition.
Open-ended responses converge with this interpretation, with women describing the strategic kindness they observe in others as occurring within workplace hierarchies, in publicized or social-media display, and in warmth that contradicts itself in private.
Adult-Onset Central Nervous System Erdheim-Chester Disease Successfully Treated With Cladribine and Cytarabine: Case Report and Literature Review.
Although targeted therapies have improved outcomes in patients with mitogen-activated protein kinase (MAPK) pathway alterations, optimal treatment strategies for adult patients with CNS ECD are still lacking.
This case suggests that combination chemotherapy may represent an optimal therapeutic strategy for adult patients with CNS ECD.
We describe a 24-year-old female with isolated CNS ECD without pathogenic genetic alterations.
Effects of different types of physical exercise interventions on aggressive behavior among children and adolescents: a network meta-analysis.
This study used a systematic review and network meta-analysis to compare how different types of physical exercise interventions affect aggression-related outcomes in children and adolescents.
Long-Term Efficacy and Allograft Loss after Immune Checkpoint Inhibitor Therapy in Solid Organ Transplant Recipients with Advanced Cutaneous Squamous Cell Carcinoma.
To evaluate long-term efficacy and allograft outcomes after ICI therapy in SOTRs with advanced CSCC.
Immune checkpoint inhibitors (ICIs) can provide effective treatment for advanced cutaneous squamous cell carcinoma (CSCC) in solid organ transplant recipients (SOTRs), but long-term oncologic and allograft outcomes remain poorly characterized.
We conducted a retrospective cohort study of SOTRs with advanced CSCC treated with systemic ICI at Mass General Brigham from 2016-2025.
Long-Term Efficacy and Allograft Loss after Immune Checkpoint Inhibitor Therapy in Solid Organ Transplant Recipients with Advanced Cutaneous Squamous Cell Carcinoma.
Five patients experienced graft loss, all kidney recipients; 4 had biopsy-confirmed rejection.
Comparative efficacy and safety of pharmacologic, laser, and combination therapies for infantile hemangioma: a systematic review and network meta-analysis with evidence certainty assessment.
In addition, we described four previously unreported patients from `` C. I. Parhon '' National Institute in Bucharest, Romania, analyzed independently from the systematic review dataset.
Associations between childhood trauma, cognitive function, and clinical symptoms in first-episode schizophrenia.
FES participants report more childhood trauma and exhibit widespread cognitive impairment, with physical neglect most strongly linked to attentional deficits.
FES participants reported significantly higher childhood trauma (except physical abuse) and performed worse on all MCCB domains (all *p* < 0.00625).
Seventy-one FES participants and 62 healthy controls were assessed using the Childhood Trauma Questionnaire (CTQ-SF), MATRICS Consensus Cognitive Battery (MCCB), Positive and Negative Syndrome Scale (PANSS), and Calgary Depression Scale (CDSS).
Within the clinical group, those with childhood trauma (71.8 %) showed nominally lower MCCB total scores (*p* = 0.042) and a trend toward higher negative symptoms (*p* = 0.083).
Genomic Insights Into the Body Size Evolution in Felidae (Mammalia: Carnivora).
Functional enrichment analysis revealed that positively selected genes (PSGs) in large-bodied Felidae were predominantly enriched in DNA repair pathways, whereas PSGs in small-bodied Felidae were primarily involved in energy metabolism and lipid metabolism processes.
Genomic Insights Into the Body Size Evolution in Felidae (Mammalia: Carnivora).
In summary, the adaptive evolution of both core signaling pathways and key functional genes has jointly driven body size diversification in Felidae.
Body size represents one of the most fundamental adaptive traits in mammals, but the genetic architecture underlying the extensive body size diversification observed in the Felidae family remains largely uncharacterized.
Baicalein attenuates extracellular matrix remodeling via FN1 in diabetic kidney disease: a multi-omics, machine-learning and mesangial-cell rescue study.
In mesangial cells, Fn1 overexpression aggravated the high-glucose-induced profibrotic molecular phenotype and partially attenuated the inhibitory effects of baicalein on ECM-associated molecular changes.
SPR detected a concentration-dependent interaction between baicalein and immobilized recombinant human FN1, with an apparent KD of 8.04 × 10-5 M. Single-cell analysis localized Fn1 expression to mesangial cells, and subsequent mouse-level pseudobulk analysis showed increased mesangial Fn1 expression in DKD mice.
The glmBoost model achieved the highest mean area under the receiver operating characteristic curve (0.938), and SHAP analysis prioritized FN1, COL1A2, VCAN, FBN1, and COL4A1.
Finally, db/db mouse experiments and an Fn1-overexpression rescue experiment in high-glucose-treated mesangial cells were performed.
Baicalein reduced serum creatinine and blood urea nitrogen levels, ameliorated renal histopathological injury, and decreased fibronectin and other fibrosis-associated molecules in db/db mice.
GSE47184 independently confirmed the direction of FN1 upregulation in DKD.
Three transcriptomic cohorts, GSE30528, GSE96804, and GSE104948, comprising 62 DKD and 59 control samples, were integrated for differential expression and weighted gene co-expression network analyses.
Baicalein attenuated renal injury and ECM remodeling in experimental DKD.
Diagnostic value of contrast-enhanced ultrasound combined with other imaging techniques in differentiating benign and malignant thyroid nodules: a network meta-analysis.
In this study, we compare these two device classes as acute recording tools by implanting them side-by-side on rat sciatic nerves under anaesthesia and recording activity evoked by nociceptive muscle stimulation or proprioceptive ankle extension.
Neobractatin mediated ZBP1 induces PANoptosis of xenografted breast tumors.
In this study, we select EMT6 cells to establish an EMT6 mouse breast cancer model, and to investigate the tumor suppression effect of NBT in vitro and in vivo.
Neobractatin mediated ZBP1 induces PANoptosis of xenografted breast tumors.
NBT ameliorates breast cancer progression by ZBP1-mediated PANoptosis in vivo and in vitro.
In vivo experiments have shown that the survival status of mice has generally improved, and the tumor volume has significantly decreased with NBT.
CCK-8, cell cloning, flow measurement of cell cycle and apoptosis, LDH, ROS, MMP, q-PCR, WB, HE staining and transcriptome sequencing were used in this study.
Complications of vertebral augmentation in metastatic spinal fractures: a systematic review of multiple study designs.
Vertebral augmentation techniques, including vertebroplasty and kyphoplasty, are widely used to relieve pain and restore spinal stability in patients with metastatic vertebral lesions.
Grand challenge in microbiome data science: recovering the microbiome as a system.
Grand challenge in microbiome data science: recovering the microbiome as a system.
Body mass index is positively associated with flatfoot and inversely associated with hindfoot valgus in school-aged children: a cross-sectional analysis of 3,292 screening records.
Body mass index is positively associated with flatfoot and inversely associated with hindfoot valgus in school-aged children: a cross-sectional analysis of 3,292 screening records.
Machine-Readable Database for Genotype-Phenotype Analyses in Rare Diseases Using FKTN-related Congenital Muscular Dystrophies as a Prototype.
To better understand the impact of specific FKTN variants in the affected individuals, we first comprehensively aggregated all publicly known and available data resulting in a database comprising all published literature that details FKTN variants and their associated clinical phenotypes.
Animal type outweighs growth stage in shaping the active antibiotic resistome in livestock manure.
Among tested animal types, layer litter showed the highest ARG number at the DNA level, with qPCR results further revealing significantly higher abundances of specific ARGs, including bla TEM and erm (B).
In this study, metagenomics, metatranscriptomics, and quantitative PCR (qPCR) were integrated to characterize microbial communities and resistome profiles in manure from five animal types across multiple growth stages.
Animal type outweighs growth stage in shaping the active antibiotic resistome in livestock manure.
Animal manure is a major reservoir of antibiotic resistance genes (ARGs), yet the factors governing their composition and activity remain insufficiently understood.
Although growth stage had limited influence on overall resistome composition, stage-dependent variations in ARG abundance were observed, with higher levels during early-life and juvenile stages.
Hippocampal surface analysis using discrete Ricci flow and Riemannian metrics for the diagnosis of Alzheimer's disease.
We conformally parameterize the hippocampus surface meshes from the MRI data using Ricci flow and retrieve three geometric descriptors, Heat Kernel Signature, Area Distortion and Conformal Factor, during the Ricci energy optimization process.
Experimental results on ADNI dataset show that AIRM achieves the best performance with 96\ % accuracy, which outperforms other metrics evaluated.
Psychiatric outcomes in the first two years after the October 7 attacks: a systematic review of posttraumatic stress, anxiety, depression, and addiction-related outcomes.
Guided by the PICOS framework, eligible studies assessed psychiatric outcomes among Israeli populations exposed to the October 7 attacks or subsequent war.
This systematic review synthesizes studies from the first two years of the war to clarify early prevalence of post-traumatic stress symptoms (PTSS), anxiety, depression, and addiction-related outcomes in the Israeli population.
Anxiety and depression were widely documented and persisted among individuals facing sustained threat, socioeconomic strain, or displacement.
Temporal changes in gait parameters and muscle activation during sustained walking in children with spastic cerebral palsy.
For energy expenditure, a significant Group × Time interaction (P = 0.047) indicated that the SCP group maintained elevated metabolic cost into the third minute while controls exhibited a declining trajectory.
These findings suggest that selected gait and EMG parameters in children with SCP begin to change after approximately 2 min of continuous walking, indicating a potential time window for closer monitoring or structured rest breaks during rehabilitation.
Similarly, significant Group × Time interactions were observed for bilateral gastrocnemius (P = 0.002) and tibialis anterior (P = 0.006) normalized root mean square amplitudes, reflecting a greater temporal decline in muscle activation in the SCP group from the second minute onward.
A portable gait analysis system and surface electromyography were used to evaluate gait characteristics during a 3-minute walking protocol in 15 children with SCP and 15 age-matched healthy controls.
Temporal changes in gait parameters and muscle activation during sustained walking in children with spastic cerebral palsy.
Linear mixed-effects model analysis revealed significant Group × Time interactions for stance phase, swing phase, step length, lower-limb forward acceleration, foot clearance angle, and walking velocity (all P < 0.05), indicating divergent temporal trajectories between children with SCP and healthy controls.
Temporal changes in spatiotemporal gait parameters and muscle activation may reflect progressive gait deterioration during prolonged walking in children with spastic cerebral palsy.
Children with SCP may exhibit gradual changes in spatial-temporal gait parameters and muscle activation patterns during the later stages of a long walking task.
Clofazimine pharmacokinetics in novel rifampicin-resistant tuberculosis regimens: an analysis of the endTB and endTB-Q trials.
For middle-aged and elderly female patients with umbilical hernia who have concurrent ascites, thickened peritoneum, or a hard and fixed hernia mass, abdominopelvic CT and ultrasound should be performed to rule out PMP to avoid blindly performing hernia repair and delaying diagnosis and treatment.
First Reported Concomitant Pulsed-Field Ablation and Left Atrial Appendage Occlusion in a Patient With Prior Atrial Septal Defect Closure Device.
Transseptal access in patients with prior atrial septal defect (ASD) closure devices is technically challenging, particularly when large-bore sheaths are required.
First Reported Concomitant Pulsed-Field Ablation and Left Atrial Appendage Occlusion in a Patient With Prior Atrial Septal Defect Closure Device.
A case of recurrent acute acalculous cholecystitis in a patient with renal cell carcinoma treated with pazopanib and axitinib: case report and literature review.
A case of recurrent acute acalculous cholecystitis in a patient with renal cell carcinoma treated with pazopanib and axitinib: case report and literature review.
The study suggests that anti-angiogenic tyrosine kinase inhibitors may induce rare episodes of cholecystitis in specific patient populations.
A 74-year-old male patient with renal cell carcinoma developed disease progression in the left adrenal gland and lungs 12.8 years after surgery.
Measuring intrinsic capacity among Canadian adults: a population-based study using the Canadian Longitudinal Study on Aging (CLSA).
The objective of this study was to develop a measure of IC in Canadian adults and to assess its psychometric properties.
Measuring intrinsic capacity among Canadian adults: a population-based study using the Canadian Longitudinal Study on Aging (CLSA).
The authors are supported by the Raymond and Margaret Labarge Chair in Research and Knowledge Application for Optimal Aging, the Canada Research Chairs Program, the Canadian Institutes of Health Research, and the Hamilton Health Sciences Foundation.
Coumarins in musculoskeletal health: a systematic review.
Musculoskeletal diseases encompass a spectrum of pathologies such as osteoporosis, rheumatoid arthritis, osteoarthritis, and osteosarcoma, characterized by degenerative alterations and aberrant hyperplasia in bone mass, synovial tissue, and cartilage.
Impaired regulatory T cell mediated immune tolerance promotes neurodegeneration in glaucoma.
Peripheral blood mononuclear cells from glaucoma patients, but not healthy donors, induced retinal ganglion cell loss following transfer into humanized immunodeficient mice without changes to the intraocular pressure, demonstrating a causal role for immune responses in the patient derived material.
We further demonstrate that transient expansion of regulatory T cells preserves visual function, reduced optic nerve axonal degeneration, and limited retinal ganglion cell loss in an experimental glaucoma model.
Here, using primary open-angle glaucoma as a model of chronic neurodegeneration, we demonstrate that dysregulated adaptive immunity is sufficient to promote retinal ganglion cell degeneration.
Study on the adsorption kinetics of natural dye by colored paper fiber raw material.
The PFO model shows better fitting performance for all systems, indicating a diffusion-controlled physisorption process.
For hemp pulp fiber at 80 mg/L, (qe) reaches 1.1184 mg/g, the PFO rate constant (k1) is 0.0012 s-1 with (R2 = 0.9980).
Hardwood pulp reaches equilibrium at ~1,500 s with the fastest initial rate, while softwood and hemp pulp require over 10000 s. This work provides fundamental kinetic data and theoretical support for formula design and process optimization of online dyeing for colored cigarette paper.
To ensure stable quality of colored cigarette paper dyed with natural dyes, real-time kinetic data of dye adsorption onto cellulosic fibers remains insufficient due to limitations of traditional offline sampling methods.
Global warming amplifies atmospheric formaldehyde exposure and widens spatial inequality.
The largest increases occur in Africa and South America, while exposure in low Human Development Index (HDI) regions globally rises by more than a factor of three, indicating a pronounced amplification of environmental inequality.
Emotional and behavioral problems in the offspring of parents with schizophrenia or bipolar disorder: a controlled comparative study.
Offspring of parents with schizophrenia or bipolar disorder show elevated emotional and behavioral problems compared with healthy controls, supporting the importance of early screening and family-oriented preventive interventions.
This study aimed to compare emotional and behavioral problems in the offspring of parents with schizophrenia, the offspring of parents with bipolar disorder, and healthy controls using the Child Behavior Checklist for ages 6-18 years (CBCL/6-18).
Emotional and behavioral problems in the offspring of parents with schizophrenia or bipolar disorder: a controlled comparative study.
Compared with healthy controls, both clinical groups had higher rates of previous child psychiatry visits and less favorable family-related sociodemographic characteristics.
In these domains, both offspring groups scored significantly higher than controls, whereas the schizophrenia and bipolar disorder groups did not significantly differ from one another.
The sample included 62 children and adolescents aged 6-18 years: 21 offspring of parents with schizophrenia, 20 offspring of parents with bipolar disorder, and 21 healthy controls.
The groups did not differ significantly in age, sex, or educational status.
This cross-sectional controlled study was conducted in the Child and Adolescent Psychiatry Outpatient Clinic of Karabük Training and Research Hospital.
Neighborhood Disadvantage, Identity-based Resilience, and Hypertension: The Healthy Aging with Resilient Identities (HARI) Study.
Identity state may moderate the association between subjective neighborhood disadvantage and hypertension, particularly among Black women, representing a potentially novel, modifiable protective factor among multiply marginalized persons living in communities with increased risk for hypertension.
Interaction terms were used to evaluate whether the association between PNP and hypertension varied by levels of IVPS within each race/gender group.
Identity state moderated this association only among Black women, such that each 1-SD increase in IVPS score was associated with 59 % lower odds of hypertension at the highest level of PNP (aOR-0.41; 95 % CI: 0.19, 0.88), with no meaningful moderation observed in other groups.
Higher PNP was associated with increased odds of hypertension among White women and men, but not consistently among Black women and men.
Models were stratified by race and gender groups (Black women, Black men, White women, White men).
Dual molecular and clinical machine-learning prognostic modeling in pancreatic ductal adenocarcinoma: a chaperone-mediated autophagy-based framework integrating multi-cohort molecular signatures and a single-center clinical nomogram.
Single-cell RNA sequencing data from GSE212966 were analyzed to characterize CMA-related transcriptional states in PDAC and adjacent non-tumor tissues.
CMA-related transcriptional activity varied among cell types, with macrophages showing prominent scores and PDAC-derived macrophages exhibiting higher CMA scores than those from adjacent tissues.
Multiple survival machine-learning approaches were compared to establish a CMA-related prognostic model.
The StepCox [ forward ] plus random survival forest model showed favorable overall performance, with C-index values of 0.903, 0.678, and 0.733 in the TCGA, PACA-CA, and PACA-AU cohorts, respectively.
These molecular and clinical models provide complementary perspectives on PDAC prognosis and warrant further evaluation in matched prospective cohorts.
KRT19, the highest-weighted model gene, was selected for in vitro validation.