Search bioRxiv⌕ Search

Biology subjects

Molnar, S.

Publications and source records attributed to Molnar, S..

4 recordsLinked to original sources

Point-in-time evidence and cross-area clinical precedent anticipate clinical entry across 100 focal areas: retrospective validation of the Intangia triage layer

Early-opportunity teams face a combinatorial problem: once a focal target, mechanism or indication is fixed, the space of plausible partners runs to thousands of candidates per area. Intangia's triage layer ranks that space from point-in-time evidence (how much literature, patent and clinical activity a candidate pairing has accumulated, and whether the partner already has clinical precedent in other contexts) so that review starts where clinical activity is most likely to begin next. This preprint validates that capability retrospectively across 100 focal areas spanning drug targets, mechanisms and disease indications, replaying 24.1 million historically scored combination-years with every area scored by a model trained on the other 99 and never on itself. The headline is operational. At a twenty-partner review shortlist per focal area, the median area's four-year first-alert precision is 0.234, against a matched random-ranker median of 0.008: roughly one in four shortlisted partners subsequently entered the focal clinical context within four years, about 38 times each area's own background rate (95% CI 31 to 45). A panel-level permutation puts the result at p = 0.0005. Discrimination generalises: the full 13-feature specification reaches a median leave-one-focal-out ROC-AUC of 0.922 (95% CI 0.911 to 0.929), with no area below chance and all 100 areas beating their strongest count-based baseline. Shortlisted entrants are anticipated with a median observed lead of two years within the evaluation window, and three years (interquartile range one to five) once the window cap is removed and every realised entrant is counted. The core ranking is carried by two interpretable signal families: cumulative co-occurrence counts and leave-one-area-out clinical precedent. Burst detection serves a complementary role: it supplies the time-stamped, source-specific momentum evidence attached to every recommendation (what is accelerating, and why now) rather than additional ranking power. A conditional view of the same landscape ranks candidates with no cross-area precedent against one another, enriched relative to matched random ranking, supporting a lower-yield emerging-opportunities capability. Two worked examples, PD-1 combination immunotherapy and CTLA-4, are point-in-time historical replays of the same architecture in familiar territory, showing what an alert looked like with the dated evidence behind it. The endpoint throughout is first clinical entry, not clinical success; prospective validation is the next stage.

bioinformatics↗

Pathogen genomic surveillance as a scalable framework for precision phage therapy

Phage therapy is gaining increasing interest in the fight against critically resistant nosocomial pathogens. However, the narrow host range of bacteriophages hampers the development of broadly effective phage therapeutics and demands precision approaches. Here we combine large-scale phylogeographical analysis with high-throughput phage typing to guide the development of precision phage cocktails targeting carbapenem-resistant Acinetobacter baumannii, a top-priority pathogen. Our analysis reveals that a few strain types dominate infections in each world region, with their geographical distribution remaining stable within six years. As we demonstrate in Eastern Europe, this spatio-temporal distribution enables preemptive preparation of region-specific phage collections that target most local infections. Finally, we showcase the efficacy of a four-phage cocktail against the most prevalent strain type in both in vitro and in vivo animal infection models. Ultimately, genomic surveillance identifies patients benefiting from the same phages across geographical scales, thus providing a scalable framework for precision phage therapy. HighlightsO_LIA few carbapenem-resistant Acinetobacter baumannii types dominate infections worldwide C_LIO_LIPhylogeography reveals stable strain composition of individual countries over a six-year period C_LIO_LIThis spatio-temporal distribution allows preemptive preparation of region-specific phage collections C_LIO_LIA four-phage cocktail is efficacious against the most prevalent strain type in Europe. C_LI

microbiology↗

Efficacy and breadth of adjuvanted SARS-CoV-2 receptor-binding domain nanoparticle vaccine in macaques

Emergence of novel variants of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) underscores the need for next-generation vaccines able to elicit broad and durable immunity. Here we report the evaluation of a ferritin nanoparticle vaccine displaying the receptor-binding domain of the SARS-CoV-2 spike protein (RFN) adjuvanted with Army Liposomal Formulation QS-21 (ALFQ). RFN vaccination of macaques using a two-dose regimen resulted in robust, predominantly Th1 CD4+ T cell responses and reciprocal peak mean neutralizing antibody titers of 14,000-21,000. Rapid control of viral replication was achieved in the upper and lower airways of animals after high-dose SARS-CoV-2 respiratory challenge, with undetectable replication within four days in 7 of 8 animals receiving 50 {micro}g RFN. Cross-neutralization activity against SARS-CoV-2 variant B.1.351 decreased only [~]2-fold relative to USA-WA1. In addition, neutralizing, effector antibody and cellular responses targeted the heterotypic SARS-CoV-1, highlighting the broad immunogenicity of RFN-ALFQ for SARS-like betacoronavirus vaccine development. Significance StatementThe emergence of SARS-CoV-2 variants of concern (VOC) that reduce the efficacy of current COVID-19 vaccines is a major threat to pandemic control. We evaluate a SARS-CoV-2 Spike receptor-binding domain ferritin nanoparticle protein vaccine (RFN) in a nonhuman primate challenge model that addresses the need for a next-generation, efficacious vaccine with increased pan-SARS breadth of coverage. RFN, adjuvanted with a liposomal-QS21 formulation (ALFQ), elicits humoral and cellular immune responses exceeding those of current vaccines in terms of breadth and potency and protects against high-dose respiratory tract challenge. Neutralization activity against the B.1.351 VOC within two-fold of wild-type virus and against SARS-CoV-1 indicate exceptional breadth. Our results support consideration of RFN for SARS-like betacoronavirus vaccine development.

immunology↗

Efficacy of a Broadly Neutralizing SARS-CoV-2 Ferritin Nanoparticle Vaccine in Nonhuman Primates

The emergence of novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants stresses the continued need for next-generation vaccines that confer broad protection against coronavirus disease 2019 (COVID-19). We developed and evaluated an adjuvanted SARS-CoV-2 Spike Ferritin Nanoparticle (SpFN) vaccine in nonhuman primates (NHPs). High-dose (50 {micro}g) SpFN vaccine, given twice within a 28 day interval, induced a Th1-biased CD4 T cell helper response and a peak neutralizing antibody geometric mean titer of 52,773 against wild-type virus, with activity against SARS-CoV-1 and minimal decrement against variants of concern. Vaccinated animals mounted an anamnestic response upon high-dose SARS-CoV-2 respiratory challenge that translated into rapid elimination of replicating virus in their upper and lower airways and lung parenchyma. SpFNs potent and broad immunogenicity profile and resulting efficacy in NHPs supports its utility as a candidate platform for SARS-like betacoronaviruses. One-Sentence SummaryA SARS-CoV-2 Spike protein ferritin nanoparticle vaccine, co-formulated with a liposomal adjuvant, elicits broad neutralizing antibody responses that exceed those observed for other major vaccines and rapidly protects against respiratory infection and disease in the upper and lower airways and lung tissue of nonhuman primates.

immunology↗