Stanford University

Secondary use and scholarly impact of a portfolio of clinical trials with shared individual participant level data: cross sectional study

Abstract Objective To assess the number, timing, characteristics, and scholarly impact of secondary publications generated using individual participant level data (IPD) from a portfolio of clinical trials shared with external investigators through a data sharing platform. Design...

A genomic catalog of Earth’s bacterial and archaeal symbionts

1 SUMMARY Microbial symbiosis drives the functional and phylogenomic diversification of life on Earth, yet remains underexplored due to culturing challenges. This study employed machine learning (ML) to predict symbiotic lifestyles in hundreds of thousands of microbial genomes fr...

MSP4BIO Deliverable 3.4: Ecological toolkit (ESE1) for MPAs prioritization and networking

The Ecological Toolkit (ESE1) was developed to support the design, establishment and management of Marine Protected Areas (MPAs) by improving decision-making processes, focusing on prioritisation of areas, integration of connectivity processes and assessment of human impacts on m...

MSP4BIO Deliverable 3.4: Ecological toolkit (ESE1) for MPAs prioritization and networking

The Ecological Toolkit (ESE1) was developed to support the design, establishment and management of Marine Protected Areas (MPAs) by improving decision-making processes, focusing on prioritisation of areas, integration of connectivity processes and assessment of human impacts on m...

Anatomical white matter tracts span the cortical hierarchy to support cognitive diversity

Long-range white matter (WM) tracts support cognition by enabling communication between distant cortical regions, which are organized along a hierarchy defined by the sensorimotor-to-association (S-A) axis. However, it remains unknown how WM tracts are positioned within the corti...

Subicular spatial codes arise from predictive mapping

Abstract The successor representation has emerged as a powerful model for understanding mammalian navigation and memory; explaining the spatial coding properties of hippocampal place cells and entorhinal grid cells. However, the diverse spatial responses of subicular neurons, the...

Functional fractionation of large-scale brain networks in the human subcortex

Brain network mapping plays a crucial role in advancing our understanding of human brain organization and the neuroanatomic foundations of cognition. Historically, the identification of large-scale brain networks has focused on the cerebral cortex. Some cortical networks have bee...

Free-Placement Optimization of Ground Station Locations for Low-Earth-Orbit Satellites

Rapidly expanding low-Earth-orbit satellite constellations are placing increasing demands on terrestrial ground networks, motivating the development of more efficient ground station network designs. Current approaches select sites from predefined locations, limiting optimization...

Incidence, risk factors, and prognostic implications of hospitalizations for heart failure among patients with myeloproliferative neoplasms

Myeloproliferative neoplasms (MPNs), including essential thrombocythemia (ET), polycythemia vera (PV), and myelofibrosis (MF), are a group of chronic leukemias associated with increased risk of heart failure (HF). Despite a link between MPNs and HF, prognostic implications and ri...

Milvexian with Antiplatelet Therapy after Acute Coronary Syndrome Event

BackgroundPatients are at increased risk for recurrent ischemic events after an acute coronary syndrome event. Milvexian, an oral factor XIa inhibitor, may reduce the risk of major adverse clinical events with minimal bleeding risk. MethodsIn this phase 3, randomized, placebo-con...

High-grade serous ovarian cancer is associated with increased TP53 mutation burden in uterine lavage

High grade serous ovarian cancer (HGSC) has low survival partly due to the lack of methods for detection, diagnosis, and risk prediction. TP53 mutations, which drive HGSC, are found in gynecological tissues as the result of somatic evolution, but it is unknown whether an excess o...

Digital Outreach to Improve Statin Refills in Patients With Low Statin Adherence

Importance Statin nonadherence is a leading, addressable driver of preventable cardiovascular events. Although health systems routinely use outreach to promote preventive care, most strategies are static and lack evidence from randomized clinical trials. Objective To determine wh...

Modeling and Design Optimization of Looped Water Distribution Networks using MS Excel: Developing the Open-Source X-WHAT Model

Abstract Cost-effective water distribution network (WDN) design is crucial for reliable urban water supply. This paper introduces the open-source Excel for Water system Hydraulic Analysis Tool (X-WHAT) for WDN simulation and preliminary design. Unlike traditional spreadsheet appr...

A suite of eight Toxoplasma gondii effectors cooperates to activate the non-canonical NF-κB pathway

ABSTRACT As a master of host-cell reprogramming, Toxoplasma gondii ( T. gondii ) tachyzoites manipulate diverse signaling networks to establish a niche permissive for long-term infection. While the parasite’s subversion of canonical NF-κB signaling (p65/p50) is well established,...

Resection Margin Status, Recurrence Pattern, and Salvageability After Resection for Colorectal Liver Metastases

Abstract Background The prognostic significance of margin status after colorectal liver metastases (CRLM) resection remains debated in the era of effective systemic therapy. This study examined the prognostic meaning of microscopically positive (R1) margins, focusing on recurrenc...

Antibody Fc receptor CD16a mediates natural killer cell activation via mechanotransduction of piconewton forces

Natural Killer(NK) cells eliminate target cells through antibody-dependent cell-mediated cytotoxicity(ADCC), initiated by CD16a(FcγRIIIa) recognizing the Fc region of antibodies bound to the target cell surface. While the recognition is considered to be driven by CD16a-Fc binding...

A Vershik–Kerov theorem for wreath products

Let G_{n,k} be the group of permutations of \{1,2,\ldots, kn\} that permutes the first k symbols arbitrarily, then the next k symbols and so on through the last k symbols. Finally, the n blocks of size k are permuted in an arbitrary way. For \sigma chosen uniformly in G_{n,k} , l...

Learning from generic language.

Generic language (e.g., "Birds have hollow bones") conveys generalizations about categories and is a fundamental and ubiquitous mechanism of learning about the world. How exactly this learning occurs, however, is unclear: Generics exhibit so much flexibility in how they are inter...

Erythropoietic protoporphyria life impact and genetic health trajectory (LIGHT) study in Europe: a cross-sectional online questionnaire

Abstract Background Erythropoietic protoporphyria and X-linked protoporphyria (collectively, EPP) are rare inherited metabolic disorders of the heme biosynthetic pathway characterized by severe photosensitivity and painful phototoxic reactions upon sunlight exposure. This study s...

De novo design of RNA pseudoknots with deep learning

RNA design has been hindered by the limited accuracy of 3D structure prediction. Here, we show that intricate RNA structures can be generated with current deep learning tools through accurate de novo design of pseudoknot secondary structures. In an Eterna competition involving 57...