David Cox
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View article: Granite Embedding R2 Models
Granite Embedding R2 Models Open
We introduce the Granite Embedding R2 models, a comprehensive family of high-performance English encoder-based embedding models engineered for enterprise-scale dense retrieval applications. Building upon our first-generation release, these…
View article: Satori-SWE: Evolutionary Test-Time Scaling for Sample-Efficient Software Engineering
Satori-SWE: Evolutionary Test-Time Scaling for Sample-Efficient Software Engineering Open
Language models (LMs) perform well on standardized coding benchmarks but struggle with real-world software engineering tasks such as resolving GitHub issues in SWE-Bench, especially when model parameters are less than 100B. While smaller m…
View article: Granite Embedding Models
Granite Embedding Models Open
We introduce the Granite Embedding models, a family of encoder-based embedding models designed for retrieval tasks, spanning dense-retrieval and sparse retrieval architectures, with both English and Multilingual capabilities. This report p…
View article: Granite Vision: a lightweight, open-source multimodal model for enterprise Intelligence
Granite Vision: a lightweight, open-source multimodal model for enterprise Intelligence Open
We introduce Granite Vision, a lightweight large language model with vision capabilities, specifically designed to excel in enterprise use cases, particularly in visual document understanding. Our model is trained on a comprehensive instru…
View article: Non-Interactions of Berberine Supplementation in Borderline Hyperlipidemia Prevention (Asymptomatic Early Atherosclerosis Subjects) and Under Chronic Therapies: A Pilot Registry Study (BERINT)
Non-Interactions of Berberine Supplementation in Borderline Hyperlipidemia Prevention (Asymptomatic Early Atherosclerosis Subjects) and Under Chronic Therapies: A Pilot Registry Study (BERINT) Open
The aim of this pilot, non-interaction, supplement registry study was to evaluate the possible interactions between chronic therapies, as antiplatelet agents, anticoagulants, anti-hypertensives, diabetic management and thyroid management, …
View article: Ribonanza: deep learning of RNA structure through dual crowdsourcing
Ribonanza: deep learning of RNA structure through dual crowdsourcing Open
Prediction of RNA structure from sequence remains an unsolved problem, and progress has been slowed by a paucity of experimental data. Here, we present Ribonanza, a dataset of chemical mapping measurements on two million diverse RNA sequen…
View article: Computational design of sequence-specific DNA-binding proteins
Computational design of sequence-specific DNA-binding proteins Open
Sequence-specific DNA-binding proteins (DBPs) play critical roles in biology and biotechnology, and there has been considerable interest in the engineering of DBPs with new or altered specificities for genome editing and other applications…
View article: Data from Postmenopausal Serum Sex Steroids and Risk of Hormone Receptor–Positive and -Negative Breast Cancer: a Nested Case–Control Study
Data from Postmenopausal Serum Sex Steroids and Risk of Hormone Receptor–Positive and -Negative Breast Cancer: a Nested Case–Control Study Open
Prediagnostic endogenous sex steroid hormone levels have well established associations with overall risk of breast cancer. While evidence toward the existence of distinct subtypes of breast cancer accumulates, few studies have investigated…
View article: Supplementary Figure Legend from Postmenopausal Serum Sex Steroids and Risk of Hormone Receptor–Positive and -Negative Breast Cancer: a Nested Case–Control Study
Supplementary Figure Legend from Postmenopausal Serum Sex Steroids and Risk of Hormone Receptor–Positive and -Negative Breast Cancer: a Nested Case–Control Study Open
PDF file - 54K
View article: Supplementary Figure 1 from Postmenopausal Serum Sex Steroids and Risk of Hormone Receptor–Positive and -Negative Breast Cancer: a Nested Case–Control Study
Supplementary Figure 1 from Postmenopausal Serum Sex Steroids and Risk of Hormone Receptor–Positive and -Negative Breast Cancer: a Nested Case–Control Study Open
PDF file - 551K
View article: Data from Postmenopausal Serum Sex Steroids and Risk of Hormone Receptor–Positive and -Negative Breast Cancer: a Nested Case–Control Study
Data from Postmenopausal Serum Sex Steroids and Risk of Hormone Receptor–Positive and -Negative Breast Cancer: a Nested Case–Control Study Open
Prediagnostic endogenous sex steroid hormone levels have well established associations with overall risk of breast cancer. While evidence toward the existence of distinct subtypes of breast cancer accumulates, few studies have investigated…
View article: Supplementary Figure 1 from Postmenopausal Serum Sex Steroids and Risk of Hormone Receptor–Positive and -Negative Breast Cancer: a Nested Case–Control Study
Supplementary Figure 1 from Postmenopausal Serum Sex Steroids and Risk of Hormone Receptor–Positive and -Negative Breast Cancer: a Nested Case–Control Study Open
PDF file - 551K
View article: Supplementary Figure Legend from Postmenopausal Serum Sex Steroids and Risk of Hormone Receptor–Positive and -Negative Breast Cancer: a Nested Case–Control Study
Supplementary Figure Legend from Postmenopausal Serum Sex Steroids and Risk of Hormone Receptor–Positive and -Negative Breast Cancer: a Nested Case–Control Study Open
PDF file - 54K
View article: Supplementary Figure 1 from Common Genetic Variants in Prostate Cancer Risk Prediction—Results from the NCI Breast and Prostate Cancer Cohort Consortium (BPC3)
Supplementary Figure 1 from Common Genetic Variants in Prostate Cancer Risk Prediction—Results from the NCI Breast and Prostate Cancer Cohort Consortium (BPC3) Open
PDF file - 71K
View article: Supplementary Tables 1-8 from Common Genetic Variants in Prostate Cancer Risk Prediction—Results from the NCI Breast and Prostate Cancer Cohort Consortium (BPC3)
Supplementary Tables 1-8 from Common Genetic Variants in Prostate Cancer Risk Prediction—Results from the NCI Breast and Prostate Cancer Cohort Consortium (BPC3) Open
PDF file - 169K
View article: Supplementary Figure 1 from Common Genetic Variants in Prostate Cancer Risk Prediction—Results from the NCI Breast and Prostate Cancer Cohort Consortium (BPC3)
Supplementary Figure 1 from Common Genetic Variants in Prostate Cancer Risk Prediction—Results from the NCI Breast and Prostate Cancer Cohort Consortium (BPC3) Open
PDF file - 71K
View article: Supplementary Tables 1-8 from Common Genetic Variants in Prostate Cancer Risk Prediction—Results from the NCI Breast and Prostate Cancer Cohort Consortium (BPC3)
Supplementary Tables 1-8 from Common Genetic Variants in Prostate Cancer Risk Prediction—Results from the NCI Breast and Prostate Cancer Cohort Consortium (BPC3) Open
PDF file - 169K
View article: Generalized Seizure following Benzodiazepine reversal with Flumazenil prior to Electroconvulsive therapy
Generalized Seizure following Benzodiazepine reversal with Flumazenil prior to Electroconvulsive therapy Open
Background: Benzodiazepines have been shown to decrease efficacy of electroconvulsive therapy (ECT) treatments (Boylan et al., 2000). Flumazenil reversal of benzodiazepines is generally a safe and effective method to restore efficacy of EC…
View article: VALHALLA: Visual Hallucination for Machine Translation
VALHALLA: Visual Hallucination for Machine Translation Open
Designing better machine translation systems by considering auxiliary inputs such as images has attracted much attention in recent years. While existing methods show promising performance over the conventional text-only translation systems…
View article: Improved Cryptosporidium case findings using immunofluorescent microscopy on concentrated stool
Improved Cryptosporidium case findings using immunofluorescent microscopy on concentrated stool Open
Background: Diarrhoea is a major cause of morbidity in Cape Town, South Africa, and mortality is attributed to a failure to recognize the severity of the condition. Cryptosporidium and Giardia are increasingly recognized as important cause…
View article: A New Grape Seed Extract Pharma Standard Supplement (ECOVITISTM) Prevents and Controls Borderline Hypertension and Endothelial Dysfunction
A New Grape Seed Extract Pharma Standard Supplement (ECOVITISTM) Prevents and Controls Borderline Hypertension and Endothelial Dysfunction Open
This registry evaluates the effect of ECOVITIS™ (grape seeds extract) in borderline hypertension (also evaluating endothelialmediated vasodilatation). The main targets of the registry were the normalization of blood pressure and of an alte…
View article: A cytosine deaminase for programmable single-base RNA editing
A cytosine deaminase for programmable single-base RNA editing Open
Adding to the RNA editing toolbox A previously developed RNA editing system called REPAIR can base edit A to I in RNA by fusing the adenine deaminase domain of ADAR2 with catalytically dead CRISPR-Cas13. Using directed evolution, Abudayyeh…
View article: Ventricular remodeling in preterm infants: computational cardiac magnetic resonance atlasing shows significant early remodeling of the left ventricle
Ventricular remodeling in preterm infants: computational cardiac magnetic resonance atlasing shows significant early remodeling of the left ventricle Open
Computational CMR demonstrates that significant LV remodeling occurs soon after preterm delivery and is associated with definable clinical situations. This suggests that neonatal interventions could reduce long-term cardiac dysfunction.
View article: Characterization and application of type VI-B RNA-targeting CRISPR systems
Characterization and application of type VI-B RNA-targeting CRISPR systems Open
Thesis: Ph. D., Massachusetts Institute of Technology, Department of Biology, 2018.
View article: RNA editing with CRISPR-Cas13
RNA editing with CRISPR-Cas13 Open
Precise transcriptome engineering Efficient and precise RNA editing to correct disease-relevant transcripts holds great promise for treating genetic disease. Cox et al. took advantage of the ability of Cas13b, an effector from a type VI CR…
View article: Correction: Corrigendum: Engineering and optimising deaminase fusions for genome editing
Correction: Corrigendum: Engineering and optimising deaminase fusions for genome editing Open
Nature Communications 7: Article number: 13330 (2016); Published 2 November 2016; Updated 9 October 2017. The original version of this Article contained an error in the email address of the corresponding author George Church. The correct e…