Genome-wide association study of virologic response with efavirenz-containing or abacavir-containing regimens in AIDS clinical trials group protocols

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Sometimes treatment effects are absent in a subgroup of the population. For example, penicillin has no effect on severe symptoms in individuals infected by resistant Staphylococcus aureus, and codeine has no effect on pain in individuals with certain polym ...

Broadly neutralizing antibodies (bNAbs) are promising candidates for the treatment and prevention of HIV-1 infections. Despite their critical importance, automatic detection of HIV-1 bNAbs from immune repertoires is still lacking. Here, we develop a straig ...

Background Each year, five million people are left disabled after stroke. Upper -extremity (UE) dysfunction is a leading problem. Neuroplasticity can be enhanced by non-invasive brain stimulation (NIBS) but evidence from large, randomized multicenter trial ...

Viral metagenomics is a useful tool for detecting multiple human viruses in urban sewage. However, more refined protocols are required for its effective use in disease surveillance. In this study, we investigated the performance of three different preampli ...

Introduction: COVID-19 remains a significant risk for the immunocompromised given their lower responsiveness to vaccination or infection. Therefore, passive immunity through long-acting monoclonal antibodies (mAbs) offers a needed approach for pre-exposure ...

How chronic mutational processes and punctuated bursts of DNA damage drive evolution of the cancer genome is poorly understood. Here, we demonstrate a strategy to disentangle and quantify distinct mechanisms underlying genome evolution in single cells, dur ...

High-throughput transcriptomics is of increasing fundamental biological and clinical interest. The generation of molecular data from large collections of samples, such as biobanks and drug libraries, is boosting the development of new biomarkers and treatm ...

Growing evidence indicates that transposable elements (TEs) play important roles in evolution by providing genomes with coding and non-coding sequences. Identification of TE-derived functional elements, however, has relied on TE annotations in individual s ...

Introduction: We have reanalyzed the genomic data of the International Collaboration for the Genomics of HIV (ICGH), centering on HIV-1 Elite Controllers.Methods: We performed a genome-wide Association Study comparing 543 HIV Elite Controllers with 3,272 u ...

The development of immune checkpoint inhibitors (ICIs) has revolutionized cancer therapy but only a fraction of patients benefits from this therapy. Model-informed drug development can be used to assess prognostic and predictive clinical factors or biomark ...

Long-term consumption of lipid-rich foods can contribute to common metabolic diseases and systemic low-grade inflammation. However, dietary responses and the development of non-communicable diseases are shaped by genetic factors and gene-by-environment int ...

Coronary heart disease (CHD) is one of the most pressing health problems of our time and a major cause of preventable death. CHD results from complex interactions between genetic and environmental factors. Using multiplex serological testing for persistent ...

The presence of competing events, such as death, makes it challenging to define causal effects on recurrent outcomes. In this thesis, I formalize causal inference for recurrent events, with and without competing events. I define several causal estimands an ...

The local physical properties - such as shape and flexibility - of the DNA double-helix is today widely believed to be influenced by nucleic acid sequence in a non-trivial way. Furthermore, there is strong evidence that these properties play a role in many ...

Retinoblastoma is the most common pediatric eye cancer. It is currently treated with a limited number of drugs, adapted from other pediatric cancer treatments. Drug toxicity and relapse of the disease warrant new therapeutic strategies for these young pati ...

The arms race between viruses and their hosts shaped the evolutionary history and the genome composition of both parties. Restriction factors are the first-line antiviral effectors encoded by the host genomes and are often conserved through evolution to pr ...

Characterizing the genetic structure of large cohorts has become increasingly important as genetic studies extend to massive, increasingly diverse biobanks. Popular methods decompose individual genomes into fractional cluster assignments with each cluster ...

The recent rise in both popularity and performance of large language models has garnered considerable interest regarding their applicability to education. Technologies like ChatGPT, which can engage in human-like dialog, have already disrupted educational ...

Glioblastoma (GBM) is the most frequent and highly malignant form of brain cancer. New therapeutic regimens are urgently needed as GBM patients present with a minimal response to currently-approved therapies. The goal of this project is to identify new the ...

Genome-wide association study of virologic response with efavirenz-containing or abacavir-containing regimens in AIDS clinical trials group protocols

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Using Negative Control Populations to Assess Unmeasured Confounding and Direct Effects

RAIN: machine learning-based identification for HIV-1 bNAbs

Efficacy and safety of transcranial direct current stimulation to the ipsilesional motor cortex in subacute stroke (NETS): a multicenter, randomized, double-blind, placebo-controlled trial

Prevalence of clonal hematopoiesis in people living with HIV

Comparison of Three Viral Nucleic Acid Preamplification Pipelines for Sewage Viral Metagenomics

A First-in-Human Randomized Study to Assess the Safety, Tolerability, Pharmacokinetics, and Neutralization Profile of Two Investigational Long-Acting Anti-SARS-CoV-2 Monoclonal Antibodies

Single-mitosis dissection of acute and chronic DNA mutagenesis and repair

Multi-well plate lid for single-step pooling of 96 samples for high-throughput barcode-based sequencing

Ancestral genome reconstruction enhances transposable element annotation by identifying degenerate integrants

The HLA-B*57:01 allele corresponds to a very large MHC haploblock likely explaining its massive effect for HIV-1 elite control

Modeling tumor size dynamics based on real-world electronic health records and image data in advanced melanoma patients receiving immunotherapy

Identifying genetic and dietary modulators of metabolic disorders using systems genetics

Associations of genetic and infectious risk factors with coronary heart disease

Interventionist estimands in event history analysis

Landscapes of DNA Mechanics and Genomes

Translational screening platform to evaluate chemotherapy in combination with focal therapy for retinoblastoma

PSGL-1 is an evolutionarily conserved antiviral restriction factor

Neural ADMIXTURE for rapid genomic clustering

Prompting Large Language Models to Power Educational Chatbots

Elucidating and modulating regulatory pathways so as to reprogram the immunosuppressive tumor microenvironment for therapeutic benefit