Hugh Murrell

Long-read deep sequencing reveals high rates of multilineage transmission and rapid viral population changes in acute HIV infection

James I. Mullins, Wenjie Deng, Elena E. Giorgi, Craig A. Magaret et autres

Understanding the selective forces acting upon HIV early in infection is crucial to design prevention strategies. By leveraging deep sequencing and the short diagnostic intervals of the FRESH and RV217 cohorts between the last-negative and first-positive RNA tests (median 4 days), we …

us, Afrique du Sud, se, gb, Kenya, th (code pays fourni par la source)

VRC01 Selects Rare HIV Escape Mutations After Acquisition in Antibody-Mediated Prevention Trials

Carolyn E. Williamson, Lyle Curry, Nonhlanhla N. Mkhize, Elena E. Giorgi et autres

Abstract Broadly neutralizing antibodies (bnAbs) show promise in HIV prevention, yet viral escape remains a challenge. In the Antibody Mediated Prevention (AMP) trials, the CD4 binding site (CD4bs) bNAb VRC01 blocked acquisition by VRC01-sensitive strains. However, its influence on viral evolution post-acquisition …

Afrique du Sud, mn, us, pk, se, Zimbabwe (code pays fourni par la source)

Rare twin cysteine residues in the HIV-1 envelope variable region 1 link to neutralization escape and breadth development

Maria C. Hesselman, Marius Zeeb, Peter Rusert, Chloé Pasin et autres

Identifying HIV-1 envelope (Env) traits associated with neutralization cross-reactivity is crucial for vaccine design. Variable loops 1 and 2 (V1V2), positioned at the Env trimer apex, are key regions linked to neutralization. We describe non-canonical cysteine (Cys) residues in V1 that are …

ch, us, Kenya, Afrique du Sud, Zimbabwe, sk (code pays fourni par la source)

Optimized SMRT-UMI protocol produces highly accurate sequence datasets from diverse populations—Application to HIV-1 quasispecies

Dylan H. Westfall, Wenjie Deng, Alec P. Pankow, Hugh Murrell et autres

Pathogen diversity resulting in quasispecies can enable persistence and adaptation to host defenses and therapies. However, accurate quasispecies characterization can be impeded by errors introduced during sample handling and sequencing, which can require extensive optimizations to overcome. We present complete laboratory and …

us, Afrique du Sud, se (code pays fourni par la source)

Optimized SMRT-UMI protocol produces highly accurate sequence datasets from diverse populations – application to HIV-1 quasispecies

Dylan H. Westfall, Wenjie Deng, Alec P. Pankow, Hugh Murrell et autres

Abstract Pathogen diversity resulting in quasispecies can enable persistence and adaptation to host defenses and therapies. However, accurate quasispecies characterization can be impeded by errors introduced during sample handling and sequencing which can require extensive optimizations to overcome. We present complete laboratory …

us, Afrique du Sud, se (code pays fourni par la source)

Dense and Deep Sarcasm Detection

Devin Pelser, Hugh Murrell

Deep and Dense Sarcasm Detection

Devin Pelser, Hugh Murrell

Recent work in automated sarcasm detection has placed a heavy focus on context and meta-data. Whilst certain utterances indeed require background knowledge and commonsense reasoning, previous works have only explored shallow models for capturing the lexical, syntactic and semantic cues present within …

Afrique du Sud (code pays fourni par la source)

Discovering General Multidimensional Associations

Ben Murrell, Daniel S Murrell, Hugh Murrell

When two variables are related by a known function, the coefficient of determination (denoted R2) measures the proportion of the total variance in the observations explained by that function. For linear relationships, this is equal to the square of the correlation coefficient, …

us, gb, Afrique du Sud (code pays fourni par la source)

R 2 -equitability is satisfiable

Ben Murrell, Daniel S Murrell, Hugh Murrell

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.

us, gb, Afrique du Sud (code pays fourni par la source)

Synchronisation of fertility with carrying capacity; an investigation using classical and agent based modeling

Hugh Murrell, John Henry Swart

A generalized Verhulst model subject to seasonal change in both fertility rate and carrying capacity is outlined. Numerical solutions to the Verhulst equations are employed to obtain optimal fertility rate phase shift with respect to carrying capacity. Possible natural selection for a …

Afrique du Sud (code pays fourni par la source)

Discovering general multidimensional associations

Ben Murrell, Daniel S Murrell, Hugh Murrell

When two variables are related by a known function, the coefficient of determination (denoted $R^2$) measures the proportion of the total variance in the observations that is explained by that function. This quantifies the strength of the relationship between variables by describing …

us, gb, Afrique du Sud (code pays fourni par la source)

Fisher Discrimination with Kernels

Hugh Murrell, Kazuo Hashimoto, Daichi Takatori

Fisher first introduced the Fisher linear discriminant back in 1938. After the popularization of the support vector machine (SVM) and the kernel trick it became inevitable that the Fisher linear discriminant would be kernelized. Sebastian Mika accomplished this task as part of …