Contested Futures: Envisioning “Personalized,” “Stratified,” and “Precision” Medicine

In recent years, discourses around “personalized,” “stratified,” and “precision” medicine have proliferated. These concepts broadly refer to the translational potential carried by new data-intensive biomedical research modes. Each describes expectations about the future of medicine and healthcare that data-intensive innovation promises to bring forth. The definitions and uses of the concepts are, however, plural, contested and characterized by diverse ideas about the kinds of futures that are desired and desirable. In this paper, we unpack key disputes around the “personalized,” “stratified,” and “precision” terms, and map the epistemic, political and economic contexts that structure them as well as the different roles attributed to patients and citizens in competing future imaginaries. We show the ethical and value baggage embedded within the promises that are manufactured through terminological choices and argue that the context and future-oriented nature of these choices helps to understanding how data-intensive biomedical innovations are made socially meaningful

HIV p24-Specific Helper T Cell Clones From Immunised Primates Recognize Highly Conserved Regions of HIV-l

We have investigated Th cell recognition of the HIV core protein p24 by using CD4+ T cell clones derived from cynomolgus macaques immunized with hybrid HIV p24:Ty virus-like particles (VLP). T cell lines from two immunized animals responded to p24:Ty-VLP, control Ty-VLP, purified p24, and whole inactivated HIV, indicating the presence of T cells specific for p24 as well as the Ty carrier protein. The HIV determinants recognized by the T cell lines were identified by using a series of overlapping peptides synthesized according to the sequence of p24. Both T cell lines recognized peptide 11 (amino acids 235-249) and peptide 14 (amino acids 265- 279). In addition, one T cell line also responded to peptide 9 (amino acids 215-229). Definitive identification of two T cell epitopes on p24 was confirmed at the clonal level: from a total of four T cell clones generated from one of the T cell lines, two respond specifically to peptide 11 and two to peptide 14. The T cell clones were CD4' and MHC class 11-restricted and secreted IL-2 in response to stimulation with purified p24, inactivated HIV or a single synthetic peptide. The specificityof the Th clones for variant peptides demonstrated cross-reactivity with two simian immunodeficiency virus isolates, but only limited responses to HIV-2 sequences. However, the Th cell epitopes identified on p24 are highly conserved between 12 HIV-1 isolates and were recognized by both of the immunized primates. These sequences may therefore be useful for priming a broadly reactive immune response to HIV-1

The atomic simulation environment — a python library for working with atoms

The Atomic Simulation Environment (ASE) is a software package written in the Python programming language with the aim of setting up, steering, and analyzing atomistic simula- tions. In ASE, tasks are fully scripted in Python. The powerful syntax of Python combined with the NumPy array library make it possible to perform very complex simulation tasks. For example, a sequence of calculations may be performed with the use of a simple "for-loop" construction. Calculations of energy, forces, stresses and other quantities are performed through interfaces to many external electronic structure codes or force fields using a uniform interface. On top of this calculator interface, ASE provides modules for performing many standard simulation tasks such as structure optimization, molecular dynamics, handling of constraints and performing nudged elastic band calculations

HMOX1 Gene Promoter Alleles and High HO-1 Levels Are Associated with Severe Malaria in Gambian Children

Heme oxygenase 1 (HO-1) is an essential enzyme induced by heme and multiple stimuli associated with critical illness. In humans, polymorphisms in the HMOX1 gene promoter may influence the magnitude of HO-1 expression. In many diseases including murine malaria, HO-1 induction produces protective anti-inflammatory effects, but observations from patients suggest these may be limited to a narrow range of HO-1 induction, prompting us to investigate the role of HO-1 in malaria infection. In 307 Gambian children with either severe or uncomplicated P. falciparum malaria, we characterized the associations of HMOX1 promoter polymorphisms, HMOX1 mRNA inducibility, HO-1 protein levels in leucocytes (flow cytometry), and plasma (ELISA) with disease severity. The (GT)n repeat polymorphism in the HMOX1 promoter was associated with HMOX1 mRNA expression in white blood cells in vitro, and with severe disease and death, while high HO-1 levels were associated with severe disease. Neutrophils were the main HO-1-expressing cells in peripheral blood, and HMOX1 mRNA expression was upregulated by heme-moieties of lysed erythrocytes. We provide mechanistic evidence that induction of HMOX1 expression in neutrophils potentiates the respiratory burst, and propose this may be part of the causal pathway explaining the association between short (GT)n repeats and increased disease severity in malaria and other critical illnesses. Our findings suggest a genetic predisposition to higher levels of HO-1 is associated with severe illness, and enhances the neutrophil burst leading to oxidative damage of endothelial cells. These add important information to the discussion about possible therapeutic manipulation of HO-1 in critically ill patients

Viral variants that initiate and drive maturation of V1V2-directed HIV-1 broadly neutralizing antibodies.

CAPRISA, 2015.Abstract available in pdf

Investigation of Central Visual Fields in Patients with Age-Related Macular Changes

The effect of early macular pigmentary and drusen changes on the central visual field was investigated in elderly patients with normal visual acuities. Visual field measurements were taken with the Humphrey Field Analyser using its 24-2 and 10-2 full threshold programs. No significant differences were found between two patients groups, one with and one without the macular changes. We conclude that fine pigmentary changes and hard drusen do not cause changes in visual functioning and can be accepted as normal age-related changes