Nonoptimal Gene Expression Creates Latent Potential for Antibiotic Resistance

This is the final version. Available from Oxford University Press (OUP) via the DOI in this record.Bacteria regulate genes to survive antibiotic stress, but regulation can be far from perfect. When regulation is not optimal, mutations that change gene expression can contribute to antibiotic resistance. It is not systematically understood to what extent natural gene regulation is or is not optimal for distinct antibiotics, and how changes in expression of specific genes quantitatively affect antibiotic resistance. Here we discover a simple quantitative relation between fitness, gene expression, and antibiotic potency, which rationalizes our observation that a multitude of genes and even innate antibiotic defense mechanisms have expression that is critically nonoptimal under antibiotic treatment. First, we developed a pooled-strain drug-diffusion assay and screened Escherichia coli overexpression and knockout libraries, finding that resistance to a range of 31 antibiotics could result from changing expression of a large and functionally diverse set of genes, in a primarily but not exclusively drug-specific manner. Second, by synthetically controlling the expression of single-drug and multidrug resistance genes, we observed that their fitness-expression functions changed dramatically under antibiotic treatment in accordance with a log-sensitivity relation. Thus, because many genes are nonoptimally expressed under antibiotic treatment, many regulatory mutations can contribute to resistance by altering expression and by activating latent defenses.National Institutes of HealthIsraeli Centers of Research Excellence I-CORE ProgramEuropean Research CouncilNational Health and Medical Research Counci

Characterization of Corrosion in Aluminum Alloys Using Nuclear Magnetic Resonance

With an ever increasing emphasis on extending the life of both military and commercial aircraft, it is critical to have nondestructive evaluation (NDE) methods capable of detecting corrosion in its earliest stages of formation. The consequences of corrosion left undetected are material thinning and a subsequent reduction in strength. Conventional NDE methods such as ultrasonics, eddy current and radiography are capable of detecting the resultant exfoliation caused by corrosion; however, some material loss must occur before reliable detection can be made using the referenced methods

The Open Access Advantage Revisited

This paper is a revision of one that appeared in 2008, incorporating the many developments and changes that have happened since then.published_or_final_versio

The Open Access Advantage

Hong Kong Open Access Committeepublished_or_final_versio

Effects of university affiliation and “school spirit” on color preferences: Berkeley versus Stanford

The ecological valence theory (EVT) posits that preference for a color is determined by people’s average affective response to everything associated with it (Palmer & Schloss, Proceedings of the National Academy of Sciences, 107, 8877–8882, 2010). The EVT thus implies the existence of sociocultural effects: Color preference should increase with positive feelings (or decrease with negative feelings) toward an institution strongly associated with a color. We tested this prediction by measuring undergraduates’ color preferences at two rival universities, Berkeley and Stanford, to determine whether students liked their university’s colors better than their rivals did. Students not only preferred their own colors more than their rivals did, but the degree of their preference increased with self-rated positive affect (“school spirit”) for their university. These results support the EVT’s claim that color preference is caused by learned affective responses to associated objects and institutions, because it is unlikely that students choose their university or develop their degree of school spirit on the basis of preexisting color preferences

High burden of viral respiratory co-infections in a cohort of children with suspected pulmonary tuberculosis

Background The presentation of pulmonary tuberculosis (PTB) in young children is often clinically indistinguishable from other common respiratory illnesses, which are frequently infections of viral aetiology. As little is known about the role of viruses in children with PTB, we investigated the prevalence of respiratory viruses in children with suspected PTB at presentation and follow-up. Methods In an observational cohort study, children < 13 years were routinely investigated for suspected PTB in Cape Town, South Africa between December 2015 and September 2017 and followed up for 24 weeks. Nasopharyngeal aspirates (NPAs) were tested for respiratory viruses using multiplex PCR at enrolment, week 4 and 8. Results Seventy-three children were enrolled [median age 22.0 months; (interquartile range 10.0–48.0); 56.2% male and 17.8% HIV-infected. Anti-tuberculosis treatment was initiated in 54.8%; of these 50.0% had bacteriologically confirmed TB. At enrolment, ≥1 virus were detected in 95.9% (70/73) children; most commonly human rhinovirus (HRV) (74.0%). HRV was more frequently detected in TB cases (85%) compared to ill controls (60.6%) (p = 0.02). Multiple viruses were detected in 71.2% of all children; 80% of TB cases and 60.6% of ill controls (p = 0.07). At follow-up, ≥1 respiratory virus was detected in 92.2% (47/51) at week 4, and 94.2% (49/52) at week 8. Conclusions We found a high prevalence of viral respiratory co-infections in children investigated for PTB, irrespective of final PTB diagnosis, which remained high during follow up. Future work should include investigating the whole respiratory ecosystem in combination with pathogen- specific immune responses

Ageing memory and glassiness of a driven vortex system

Many systems in nature, glasses, interfaces and fractures being some examples, cannot equilibrate with their environment, which gives rise to novel and surprising behaviour such as memory effects, ageing and nonlinear dynamics. Unlike their equilibrated counterparts, the dynamics of out-of- equilibrium systems is generally too complex to be captured by simple macroscopic laws. Here we investigate a system that straddles the boundary between glass and crystal: a Bragg glass formed by vortices in a superconductor. We find that the response to an applied force evolves according to a stretched exponential, with the exponent reflecting the deviation from equilibrium. After the force is removed, the system ages with time and its subsequent response time scales linearly with its age (simple ageing), meaning that older systems are slower than younger ones. We show that simple ageing can occur naturally in the presence of sufficient quenched disorder. Moreover, the hierarchical distribution of timescales, arising when chunks of loose vortices cannot move before trapped ones become dislodged, leads to a stretched-exponential response.Comment: 16 pages, 5 figure

Optimising computer aided detection to identify intra-thoracic tuberculosis on chest x-ray in South African children

Diagnostic tools for paediatric tuberculosis remain limited, with heavy reliance on clinical algorithms which include chest x-ray. Computer aided detection (CAD) for tuberculosis on chest x-ray has shown promise in adults. We aimed to measure and optimise the performance of an adult CAD system, CAD4TB, to identify tuberculosis on chest x-rays from children with presumptive tuberculosis. Chest x-rays from 620 children <13 years enrolled in a prospective observational diagnostic study in South Africa, were evaluated. All chest x-rays were read by a panel of expert readers who attributed each with a radiological reference of either 'tuberculosis' or 'not tuberculosis'. Of the 525 chest x-rays included in this analysis, 80 (40 with a reference of 'tuberculosis' and 40 with 'not tuberculosis') were allocated to an independent test set. The remainder made up the training set. The performance of CAD4TB to identify 'tuberculosis' versus 'not tuberculosis' on chest x-ray against the radiological reference read was calculated. The CAD4TB software was then fine-tuned using the paediatric training set. We compared the performance of the fine-tuned model to the original model. Our findings were that the area under the receiver operating characteristic curve (AUC) of the original CAD4TB model, prior to fine-tuning, was 0.58. After fine-tuning there was an improvement in the AUC to 0.72 (p = 0.0016). In this first-ever description of the use of CAD to identify tuberculosis on chest x-ray in children, we demonstrate a significant improvement in the performance of CAD4TB after fine-tuning with a set of well-characterised paediatric chest x-rays. CAD has the potential to be a useful additional diagnostic tool for paediatric tuberculosis. We recommend replicating the methods we describe using a larger chest x-ray dataset from a more diverse population and evaluating the potential role of CAD to replace a human-read chest x-ray within treatment-decision algorithms for paediatric tuberculosis

Toward a conceptual framework of the acceptability of tuberculosis treatment in children using a theory generative approach

To describe an early-stage holistic framework towards evaluating factors that impact the overall acceptability of TB treatment along the TB care cascade in children. We developed a conceptual framework utilising a theory generative approach. Domains were developed through review of existing definitions and analysis of existing qualitative data undertaken in acceptability studies of TB treatment in children. Clarity of domain definitions was achieved through iterative refinement among the research team. Three domains, each comprising several dimensions, were identified to holistically evaluate treatment acceptability: (1) usability, which involves the alignment between the requirements of treatment use and caregivers’ and children’s ability to integrate TB treatment into their everyday routines, (2) receptivity, which describes the end-user’s perception and expectations of treatment and its actual use, and (3) integration, which describes the relationship between available health services and caregivers/children’s capacity to make use of those services. Our framework addresses the gaps in current research which do not account for the influence of caregivers’ and children’s contexts on TB treatment uptake and overall acceptability. This approach may support the development of more standard, holistic measures to improve TB treatment delivery and experiences and future research in children