Characterising Retroviral Restriction by TRIM Proteins

Tripartite motif (TRIM) proteins are numerous in the human proteome, and a number of these molecules are known to restrict retroviral replication. TRIM5α (T5α) is one such factor. It targets the viral capsid and imposes a block to infection between entry and reverse transcription. Capsid recognition is mediated by the C-terminal B30.2 domain, which contains surface-exposed loops of high amino acid variability. Restriction is then effected via proteasome recruitment and the induction of innate immune cascades. Although T5α is well-characterised in this respect, other factors – such as the highly divergent TRIM1 (T1) – remain poorly understood. To further characterise the T1 restriction phenotype, chimeras of this protein and its non-restricting paralogue, T18, were generated by overlapping PCR. The restriction activities of the resulting molecules were then measured using an established flow cytometry assay. These experiments revealed that T1 also binds capsid via the B30.2 domain, although the majority of this region can be functionally replaced. Other aspects of T1 biology addressed in this work include the contribution of N-terminal components to restriction potency, and the relationship between protein expression level and restriction activity. Following a number of attempts to generate a functional chimera of T1 and 5α, the latter half of this thesis explores how the spacing between capsid-binding and effector domains can influence restriction activity. To this end, a panel of mutations were made in the linker 2 (L2) region of T5α, and their effects on restriction measured. These experiments revealed that even small changes in interdomain spacing can have profound phenotypic consequences. Collectively, this work reinforces the notion that TRIM family members share a common overall design, allowing individual components to be shuffled between them. At the same time, each molecule has been shaped by unique evolutionary pressures, which can render them sensitive even to relatively minor modifications

Synchrotron validation of inline coherent imaging for tracking laser keyhole depth

In situ monitoring is critical to the increasing adoption of laser powder bed fusion (LPBF) and laser welding by industry for manufacture of complex metallic components. Optical coherence tomography (OCT), an interferometric imaging technique adapted from medical applications, is now widely used for operando monitoring of morphology during high-power laser material processing. However, even in stable processing regimes, some OCT depth measurements from the keyhole (vapor cavity formed at laser beam spot) appear too shallow or too deep when compared to ex situ measurements of weld depth. It has remained unclear whether these outliers are due to imaging artifacts, multiple scattering of the imaging beam within the keyhole, or real changes in keyhole depth, making it difficult to accurately extract weld depth and determine error bounds. To provide a definitive explanation, we combine inline coherent imaging (ICI), a type of OCT, with synchrotron X-ray imaging for simultaneous, operando monitoring of the full 2-dimensional keyhole profile at high-speed (280 kHz and 140 kHz, respectively). Even in a highly turbulent pore-generation mode, the depth measured with ICI closely follows the keyhole depth extracted from radiography (>80% within ± 14 µm). Ray-tracing simulations are used to confirm that the outliers in ICI depth measurements (that significantly disagree with radiography) primarily result from multiple reflections of the imaging light (57%). Synchrotron X-ray imaging also enables tracking of bubble and pore formation events. Pores are generated during laser welding when the sidewalls of the keyhole rapidly (>10 m/s) collapse inwards, pinching off a bubble from the keyhole root and resulting in a rapid decrease in keyhole depth. Evidence of bubble formation can be found in ICI depth profiles alone, as rapid depth changes exhibit moderate correlation with bubble formation events (0.26). This work moves closer to accurate, localized defect detection during laser welding and LPBF using ICI

Revisiting the Thermodynamic Stability of Indomethacin Polymorphs with Low-Frequency Vibrational Spectroscopy and Quantum Mechanical Simulations

The two major polymorphs of the active pharmaceutical ingredient indomethacin were studied using a combination of experimental low-frequency vibrational spectroscopies, theoretical solid-state density functional theory and ab initio molecular dynamics calculations. The results enable a complete spectral assignment of the low-frequency IR and Raman spectra, and yield new insight into the energetic and dynamical factors present within the solids to be understood. Ultimately, these results are used to rationalize the thermodynamic properties of the two crystals, which result in a contradiction to the long-held belief that the γ-form is the more stable polymorph at ambient conditions due to its predominant abundance. Overall, the study highlights the combined role that molecular conformation, bulk packing arrangement, and intermolecular forces have on the ultimate properties of pharmaceutical crystals, and the need for detailed analyses into all of these effects in order to predict the properties of materials

Cost-effectiveness of strategies preventing late-onset infection in preterm infants

OBJECTIVE: Developing a model to analyse the cost-effectiveness of interventions preventing late-onset infection (LOI) in preterm infants and applying it to the evaluation of anti-microbial impregnated peripherally inserted central catheters (AM-PICCs) compared with standard PICCs (S-PICCs). DESIGN: Model-based cost-effectiveness analysis, using data from the Preventing infection using Antimicrobial Impregnated Long Lines (PREVAIL) randomised controlled trial linked to routine healthcare data, supplemented with published literature. The model assumes that LOI increases the risk of neurodevelopmental impairment (NDI). SETTING: Neonatal intensive care units in the UK National Health Service (NHS). PATIENTS: Infants born ≤32 weeks gestational age, requiring a 1 French gauge PICC. INTERVENTIONS: AM-PICC and S-PICC. MAIN OUTCOME MEASURES: Life expectancy, quality-adjusted life years (QALYs) and healthcare costs over the infants' expected lifetime. RESULTS: Severe NDI reduces life expectancy by 14.79 (95% CI 4.43 to 26.68; undiscounted) years, 10.63 (95% CI 7.74 to 14.02; discounted) QALYs and costs £19 057 (95% CI £14 197; £24697; discounted) to the NHS. If LOI causes NDI, the maximum acquisition price of an intervention reducing LOI risk by 5% is £120. AM-PICCs increase costs (£54.85 (95% CI £25.95 to £89.12)) but have negligible impact on health outcomes (-0.01 (95% CI -0.09 to 0.04) QALYs), compared with S-PICCs. The NHS can invest up to £2.4 million in research to confirm that AM-PICCs are not cost-effective. CONCLUSIONS: The model quantifies health losses and additional healthcare costs caused by NDI and LOI during neonatal care. Given these consequences, interventions preventing LOI, even by a small extent, can be cost-effective. AM-PICCs, being less effective and more costly than S-PICC, are not likely to be cost-effective. TRIAL REGISTRATION NUMBER: NCT03260517

Learning environment associated with use of mixed mode delivery model among secondary business studies students in Singapore

At many teacher education institutes around the world, preservice teachers are empowered to use pedagogical tools and strategies that engage their students. We used a modified version of the Constructivist Learning Environment Survey (CLES) to evaluate the effectiveness of a pedagogical model known as the Mixed Mode Delivery (MMD) model in terms of the CLES’s five scales of personal relevance, uncertainty, critical voice, shared control and negotiation. Comparisons were made between 2,216 secondary school students taught by the preservice teachers in an MMD group and 991 students in a control group in terms of the relative magnitudes of the gap between the actual and preferred learning environment in students’ school classrooms. The findings supported the positive impact of using MMD in terms of students’ perceptions of their classroom environments for all CLES scales

Cutaneous melanoma: an updated SIGN Guideline

No abstrac

A single sub-km Kuiper Belt object from a stellar Occultation in archival data

The Kuiper belt is a remnant of the primordial Solar System. Measurements of its size distribution constrain its accretion and collisional history, and the importance of material strength of Kuiper belt objects (KBOs). Small, sub-km sized, KBOs elude direct detection, but the signature of their occultations of background stars should be detectable. Observations at both optical and X-ray wavelengths claim to have detected such occultations, but their implied KBO abundances are inconsistent with each other and far exceed theoretical expectations. Here, we report an analysis of archival data that reveals an occultation by a body with a 500 m radius at a distance of 45 AU. The probability of this event to occur due to random statistical fluctuations within our data set is about 2%. Our survey yields a surface density of KBOs with radii larger than 250 m of 2.1^{+4.8}_{-1.7} x 10^7 deg^{-2}, ruling out inferred surface densities from previous claimed detections by more than 5 sigma. The fact that we detected only one event, firmly shows a deficit of sub-km sized KBOs compared to a population extrapolated from objects with r>50 km. This implies that sub-km sized KBOs are undergoing collisional erosion, just like debris disks observed around other stars.Comment: To appear in Nature on December 17, 2009. Under press embargo until 1800 hours London time on 16 December. 19 pages; 7 figure

Temporal trends in mode, site and stage of presentation with the introduction of colorectal cancer screening: a decade of experience from the West of Scotland

background:  Population colorectal cancer screening programmes have been introduced to reduce cancer-specific mortality through the detection of early-stage disease. The present study aimed to examine the impact of screening introduction in the West of Scotland. methods:  Data on all patients with a diagnosis of colorectal cancer between January 2003 and December 2012 were extracted from a prospectively maintained regional audit database. Changes in mode, site and stage of presentation before, during and after screening introduction were examined. results:  In a population of 2.4 million, over a 10-year period, 14 487 incident cases of colorectal cancer were noted. Of these, 7827 (54%) were males and 7727 (53%) were socioeconomically deprived. In the postscreening era, 18% were diagnosed via the screening programme. There was a reduction in both emergency presentation (20% prescreening vs 13% postscreening, P0.001) and the proportion of rectal cancers (34% prescreening vs 31% pos-screening, P0.001) over the timeframe. Within non-metastatic disease, an increase in the proportion of stage I tumours at diagnosis was noted (17% prescreening vs 28% postscreening, P0.001). conclusions:  Within non-metastatic disease, a shift towards earlier stage at diagnosis has accompanied the introduction of a national screening programme. Such a change should lead to improved outcomes in patients with colorectal cancer

Field-study science classrooms as positive and enjoyable learning environments

We investigated differences between field-study classrooms and traditional science classrooms in terms of the learning environment and students’ attitudes to science, as well as the differential effectiveness of field-study classrooms for students differing in sex and English proficiency. A modified version of selected scales from the What Is Happening In this Class? questionnaire was used to assess the learning environment, whereas students’ attitudes were assessed with a shortened version of a scale from the Test of Science Related Attitudes. A sample of 765 grade 5 students from 17 schools responded to the learning environment and attitude scales in terms of both their traditional science classrooms and classrooms at a field-study centre in Florida. Large effect sizes supported the effectiveness of the field-studies classroom in terms of both the learning environment and student attitudes. Relative to the home school science class, the field-study class was considerably more effective for students with limited English proficiency than for native English speakers