Unravelling the genomic landscape of acute lymphoblastic leukaemia in older adults

Ph. D, ThesisThe objectives of this study were to characterise the primary genetic abnormalities, genomic copy number changes and mutational landscape of ALL in older adults. The primary chromosomal abnormalities from patients aged ≥60 years recruited into the UKALL14 (n=94) and UKALL60+ (N=116) trials were first evaluated. B-cell precursor (BCP) ALL patients lacking a primary chromosomal abnormality (B-other ALL) were screened for ABL-class fusions, JAK-STAT abnormalities and other rearrangements using fluorescence in situ hybridisation (FISH). CRLF2 and ZNF384 rearrangements were detected in 17% and 7% of tested patients respectively. ABLclass fusions were notably absent. Next, single nucleotide polymorphism (SNP) arrays were performed to identify copy number abnormalities in patients with suitable material (n=83). Deletions were detected in IKZF1 (52%), CDKN2A/B (45%) and PAX5 (39%), as well as arm level events including del(9p) (21%), monosomy 7 (10%) and gain 1q (10%). Selected novel abnormalities were then validated using a customised sequencing approach. Recurrent novel deletions were confirmed in LEMD3, KDM6A and CXCR4, potentially contributing to leukaemogenesis. Separately, SNP arrays were performed on DNA from patients with low hypodiploidy or high hyperdiploidy (n=88) and machine-learning techniques were used to cluster cases based on log2 ratio data. Discrepancies between the cytogenetic-derived and SNP array-derived genetic subgroup were identified. A diagnostic classifier based on chromosomal log2 ratios was then designed using classification and regression tree analysis (CART). Finally, the mutational landscape of ALL in older adults was characterised in selected patients using exome sequencing (n=6) and a customised sequencing panel (n=30). Pathogenic variants were identified in TP53, NF1, JAK2 as well as members of the RAS signalling pathway, and were closely related to specific primary chromosomal abnormalities. This project has helped characterise the landscape of genetic prognostic biomarkers in older adults with ALL, and identified novel therapeutically actionable abnormalities meriting further assessment.Bright Red, NIHR Newcastle Biomedical Research Centr

Case Studies to Develop a Highway-Rail Grade Crossing Analysis Framework Using Microsimulation

693JJ621C000017There are approximately 126,700 highway-rail at-grade crossings in the U.S. A portion of those involve high-volume public streets where crossing events result in measurable traffic backups and delays to the extent that mitigation efforts are needed. Conventional traffic analysis methods such as those in the Highway Capacity Manual are limited in their ability to quantify the impacts of traffic interruptions due to a train crossing. Microscopic traffic simulation methods are capable of analyzing these events and simulation software has been a part of the practitioner\u2019s toolbox now for 30 years. However, there has been no technical guidance nor consistency on how these tools should be applied to evaluate crossing events. Using microscopic simulation, researchers performed two case studies from which a framework has been developed that can be used by practitioners and decision makers for performing traffic operations analyses of at-grade crossings. The framework offers guidance for a consistent approach to the development and application of such models

A 1RM Strengthening and Exercise Programme for the Treatment of Knee Osteoarthritis: A Quality-Improvement Study

Background: The Kneefit programme is a 12-week strengthening and exercise programme, personalised using body-weight ratios, for people with knee osteoarthritis. Objectives and Design: This quality-improvement study was conducted to evaluate the effectiveness of the programme for managing symptomatic knee osteoarthritis. Methods: The Kneefit programme was delivered between 20 August 2013 and 7 January 2014 and included six weeks of supervised strengthening, balance, and cardiovascular exercise in a group at the local hospital, followed by six weeks of unsupervised exercise. Leg-press and knee-extension 1RM scores were assessed at baseline, six weeks, and twelve weeks. In addition, patient-reported outcome measures (Oxford Knee Score, EQ5D, Patient Specific Function Score (PSFS)) were assessed. Wilcoxon Signed Rank tests were used to evaluate the changes from week 1 to week 6 and week 12. Results: Thirty-six patients were included at baseline and at six weeks, and 31 patients completed their twelve-week assessment. Statistically significant improvements were found at 6 and 12 weeks for change for the Oxford Knee Score (median change: 4.0, IQR 4.0 to 9.0, p < 0.001 and 4.0, IQR 0 to 8.0, p < 0.001), EQ5D-5L (median change: 0.078, IQR 0.03 to 0.20, p < 0.001 and 0.071, IQR 0.02 to 0.25, p < 0.001) and the PSFS (median change: 1.3 IQR 0 to 2.6, p = 0.005 and 2.3 IQR −0.3 to 3.3, p = 0.016). In addition, significant improvements were found for 1RM leg-press and knee-extension scores on both the affected and unaffected legs. Conclusion: The Kneefit programme was successful at improving both functional and strength-related outcome measures in patients with knee osteoarthritis. Our findings suggest that tailoring strength exercises based on the 1RM strength-training principles is feasible in this population

Recycled stellar ejecta as fuel for star formation and implications for the origin of the galaxy mass-metallicity relation

We use cosmological, hydrodynamical simulations from the Evolution and Assembly of GaLaxies and their Environments and OverWhelmingly Large Simulations projects to assess the significance of recycled stellar ejecta as fuel for star formation. The fractional contributions of stellar mass-loss to the cosmic star formation rate (SFR) and stellar mass densities increase with time, reaching 35 and 19 per cent, respectively, at z = 0. The importance of recycling increases steeply with galaxy stellar mass forM* < 1010.5M_, and decreases mildly at higher mass. This trend arises from the mass dependence of feedback associated with star formation and AGN, which preferentially suppresses star formation fuelled by recycling. Recycling is more important for satellites than centrals and its contribution decreases with galactocentric radius. The relative contribution of asymptotic giant branch (AGB) stars increases with time and towards galaxy centres. This is a consequence of the more gradual release of AGB ejecta compared to that of massive stars, and the preferential removal of the latter by star formation driven outflows and by lock up in stellar remnants. Recycling-fuelled star formation exhibits a tight, positive correlation with galaxy metallicity, with a secondary dependence on the relative abundance of alpha elements (which are predominantly synthesized in massive stars), that is insensitive to the subgrid models for feedback. Hence, our conclusions are directly relevant for the origin of the mass–metallicity relation and metallicity gradients. Applying the relation between recycling and metallicity to the observed mass–metallicity relation yields our best estimate of the mass-dependent contribution of recycling. For centrals with a mass similar to that of the Milky Way, we infer the contributions of recycled stellar ejecta to the SFR and stellar mass to be 35 and 20 per cent, respectively

Experimental evolution, genetic analysis and genome re-sequencing reveal the mutation conferring artemisinin resistance in an isogenic lineage of malaria parasites

<p>Abstract</p> <p>Background</p> <p>Classical and quantitative linkage analyses of genetic crosses have traditionally been used to map genes of interest, such as those conferring chloroquine or quinine resistance in malaria parasites. Next-generation sequencing technologies now present the possibility of determining genome-wide genetic variation at single base-pair resolution. Here, we combine <it>in vivo </it>experimental evolution, a rapid genetic strategy and whole genome re-sequencing to identify the precise genetic basis of artemisinin resistance in a lineage of the rodent malaria parasite, <it>Plasmodium chabaudi</it>. Such genetic markers will further the investigation of resistance and its control in natural infections of the human malaria, <it>P. falciparum</it>.</p> <p>Results</p> <p>A lineage of isogenic <it>in vivo </it>drug-selected mutant <it>P. chabaudi </it>parasites was investigated. By measuring the artemisinin responses of these clones, the appearance of an <it>in vivo </it>artemisinin resistance phenotype within the lineage was defined. The underlying genetic locus was mapped to a region of chromosome 2 by Linkage Group Selection in two different genetic crosses. Whole-genome deep coverage short-read re-sequencing (Illumina^®Solexa) defined the point mutations, insertions, deletions and copy-number variations arising in the lineage. Eight point mutations arise within the mutant lineage, only one of which appears on chromosome 2. This missense mutation arises contemporaneously with artemisinin resistance and maps to a gene encoding a de-ubiquitinating enzyme.</p> <p>Conclusions</p> <p>This integrated approach facilitates the rapid identification of mutations conferring selectable phenotypes, without prior knowledge of biological and molecular mechanisms. For malaria, this model can identify candidate genes before resistant parasites are commonly observed in natural human malaria populations.</p

Continuous Deployment Transitions at Scale

Predictable, rapid, and data-driven feature rollout; lightning-fast; and automated fix deployment are some of the benefits most large software organizations worldwide are striving for. In the process, they are transitioning toward the use of continuous deployment practices. Continuous deployment enables companies to make hundreds or thousands of software changes to live computing infrastructure every day while maintaining service to millions of customers. Such ultra-fast changes create a new reality in software development. Over the past four years, the Continuous Deployment Summit, hosted at Facebook, Netflix, Google, and Twitter has been held. Representatives from companies like Cisco, Facebook, Google, IBM, Microsoft, Netflix, and Twitter have shared the triumphs and struggles of their transition to continuous deployment practices—each year the companies press on, getting ever faster. In this chapter, the authors share the common strategies and practices used by continuous deployment pioneers and adopted by newcomers as they transition and use continuous deployment practices at scale

Facile route to conformal hydrotalcite coatings over complex architectures:a hierarchically ordered nanoporous base catalyst for FAME production

An alkali- and nitrate-free hydrotalcite coating has been grafted onto the surface of a hierarchically ordered macroporous-mesoporous SBA-15 template via stepwise growth of conformal alumina adlayers and their subsequent reaction with magnesium methoxide. The resulting low dimensional hydrotalcite crystallites exhibit excellent per site activity for the base catalysed transesterification of glyceryl triolein with methanol for FAME production

Unstructured proteins of the malaria parasite Plasmodium falciparum as vaccine candidates

Malaria vaccine research has been battling with persistent challenges, including polymorphisms of vaccine antigens, difficulties with production processes, and limited immune protection against the disease. Intrinsically unstructured proteins (IUPs) are a fairly newly classified group of proteins that have no stable 3D structure and are generally heat-resistant. They usually contain low complexity regions and repetitive sequences, both of which are distinct characteristics of the malaria proteome. Surprisingly, some of the vaccine candidates that have been extensively studied were later reported to have unstructured regions, some of which serve as targets of protective immunity. In keeping with their interesting immunological profiles and their unique properties, which are exceptionally beneficial for vaccine production, malarial IUP antigens may be good vaccine candidates. This PhD project has the following aims:- 1) to develop a synthetic unstructured protein antigen based on the Block 2 region of MSP-1, named the MSP-1 hybrid 2) to characterize a novel vaccine antigen derived from the MSP-3.3 protein, namely an IUP region of PF10_0347 gene product, for its potential as a vaccine candidate 3) to develop a second-generation vaccine by combining the MSP-1 hybrid, with two allelic variants of MSP-2, to overcome antigenic polymorphism and strain-specific immune responses 4) to validate protocols for IUP identification from proteins extracted from the malaria parasite. This study showed that 1) MSP-1 hybrid production was scalable, yielding high protein yields with comparable immunological properties to small-scale production. MSP-1 hybrid was shown to be compatible with different adjuvants, and elicited specific antibodies covering the whole range of Block 2 allelic diversities. 2) A novel antigen, MSP-3.3C, an IUP based on the 3’ region of the PF10_0347 gene, was cloned, expressed and purified. Anti-MSP3.3C antibodies showed very strong parasite growth inhibitory effects in vitro. 3) The MSP-multihybrid antigen was expressed using simple techniques, but only at low levels. It contains epitopes from all three parasite antigen components, and is recognized by specific naturally acquired antibodies. 4) an unconventional 2D gel technique was tested as a method of malaria parasite IUP identification. Plans for further validation of this technique were discussed