HM850K methylation profiling of buffy coat and urine gDNA.

<p>Multidimensional Scaling Plot analysis showing the relationship between samples for the most variable 1000 probes within the dataset.</p

Strategies for optimising gDNA isolation from urine.

<p>The impact of several variables on the yield (quantity and quality) of genomic DNA from urine were tested in the current study. These included fresh vs frozen urine, starting volume and isolation kit. For comparison, buffy coat gDNA was isolated using a standard commercially available kit. *Two buffy coat samples matched to two corresponding frozen urine from Method 1.</p

HM850K methylation profiling of buffy coat and urine gDNA.

<p>Multidimensional Scaling Plot analysis of top 742 differentially methylated probes, separated by tissue type.</p

HM850K methylation profiling of buffy coat and urine gDNA.

<p>Heat map of methylation for 742 most differential probes by tissue type.</p

HM850K methylation profiling of buffy coat and urine gDNA.

<p>Hierarchical clustering and heatmap of methylation for 1000 most variable probes. Yellow–unmethylated, red–fully methylated.</p

HM850K methylation profiling of buffy coat and urine gDNA.

<p>Distribution of all methylation values showing a typical bimodal pattern of methylation associated with the majority of being completely unmethylated or completely methylated.</p

The stability of miRNA species expression in hematopoietic samples.

<p>The stability of miRNA species expression using 41 samples of leukaemic and non-leukaemic cell lines, paediatric archived bone marrow aspirate slides (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0042951#pone.0042951.s002" target="_blank">Table S1</a>), and 14 potential miRNA candidates (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0042951#pone.0042951.s003" target="_blank">Table S2</a>). geNorm and NormFinder (NF) were used to calculate the expression stability values for each miRNA tested. The most ‘stably’ expressed gene in a sample group is that with an average expression stability value (<i>M</i>) closest to zero. The most stably expressed miRNA were; NF Ungrouped: hsa-miR-16 <i>M</i> = 1.143; NF Grouped by Cancer Status: hsa-miR-16 <i>M</i> = 0.457; NF Grouped by Leukaemia subtype: hsa-miR-16 <i>M</i> = 0.573; geNorm: hsa-miR-16 and hsa-miR-26b are equal at <i>M</i> = 1.817.</p

A comparison of RNA extraction methods for the evaluation of RNA concentration (ng/µl) and miRNA expression from archived bone marrow aspirate slides.

<p>The comparison of miRNA extraction methods from matched unstained archived bone marrow smears (n = 6 or n = 8 patients; <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0042951#pone.0042951.s004" target="_blank">Table S3</a>). Six different methods were used based on traditional TRIzol or using the Roche High Pure miRNA Column extraction kit (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0042951#pone-0042951-t001" target="_blank">Table 1</a>). (<b>A</b>) <b>Comparison of Total RNA yield from experimental extraction protocols</b>. The average RNA concentration was measured by NanoDrop (ng/µl ±s.e.m.). Kit Total RNA extraction methods with a Proteinase K digestion (‘FFPE protocol’) are higher in RNA yield compared to kit methods without a digestion step (‘Tissue protocol’), or when extracting small RNA only. These methods are also significantly better than TRIzol extractions. The archived slide extraction method with the highest RNA yield was the Roche kit ‘isolation from FFPE Tissue’ Total RNA extraction with an overnight Proteinase K digestion. * Indicates RNA concentration is significantly different to the Kit Overnight FFPE: Total RNA protocol. (<b>B</b>) <b>Comparison of hsa-miR-16 expression from experimental extraction protocols</b>. The average expression of our reverence gene (hsa-miR-16) measured by qRT-PCR (raw C_t ±s.e.m.). Raw C_t value tracks with total RNA yield, whereby as the concentration of RNA increases the C_t value decreases. This analysis shows extractions with a Proteinase K digestion return a lower C_t value compared to extractions without a digestion step. TRIzol extractions also return a higher C_t value than the Proteinase K digestion protocols.</p

Hazard Detection and Avoidance in Lunar Conditions through the use of a Time of Flight camera

The field of Space Exploration has traditionally been the realm of government agencies, mainly due to the high costs and low material gains from such ventures. However, this is changing and private ventures in the field are increasing. This report details work done as part of Team HAKUTO, a participant in the Google Lunar XPRIZE competition. This report details work on a Time of Flight camera used for autonomous hazard detection and avoidance in a lunar environment. The method with which to achieve this was determined previously to the beginning of this project. Due to the limited computational and memory resources available during the mission, it was decided to use a fairly simple method which identified each potentially interesting feature as a Region of Interest. These Regions of Interest were then evaluated by their overall physical dimensions in order to determine whether or not they would pose a threat to the Rover. The work methodology was largely focused on repeated optimizations and improvements. These efforts were then evaluated against standardized testing with logged environmental data. The main focus of the report is on the optimization of code to meet strict Real-Time limitations as well as improvements to the Hazard Classification Conditions used to classify potential hazards. It also contains discussions about the results and potential future work to be carried out in the HAKUTO project, as well as lightly touching upon the desired outcome of the HAKUTO project.Rymdforskning är ett fält som traditionellt har fyllts av regerings-organisationer, framför allt på grund av de höga kostnaderna och den låga materiella avkastningen från sådana satsningar. Emellertid, detta håller på att ändras och privata satsningar i fältet ökar. Denna rapport beskriver arbete gjort som del av Team HAKUTO, en deltagare i tävlingen Google Lunar XPRIZE. Denna rapport beskriver arbete med en Time of Flight-kamera som används för autonom upptäckt och undvikande av faror i en månmiljö. Metoden för att uppnå detta fastställdes innan starten på detta projekt. På grund av de begränsade beräkningsoch minnes-resurser som är tillgängliga under uppdraget, bestämdes det att använda en tämligen enkel metod som identifierar varje potentiellt intressant särdrag i månmiljön som en Region av Intresse. Dessa Regioner av Intresse utvärderades sedan efter deras övergripande fysiska dimensioner för att avgöra om de skulle kunna utgöra en fara för Rovern. Arbetsmetodiken var till största del fokuserad på upprepade optimeringar och förbättringar. Resultaten från dessa ansträngningar utvärderades sedan mot standardiserade tester med loggad miljödata. Det huvudsakliga fokuset av denna raport är om optimiseringen av koden för att möta strikta realtidsbegränsningar, samt förbättringar av Faroklassificeringsvilkoren som används för att klassifiera potentiella faror. Den innehåller också diskussioner om resultaten och potentiellt framtida arbete att utföras i HAKUTO projektet, samt en övergripande bild av det önskvärda resultatet av HAKUTO projektet

Modified protocols used for the extraction of RNA from archived bone marrow aspirate slides.

<p>The modified extraction protocols used in this study for the extraction of total RNA and small RNA from unstained archived bone marrow aspirate slides. Two main methods were used, the Roche High Pure miRNA Isolation Kit and TRIzol. We followed two provided extraction protocols for the kit; ‘miRNA isolation from tissue’, and ‘miRNA isolation from FFPE tissue’. The methods provided by the manufacturers were modified to include a slide scraping step, and a digestion/homogenization step to break down the slide material. The kit allows for the extraction of total RNA as well as small RNA only; both these methods were trialled here; samples listed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0042951#pone.0042951.s004" target="_blank">Table S3</a>.</p