Explore the vast range of titles available.

12 microRNA expression profiling platforms are compared for their reproducibility, sensitivity, accuracy and specificity, and the strengths and weaknesses of each platform are discussed. MicroRNAs are important negative regulators of protein-coding gene expression and have been studied intensively over the past years. Several measurement platforms have been developed to determine relative miRNA abundance in biological samples using different technologies such as small RNA sequencing, reverse transcription–quantitative PCR (RT-qPCR) and (microarray) hybridization. In this study, we systematically compared 12 commercially available platforms for analysis of microRNA expression. We measured an identical set of 20 standardized positive and negative control samples, including human universal reference RNA, human brain RNA and titrations thereof, human serum samples and synthetic spikes from microRNA family members with varying homology. We developed robust quality metrics to objectively assess platform performance in terms of reproducibility, sensitivity, accuracy, specificity and concordance of differential expression. The results indicate that each method has its strengths and weaknesses, which help to guide informed selection of a quantitative microRNA gene expression platform for particular study goals.

The stratum corneum and DNA repair do not completely protect keratinocytes from ultraviolet B. A third defense prevents cells with DNA photoproducts from becoming precancerous mutant cells: apoptosis of ultraviolet-damaged keratinocytes (“sunburn cells”). As signals for ultraviolet-induced apoptosis, some studies implicate DNA photoproducts in actively transcribed genes; other studies implicate non-nuclear signals. We traced and quantitated the in vivo DNA signal through several steps in the apoptosis-signaling pathway in haired mice. Homozygous inactivation of Xpa, Csb, or Xpc nucleotide excision repair genes directed the accumulation of DNA photoproducts to specific genome regions. Repair-defective Xpa−/− mice were 7–10-fold more sensitive to sunburn cell induction than wild-type mice, indicating that 86–90% of the ultraviolet B signal for keratinocyte apoptosis involved repairable photoproducts in DNA; the remainder involves unrepaired DNA lesions or nongenomic targets. Csb−/− mice, defective only in excising photoproducts from actively transcribed genes, were as sensitive as Xpa−/−, indicating that virtually all of the DNA signal originates from photoproducts in active genes. Conversely, Xpc−/− mice, defective in repairing the untranscribed majority of the genome, were as resistant to apoptosis as wild type. Sunburn cell formation requires the Trp53 tumor suppressor protein; 90–96% of the signal for its induction in vivo involved transcribed genes. Mdm2, which regulates the stability of Trp53 through degradation, was induced in vivo by low ultraviolet B doses but was suppressed at erythemal doses. DNA photoproducts in actively transcribed genes were involved in ≈ 89% of the Mdm2 response.

Nat. Methods 11, 809–815 (2014); published online 29 June 2014; corrected after print 30 July 2014 In the version of this article initially published, the author Linda Wong was omitted from the author list. The error has been corrected in the HTML and PDF versions of the article.

To elucidate the regulatory mechanisms that control expression of the SOS system in Bacillus subtilis promoter regions from three DNA damage-inducible genes dinA, dinB and dinC, were cloned (chapter 1). Sequences required for damage-inducible expression of the dinA, dinB and dinC promoters were localized to within 120 bp, 138 bp and 420 bp DNA fragments, respectively. Within these promoter regions a consensus sequence (Cheo Box) GAAC-N4-GTTC was identified. Similar sequences were identified within the promoter regions of the dinR and recA genes. No sequences similar to the E. coli LexA binding site were found within any of these damage-inducible promoter regions. I have proposed that this novel consensus sequence functions as an operator site that is required for damage-inducible regulation in Bacillus subtilis. This hypothesis was tested by the construction of deletions within the dinA and recA promoter regions (chapters 2 and 3). Deletion of the Cheo Boxes upstream of the dinA and recA promoters derepressed expression and abolished damage-inducible regulation. Components of the SOS system of B. subtilis are spontaneously induced specifically within cells that have differentiated to the state of natural competence. Expression of SOS phenomena within competent cells is dependent upon the competence-specific induction of the recA gene. However, the expression of recA within competent cells occurs by a RecA-independent mechanism. Thus, the recA gene is controlled by two different regulatory mechanisms: RecA-dependent damage-induction and RecA-independent competence-induction. The expression of recA within competent cells is dependent upon the spo0A, spo0H, comA, srfA and degU loci. Therefore the competence-specific induction of recA is controlled by the same regulatory pathway that induces the late competence genes. A 1.2 kb recA-specific mRNA transcript was induced following treatment with mitomycin and within competent cells. The damage-inducible and competence inducible transcripts initiate at identical positions within the recA promoter. Thus the recA gene is transcribed from a single promoter that is controlled by two different regulatory mechanisms. Based upon the results of a deletion analysis of the recA promoter region I have proposed that multiple regulatory elements are required for the competence-specific induction of the recA gene.

Background Coincidence imaging of low-abundance yttrium-90 ( 90 Y) internal pair production by positron emission tomography with integrated computed tomography (PET/CT) achieves high-resolution imaging of post-radioembolization microsphere biodistribution. Part 2 analyzes tumor and non-target tissue dose-response by 90 Y PET quantification and evaluates the accuracy of tumor 99m Tc macroaggregated albumin (MAA) single-photon emission computed tomography with integrated CT (SPECT/CT) predictive dosimetry. Methods Retrospective dose quantification of 90 Y resin microspheres was performed on the same 23-patient data set in part 1. Phantom studies were performed to assure quantitative accuracy of our time-of-flight lutetium-yttrium-oxyorthosilicate system. Dose-responses were analyzed using 90 Y dose-volume histograms (DVHs) by PET voxel dosimetry or mean absorbed doses by Medical Internal Radiation Dose macrodosimetry, correlated to follow-up imaging or clinical findings. Intended tumor mean doses by predictive dosimetry were compared to doses by 90 Y PET. Results Phantom studies demonstrated near-perfect detector linearity and high tumor quantitative accuracy. For hepatocellular carcinomas, complete responses were generally achieved at D 70 > 100 Gy ( D 70 , minimum dose to 70% tumor volume), whereas incomplete responses were generally at D 70 < 100 Gy; smaller tumors (<80 cm 3 ) achieved D 70 > 100 Gy more easily than larger tumors. There was complete response in a cholangiocarcinoma at D 70 90 Gy and partial response in an adrenal gastrointestinal stromal tumor metastasis at D 70 53 Gy. In two patients, a mean dose of 18 Gy to the stomach was asymptomatic, 49 Gy caused gastritis, 65 Gy caused ulceration, and 53 Gy caused duodenitis. In one patient, a bilateral kidney mean dose of 9 Gy ( V 20 8%) did not cause clinically relevant nephrotoxicity. Under near-ideal dosimetric conditions, there was excellent correlation between intended tumor mean doses by predictive dosimetry and those by 90 Y PET, with a low median relative error of +3.8% (95% confidence interval, -1.2% to +13.2%). Conclusions Tumor and non-target tissue absorbed dose quantification by 90 Y PET is accurate and yields radiobiologically meaningful dose-response information to guide adjuvant or mitigative action. Tumor 99m Tc MAA SPECT/CT predictive dosimetry is feasible. 90 Y DVHs may guide future techniques in predictive dosimetry.

Randomised controlled trials are increasingly conducted as embedded, nested, or using cohorts or routinely collected data, including registries, electronic health records, and administrative databases, to assess if participants are eligible for the trial and to facilitate recruitment, to deliver an embedded intervention, to collect trial outcome data, or a combination of these purposes. This report presents the Consolidated Standards of Reporting Trials (CONSORT) extension for randomised controlled trials conducted using cohorts and routinely collected data (CONSORT-ROUTINE). The extension was developed to look at the unique characteristics of trials conducted with these types of data with the goal of improving reporting quality in the long term by setting standards early in the process of uptake of these trial designs. The extension was developed with a sequential approach, including a Delphi survey, a consensus meeting, and piloting of the checklist. The checklist was informed by the CONSORT 2010 statement and two reporting guidelines for observational studies, the Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) statement and the REporting of studies Conducted using Observational Routinely collected Data (RECORD) statement. The extension includes eight items modified from the CONSORT 2010 statement and five new items. Reporting items with explanations and examples are provided, including key aspects of trials conducted using cohorts or routinely collected data that require specific reporting considerations.

The aim of this study was to review the outcomes of palliative radiotherapy (RT) for hematuria treated with modern RT techniques. This was a retrospective cohort study. The primary endpoint was symptom response rate. Secondary endpoints included symptom recurrence rate, overall survival and treatment-related toxicity. Median age was 82 years (range=36-98 years). Median biologically effective dose (BED) was 36 Gy. Sixty-seven percent of patients (39/58) responded to RT. The median survival duration was 5.6 months (range=0.02-47.6 months). One third (13/39) of responders had recurrence of hematuria. Competing Risk regression with death as the competing risk showed that patients treated with low BED regimen (<36 Gy) had 5.76 times the hazard of recurrence compared to high BED regimen (>36 Gy) (p=0.01). One patient (2%) developed grade 3 nausea and vomiting which required admission for intravenous hydration. BED regimens should be recommended as they are associated with a significantly lower rate of recurrent hematuria.