Transformation and Preprocessing of Single-Cell RNA-Seq Data

The count table, a numeric matrix of genes × cells, is a basic input data structure in the analysis of single-cell RNA-seq data. A common preprocessing step is to adjust the counts for variable sampling efficiency and to transform them so that the variance is similar across the dynamic range. These steps are intended to make subsequent application of generic statistical methods more palatable. Here, we describe three transformations (based on the delta method, model residuals, or inferred latent expression state) and compare their strengths and weaknesses. We conclude with an outlook on future needs for the development of transformations for single-cell count data.

PP19 Paramedic research literature 2011–2019. A bibliographic analysis of the contents of amber, the ambulance research repository

BackgroundThe data held by amber presents an opportunity to understand the structure of the published paramedic literature, specifically the output of NHS staff working in English ambulance services 2011–2019. This period is of interest because it represents part of the development phase of paramedic research in England. The authors apply a series of bibliometric measures to generate a profile of the published literature.MethodThe metadata was downloaded from amber for the period from 2011–2019. The metadata was used to create a series of tables that describe the contents of amber. The data was augmented by Altmetric Scores and Citation Counts (SCOPUS) to provide a measure of the quality of the articles contained in amber.ResultsThe data shows a characteristic long tail with 1) Few very high scoring articles (Altmetric and Citation) and many lower scoring articles, 2) A few journals titles publish the majority of articles in paramedicine with many publishing just 1–3 articles. Altmetric scores do not predict citation counts for this data. Only six of the articles that appear in the top 20 journal articles by Altmetric score also appear in the top 20 journal articles by citation count table. Nearly 50% of article achieve an Altmetric score, only 20% of the research is cited one or more times. 68% of articles are written by more than one author including all the articles included in the top 20 article tables. Only 10 of the top 20 cited articles are published in core emergency medicine journals in this instance Resuscitation and Emergency Medicine Journal.ConclusionsBroadly, the data describes the body of research in paramedicine growing overtime in volume and quality.

P1611PRE-ANALYTICAL CONSIDERATIONS IN STUDYING CIRCULATING MICRORNA EXPRESSION: COMPARISON BETWEEN PAIRED EDTA PLASMA, EDTA WHOLE BLOOD AND PAXGENE BLOOD RNA TUBES

Background and Aims microRNA (miRNA) dysregulations have been related to pathological processes, including kidney disease. Relative stability in blood makes miRNAs attractive biomarkers. The current recommendation is to use fresh EDTA plasma samples (i.e. processed within 30 min. from sampling) to study circulating miRNA. However, cumbersome logistics might preclude broad implementation. Therefore, we investigated the potential of whole blood EDTA and PAXgene blood RNA tubes as alternative sources to study circulating microRNA expression profiling. Method Paired EDTA plasma, EDTA whole blood and PAXgene blood RNA tubes were obtained from 10 healthy adults (50% male). EDTA plasma samples were processed within 30 min. after sampling and immediately stored at -80°C. EDTA whole blood tubes and PAXgene tubes were kept at room temperature for 48 hours after sampling. Subsequently, the content of the EDTA whole blood samples was transferred to a 15 mL Falcon tube and stored at -80°C. PAXgene tubes were transferred to -20°C following the manufacturer’s protocol. Within 1 month of storage, all samples were thawed and miRNA was extracted using the Qiagen miRNeasy serum/plasma kit and subjected to RNA-sequencing (Oxford Genomics Centre). Based on the raw data, a count table was created using the online tool miRDeep* for the identification of both novel and known microRNAs. Subsequent downstream bio-informatic analyses approaches consisted of 1) unsupervised hierarchical clustering with principal component analysis (PCA); 2) calculation of differential miRNA expression using generalized linear models with differences considered significant if the false discovery rate-adjusted p-value was inferior to 10%. Results Initial assessment of the count table showed significant differences in the number of detected microRNAs. A median of 220 different microRNAs was detected in EDTA plasma samples versus 661 in PaxGene samples (p < 0.05) and 490 in EDTA whole blood samples (p < 0.05) (Figure 1A). We also found fewer novel miRNAs in EDTA plasma samples than in PAXgene samples (p < 0.001) and EDTA whole blood samples (p < 0.05). Low count microRNAs, defined as below 10 reads in more than 20% of the samples, were more abundant in Paxgene samples versus EDTA plasma samples (p = 0.0039), but this difference was not significant when comparing EDTA whole blood samples with EDTA plasma samples (Figure 1B). PCA analysis (Figure 1C) showed a clear separation of samples according to the blood collection method, strongly suggesting that the blood collection method predominantly determines the miRNA expression profile. Conclusion Bio-informatic analyses demonstrated different miRNA expression profiles according to three different blood collection methods, underpinning the importance of a standardized method for the collection of blood aimed at studying circulating miRNAs. As such, this study has important implications for the design of novel studies aiming to investigate circulating miRNAs.

FAKTOR FAKTOR YANG MEMPENGARUHI PENYUSUNAN ANGGARAN PENDAPATAN DAN BELANJA DAERAH BERBASIS KINERJA (APBD) KABUPATEN PESISIR SELATAN

Factors Affecting the preparation of the budget of income and Expenditure performance-based area of South Coast District. The purpose of this research is: 1. To explain whether there are Factors that affect the compilation of Budgetary revenue and Expenditures performance-based Regions (NATIONAL) South Pesisir Regency and 2. Measuring the magnitude of Factors Affecting the preparation of the budget of income and Expenditure performance-based Regions (NATIONAL) South Pesisir Regency. This research was conducted in February-March 2016 in regional development planning board and the South Pesisir Regency.The sample used in this study as many as 63 respondents using a sampling of saturated. As for the independent variable in this study was organizational commitment (X 1), Financial Information System area (X 2) and Regional Financial Resources (X 3). The dependent variable was the budget of income and Expenditure performance-based Regions (NATIONAL) South Pesisir Regency. The method of data collection is the kuestioner. Data analysis techniques using Descriptive Analysis and Inferensial Analysis.To know how the variables are independent of the dependent variable are partial, used test t. Whereas to know the influence of the variables are independent of the dependent variables simultaneously, use the test F. Assumptions used in the test of validity is if R-R count-table item is declared valid. R-count shown in the table above, from individual items suggests that R-R count-table so that the items are declared valid. Based on a test of the validity of an instrument of organizational commitment (X1), Financial Information System area (X2) and Regional Financial Resources (X3). Note all items are declared valid and reliability test results show that the instruments have a high reliability and meets the criteria of valid instruments and reliability requirements. The free variables of organizational commitment (X ) do not affect government BUDGETS significantly to the southern coast (Y), the Financial Information System area (X2) and Regional Financial Resources (X3) influential Government BUDGETS significantly to the southern coast (Y).

REVITALISASI SUMBER DAYA MANUSIA POLISI MELALUI GAYA KEPEMIMPINAN DAN SINKRONISASI PENDIDIKAN POLISI DENGAN AKTOR UNTUK INTEGRITAS KINERJA DALAM INTEGRATED CRIMINAL JUSTICE SYSTEM KEPOLISIAN REPUBLIK INDONESIA RESOR PESISIR SELATAN

The purpose of this research is: 1. To clarify whether or not there is Revitalizing human resources Police through a leadership style and synchronization with the Police Education actors to the integrity of the performance in the Integrated Criminal Justice System police of Republic of Indonesia South Coast Resort. 2. Measure the magnitude of Revitalizing human resources Police through a leadership style and synchronization with the Police Education actors to the integrity of the performance in the Integrated Criminal Justice System police of Republic of Indonesia South Coast Resort. This research was conducted in February-March 2016 at Polres southern coast.The sample used in this study as many as 85 respondents using a sampling of saturated. As for the independent variable in this research is Revitalizing HUMAN RESOURCES Police (X 1), leadership style (X 2) and synchronization Dikpol (X 3). The dependent variable is the integrity of the coastal South Polres PerformanceThe method of data collection is the kuestioner. Data analysis techniques using Descriptive Analysis and Inferensial Analysis.To know how the variables are independent of the dependent variable are partial, used test t. Whereas to know the influence of the variables are independent of the dependent variables simultaneously, use the test F. Assumptions used in the test of validity is if R-R count-table item is declared valid. R-count shown in the table above, from individual items suggests that R-R count-table so that the items are declared valid. Based on a test of the validity of the instrument is Revitalizing HUMAN RESOURCES Police (X 1), leadership style (X 2) and synchronization Dikpol (X 3) all items are declared valid and reliability test results show that the instruments have a high reliability and meets the criteria of valid instruments and reliability requirements. Revitalizing HUMAN RESOURCES Police free variables (X 1), leadership style (X 2) and synchronization Dikpol (X 3) effect significantly to the integrity of the performance of the South Coast Polres (Y).

deltaRpkm: an R package for a rapid detection of differential gene presence between related bacterial genomes

Background Comparative genomics has seen the development of many software performing the clustering, polymorphism and gene content analysis of genomes at different phylogenetic levels (isolates, species). These tools rely on de novo assembly and/or multiple alignments that can be computationally intensive for large datasets. With a large number of similar genomes in particular, e.g., in surveillance and outbreak detection, assembling each genome can become a redundant and expensive step in the identification of genes potentially involved in a given clinical feature. Results We have developed deltaRpkm, an R package that performs a rapid differential gene presence evaluation between two large groups of closely related genomes. Starting from a standard gene count table, deltaRpkm computes the RPKM per gene per sample, then the inter-group δRPKM values, the corresponding median δRPKM (m) for each gene and the global standard deviation value of m (sm). Genes with m > = 2 ∗ sm (standard deviation s of all the m values) are considered as “differentially present” in the reference genome group. Our simple yet effective method of differential RPKM has been successfully applied in a recent study published by our group (N = 225 genomes of Listeria monocytogenes) (Aguilar-Bultet et al. Front Cell Infect Microbiol 8:20, 2018). Conclusions To our knowledge, deltaRpkm is the first tool to propose a straightforward inter-group differential gene presence analysis with large datasets of related genomes, including non-coding genes, and to output directly a list of genes potentially involved in a phenotype.