Statistical analysis in microbiology:statnotes

This book is aimed primarily at microbiologists who are undertaking research and who require a basic knowledge of statistics to analyse their experimental data. Computer software employing a wide range of data analysis methods is widely available to experimental scientists. The availability of this software, however, makes it essential that investigators understand the basic principles of statistics. Statistical analysis of data can be complex with many different methods of approach, each of which applies in a particular experimental circumstance. Hence, it is possible to apply an incorrect statistical method to data and to draw the wrong conclusions from an experiment. The purpose of this book, which has its origin in a series of articles published in the Society for Applied Microbiology journal ‘The Microbiologist’, is an attempt to present the basic logic of statistics as clearly as possible and therefore, to dispel some of the myths that often surround the subject. The 28 ‘Statnotes’ deal with various topics that are likely to be encountered, including the nature of variables, the comparison of means of two or more groups, non-parametric statistics, analysis of variance, correlating variables, and more complex methods such as multiple linear regression and principal components analysis. In each case, the relevant statistical method is illustrated with examples drawn from experiments in microbiological research. The text incorporates a glossary of the most commonly used statistical terms and there are two appendices designed to aid the investigator in the selection of the most appropriate test.

A tale of two analyses: the use of archived qualitative data

This article provides a unique contribution to the debates about archived qualitative data by drawing on two uses of the same data - British Migrants in Spain: the Extent and Nature of Social Integration, 2003-2005 - by Jones (2009) and Oliver and O'Reilly (2010), both of which utilise Bourdieu's concepts analytically and produce broadly similar findings. We argue that whilst the insights and experiences of those researchers directly involved in data collection are important resources for developing contextual knowledge used in data analysis, other kinds of critical distance can also facilitate credible data use. We therefore challenge the assumption that the idiosyncratic relationship between context, reflexivity and interpretation limits the future use of data. Moreover, regardless of the complex genealogy of the data itself, given the number of contingencies shaping the qualitative research process and thus the potential for partial or inaccurate interpretation, contextual familiarity need not be privileged over other aspects of qualitative praxis such as sustained theoretical insight, sociological imagination and methodological rigour. © Sociological Research Online, 1996-2012.

Efficacy and safety of second-generation antipsychotic long-acting injections (SGA LAIs) in maintenance treatment of bipolar disorder:protocol for a systematic review and meta-analysis

INTRODUCTION: Bipolar disorder requires long-term treatment but non-adherence is a common problem. Antipsychotic long-acting injections (LAIs) have been suggested to improve adherence but none are licensed in the UK for bipolar. However, the use of second-generation antipsychotics (SGA) LAIs in bipolar is not uncommon albeit there is a lack of systematic review in this area. This study aims to systematically review safety and efficacy of SGA LAIs in the maintenance treatment of bipolar disorder. METHODS AND ANALYSIS: The protocol is based on Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) and will include only randomised controlled trials comparing SGA LAIs in bipolar. PubMed, EMBASE, CINAHL, Cochrane Library (CENTRAL), PsychINFO, LiLACS, http://www.clinicaltrials.gov will be searched, with no language restriction, from 2000 to January 2016 as first SGA LAIs came to the market after 2000. Manufacturers of SGA LAIs will also be contacted. Primary efficacy outcome is relapse rate or delayed time to relapse or reduction in hospitalisation and primary safety outcomes are drop-out rates, all-cause discontinuation and discontinuation due to adverse events. Qualitative reporting of evidence will be based on 21 items listed on standards for reporting qualitative research (SRQR) focusing on study quality (assessed using the Jadad score, allocation concealment and data analysis), risk of bias and effect size. Publication bias will be assessed using funnel plots. If sufficient data are available meta-analysis will be performed with primary effect size as relative risk presented with 95% CI. Sensitivity analysis, conditional on number of studies and sample size, will be carried out on manic versus depressive symptoms and monotherapy versus adjunctive therapy.

Approximation of Experimental Data by Bezier Curves

Very often the experimental data are the realization of the process, fully determined by some unknown function, being distorted by hindrances. Treatment and experimental data analysis are substantially facilitated, if these data to represent as analytical expression. The experimental data processing algorithm and the example of using this algorithm for spectrographic analysis of oncologic preparations of blood is represented in this article.

Oxidiative lipidomics coming of age:advances in analysis of oxidized phospholipids in physiology and pathology

Significance: Oxidized phospholipids are now well-recognized as markers of biological oxidative stress and bioactive molecules with both pro-inflammatory and anti-inflammatory effects. While analytical methods continue to be developed for studies of generic lipid oxidation, mass spectrometry (MS) has underpinned the advances in knowledge of specific oxidized phospholipids by allowing their identification and characterization, and is responsible for the expansion of oxidative lipidomics. Recent Advances: Studies of oxidized phospholipids in biological samples, both from animal models and clinical samples, have been facilitated by the recent improvements in MS, especially targeted routines that depend on the fragmentation pattern of the parent molecular ion and improved resolution and mass accuracy. MS can be used to identify selectively individual compounds or groups of compounds with common features, which greatly improves the sensitivity and specificity of detection. Application of these methods have enabled important advances in understanding the mechanisms of inflammatory diseases such as atherosclerosis, steatohepatitis, leprosy and cystic fibrosis, and offer potential for developing biomarkers of molecular aspects of the diseases. Critical Issues and Future Directions: The future in this field will depend on development of improved MS technologies, such as ion mobility, novel enrichment methods and databases and software for data analysis, owing to the very large amount of data generated in these experiments. Imaging of oxidized phospholipids in tissue MS is an additional exciting direction emerging that can be expected to advance understanding of physiology and disease.

Analyzing the Data in OLAP Data Cubes

* Supported partially by the Bulgarian National Science Fund under Grant MM-1405/2004

XML Presentation of Documents Used for Data Exchange in Management of Genetic Resources

In the global strategy for preservation genetic resources of farm animals the implementation of information technology is of great importance. In this regards platform independent information tools and approaches for data exchange are needed in order to obtain aggregate values for regions and countries of spreading a separate breed. The current paper presents a XML based solution for data exchange in management genetic resources of farm animals’ small populations. There are specific requirements to the exchanged documents that come from the goal of data analysis. Three main types of documents are distinguished and their XML formats are discussed. DTD and XML Schema for each type are suggested. Some examples of XML documents are given also.

Algorithms for Data Flows

* The research was supported by INTAS 00-397 and 00-626 Projects.

Cluster Analysis of Some Clases of Objects by Application of the Test Recognition Algorithms

The paper treats the task for cluster analysis of a given assembly of objects on the basis of the information contained in the description table of these objects. Various methods of cluster analysis are briefly considered. Heuristic method and rules for classification of the given assembly of objects are presented for the cases when their division into classes and the number of classes is not known. The algorithm is checked by a test example and two program products (PP) – learning systems and software for company management. Analysis of the results is presented.

Application of Regularized Discriminant Analysis

2000 Mathematics Subject Classification: 62H30, 62P99

Manageable Workflows for Processing Parallel Sequencing Data

ACM Computing Classification System (1998): D.2.11, D.1.3, D.3.1, J.3, C.2.4.

Integration of Satellite and Financial Data to Model Future Economic Impact of Citrus Crops (Final Project Report)

This study analyzed the health and overall landcover of citrus crops in Florida. The analysis was completed using Landsat satellite imagery available free of charge from the University of Maryland Global Landcover Change Facility. The project hypothesized that combining citrus production (economic) data with citrus area per county derived from spectral signatures would yield correlations between observable spectral reflectance throughout the year, and the fiscal impact of citrus on local economies. A positive correlation between these two data types would allow us to predict the economic impact of citrus using spectral data analysis to determine final crop harvests.

A qualitative analysis of the congruency of Jungian psychological preferences identified by the Myers-Briggs Type Indicator (MBTI) and the human resource development role of instructor/facilitator

The purpose of this ethnographic study was to describe and explain the congruency of psychological preferences identified by the Myers-Briggs Type Indicator (MBTI) and the human resource development (HRD) role of instructor/facilitator. This investigation was conducted with 23 HRD professionals who worked in the Miami, Florida area as instructors/facilitators with adult learners in job-related contexts.^ The study was conducted using qualitative strategies of data collection and analysis. The research participants were selected through a purposive sampling strategy. Data collection strategies included: (a) administration and scoring of the MBTI, Form G, (b) open-ended and semi-structured interviews, (c) participant observations of the research subjects at their respective work sites and while conducting training sessions, (d) field notes, and (e) contact summary sheets to record field research encounters. Data analysis was conducted with the use of a computer program for qualitative analysis called FolioViews 3.1 for Windows. This included: (a) coding of transcribed interviews and field notes, (b) theme analysis, (c) memoing, and (d) cross-case analysis.^ The three major themes that emerged in relation to the congruency of psychological preferences and the role of instructor/facilitator were: (1) designing and preparing instruction/facilitation, (2) conducting training and managing group process, and (3) interpersonal relations and perspectives among instructors/facilitators.^ The first two themes were analyzed through the combination of the four Jungian personality functions. These combinations are: sensing-thinking (ST), sensing-feeling (SF), intuition-thinking (NT), and intuition-feeling (NF). The third theme was analyzed through the combination of the attitudes or energy focus and the judgment function. These combinations are: extraversion-thinking (ET), extraversion-feeling (EF), introversion-thinking (IT), and introversion-feeling (IF).^ A last area uncovered by this ethnographic study was the influence exerted by a training and development culture on the instructor/facilitator role. This professional culture is described and explained in terms of the shared values and expectations reported by the study respondents. ^

A qualitative analysis of the lived experience of nursing staff developers in the process of changing to a new educational model

The purpose of this study was to document and critically analyze the lived experience of selected nursing staff developers in the process of moving toward a new model for hospital nursing education. Eleven respondents were drawn from a nation-wide population of about two hundred individuals involved in nursing staff development. These subjects were responsible for the implementation of the Performance Based Development System (PBDS) in their institutions.^ A purposive, criterion-based sampling technique was used with respondents being selected according to size of hospital, primary responsibility for orchestration of the change, influence over budgetary factors and managerial responsibility for PBDS. Data were gathered by the researcher through both in-person and telephone interviews. A semi-structured interview guide, designed by the researcher was used, and respondents were encouraged to amplify on their recollections as desired. Audiotapes were transcribed and resulting computer files were analyzed using the program "Martin". Answers to interview questions were compiled and reported across cases. The data was then reviewed a second time and interpreted for emerging themes and patterns.^ Two types of verification were used in the study. Internal verification was done through interview transcript review and feedback by respondents. External verification was done through review and feedback on data analysis by readers who were experienced in management of staff development departments.^ All respondents were female, so Gilligan's concept of the "ethic of care" was examined as a decision making strategy. Three levels of caring which influenced decision making were found. They were caring: (a) for the organization, (b) for the employee, and (c) for the patient. The four existentials of the lived experience, relationality, corporeality, temporality and spatiality were also examined to reveal the everydayness of making change. ^

Elemental analysis of glass and ink by laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) and laser induced breakdown spectroscopy (LIBS)

The necessity of elemental analysis techniques to solve forensic problems continues to expand as the samples collected from crime scenes grow in complexity. Laser ablation ICP-MS (LA-ICP-MS) has been shown to provide a high degree of discrimination between samples that originate from different sources. In the first part of this research, two laser ablation ICP-MS systems were compared, one using a nanosecond laser and another a femtosecond laser source for the forensic analysis of glass. The results showed that femtosecond LA-ICP-MS did not provide significant improvements in terms of accuracy, precision and discrimination, however femtosecond LA-ICP-MS did provide lower detection limits. In addition, it was determined that even for femtosecond LA-ICP-MS an internal standard should be utilized to obtain accurate analytical results for glass analyses. In the second part, a method using laser induced breakdown spectroscopy (LIBS) for the forensic analysis of glass was shown to provide excellent discrimination for a glass set consisting of 41 automotive fragments. The discrimination power was compared to two of the leading elemental analysis techniques, μXRF and LA-ICP-MS, and the results were similar; all methods generated >99% discrimination and the pairs found indistinguishable were similar. An extensive data analysis approach for LIBS glass analyses was developed to minimize Type I and II errors en route to a recommendation of 10 ratios to be used for glass comparisons. Finally, a LA-ICP-MS method for the qualitative analysis and discrimination of gel ink sources was developed and tested for a set of ink samples. In the first discrimination study, qualitative analysis was used to obtain 95.6% discrimination for a blind study consisting of 45 black gel ink samples provided by the United States Secret Service. A 0.4% false exclusion (Type I) error rate and a 3.9% false inclusion (Type II) error rate was obtained for this discrimination study. In the second discrimination study, 99% discrimination power was achieved for a black gel ink pen set consisting of 24 self collected samples. The two pairs found to be indistinguishable came from the same source of origin (the same manufacturer and type of pen purchased in different locations). It was also found that gel ink from the same pen, regardless of the age, was indistinguishable as were gel ink pens (four pens) originating from the same pack.