DiveRsity: An R package for the estimation and exploration of population genetics parameters and their associated errors

Summary: We present a new R package, diveRsity, for the calculation of various diversity statistics, including common diversity partitioning statistics (?, G) and population differentiation statistics (D, GST ', ? test for population heterogeneity), among others. The package calculates these estimators along with their respective bootstrapped confidence intervals for loci, sample population pairwise and global levels. Various plotting tools are also provided for a visual evaluation of estimated values, allowing users to critically assess the validity and significance of statistical tests from a biological perspective. diveRsity has a set of unique features, which facilitate the use of an informed framework for assessing the validity of the use of traditional F-statistics for the inference of demography, with reference to specific marker types, particularly focusing on highly polymorphic microsatellite loci. However, the package can be readily used for other co-dominant marker types (e.g. allozymes, SNPs). Detailed examples of usage and descriptions of package capabilities are provided. The examples demonstrate useful strategies for the exploration of data and interpretation of results generated by diveRsity. Additional online resources for the package are also described, including a GUI web app version intended for those with more limited experience using R for statistical analysis. © 2013 British Ecological Society.

Statistics sunspots and settlement: Influences on sum of probability curves

Large data sets of radiocarbon dates are becoming a more common feature of archaeological research. The sheer numbers of radiocarbon dates produced, however, raise issues of representation and interpretation. This paper presents a methodology which both reduces the visible impact of dating fluctuations, but also takes into consideration the influence of the underlying radiocarbon calibration curve. By doing so, it may be possible to distinguish between periods of human activity in early medieval Ireland and the statistical tails produced by radiocarbon calibration.

Extremely Complex Populations of Small RNAs in the Mouse Retina and RPE/Choroid

Purpose: MicroRNAs (miRNAs) are small non-coding RNAs of ~18-22 nucleotides in length that regulate gene expression. They are widely expressed in the retina, being both required for its normal development and perturbed in disease. The aim of this study was to apply new high-throughput sequencing techniques to more fully characterise the microRNAs and other small RNAs expressed in the retina and retinal pigment epithelium (RPE)/choroid of the mouse.

Methods: Retina and RPE/choroid were dissected from eyes of 3 month-old C57BL/6J mice. Small RNA libraries were prepared and deep sequencing performed on a Genome Analyzer (Illumina). Reads were annotated by alignment to miRBase, other non-coding RNA databases and the mouse genome.

Results: Annotation of 9 million reads to 320 microRNAs in retina and 340 in RPE/choroid provides the most comprehensive profiling of microRNAs to date. Two novel microRNAs were identified in retina. Members of the sensory organ specific miR-183,-182,-96 cluster were amongst the most highly expressed, retina-enriched microRNAs. Remarkably, microRNA 'isomiRs', which vary slightly in length and are differentially detected by Taqman RT-PCR assays, existed for all the microRNAs identified in both tissues. More variation occurred at the 3' ends, including non-templated additions of T and A. Drosha-independent mirtron microRNAs and other small RNAs derived from snoRNAs were also detected.

Conclusions: Deep sequencing has revealed the complexity of small RNA expression in the mouse retina and RPE/choroid. This knowledge will improve the design and interpretation of future functional studies of the role of microRNAs and other small RNAs in retinal disease.

Scientific standards for human intervention trials evaluating health benefits of foods, and their application to infants, children and adolescents

Associations between the consumption of particular foods and health outcomes may be indicated by observational studies. However, intervention trials that evaluate the health benefits of foods provide the strongest evidence to support dietary recommendations for health. Thus, it is important that these trials are carried out safely, and to high scientific standards. Accepted standards for the reporting of the health benefits of pharmaceutical and other medical interventions have been provided by the Consolidated Standards of Reporting Trials (CONSORT) statement. However, there are no generally accepted standards for trials to evaluate the health benefits of foods. Trials with foods differ from medical trials in issues related to safety, ethics, research governance and practical implementation. Furthermore, these important issues can deter the conduct of both medical and nutrition trials in infants, children and adolescents. This paper provides standards for the planning, design, conduct, statistical analysis and interpretation of human intervention trials to evaluate the health benefits of foods that are based on the CONSORT guidelines, and outlines the key issues that need to be addressed in trials in participants in the paediatric age range.

Doing Focus Groups and Interviews with Recent Migrants to Northern Ireland: A Dynamic Interplay of Ethics, Language and Access

This case describes a qualitative social science research project that was conducted in 2009 and that examined the experiences of recent migrants to Northern Ireland. While background to the research and key findings are presented, the topic forms a backdrop to the case. The following aspects of the study are presented: the theoretical context; formulating the research question, design and methodology; key methodological issues; data collection and analysis; project dissemination; and research funding and reporting. The case pays particular attention to the needs and impact of different groups including the researcher, the funding body, the researcher’s employer and the researched. The significance of access, language and ethics to this study are examined. Finally, the way in which the research unfolded in an often-unpredictable way throughout the implementation process is highlighted in the narrative.

RAS testing of colorectal carcinoma—a guidance document from the Association of Clinical Pathologists Molecular Pathology and Diagnostics Group

Analysis of colorectal carcinoma (CRC) tissue for KRAS codon 12 or 13 mutations to guide use of anti-epidermal growth factor receptor (EGFR) therapy is now considered mandatory in the UK. The scope of this practice has been recently extended because of data indicating that NRAS mutations and additional KRAS mutations also predict for poor response to anti-EGFR therapy. The following document provides guidance on RAS (i.e., KRAS and NRAS) testing of CRC tissue in the setting of personalised medicine within the UK and particularly within the NHS. This guidance covers issues related to case selection, preanalytical aspects, analysis and interpretation of such RAS testing.

From the past to the Future: integrating archaeology and conflict resolution in Northern Ireland

Contested understandings about the past continue to reify the divided character of post-Troubles Northern Ireland. In particular, the unresolved legacies of the extension of English control over Ireland in the late sixteenth and early seventeenth centuries through warfare and plantation continue to structure daily lives in the province. Yet the archaeological record of this period complicates the accepted dichotomous narratives through highlighting complexity. These nuances, however, have been lost in recent decades as an overly simplistic model of colonizer versus colonized has emerged as the dominant political paradigm. The management and presentation of sites associated with the process of plantation can arguably create the space necessary to bridge the divide, and to challenge accepted understandings. Cross-community engagement in the process of archaeological discovery and interpretation on plantation-period sites in Northern Ireland highlights the critical role archaeology can play in peace and reconciliation in post-conflict societies.

How individual participant data meta-analyses have influenced trial design, conduct, and analysis

OBJECTIVES: To demonstrate how individual participant data (IPD) meta-analyses have impacted directly on the design and conduct of trials and highlight other advantages IPD might offer.

STUDY DESIGN AND SETTING: Potential examples of the impact of IPD meta-analyses on trials were identified at an international workshop, attended by individuals with experience in the conduct of IPD meta-analyses and knowledge of trials in their respective clinical areas. Experts in the field who did not attend were asked to provide any further examples. We then examined relevant trial protocols, publications, and Web sites to verify the impacts of the IPD meta-analyses. A subgroup of workshop attendees sought further examples and identified other aspects of trial design and conduct that may inform IPD meta-analyses.

RESULTS: We identified 52 examples of IPD meta-analyses thought to have had a direct impact on the design or conduct of trials. After screening relevant trial protocols and publications, we identified 28 instances where IPD meta-analyses had clearly impacted on trials. They have influenced the selection of comparators and participants, sample size calculations, analysis and interpretation of subsequent trials, and the conduct and analysis of ongoing trials, sometimes in ways that would not possible with systematic reviews of aggregate data. We identified additional potential ways that IPD meta-analyses could be used to influence trials.

CONCLUSIONS: IPD meta-analysis could be better used to inform the design, conduct, analysis, and interpretation of trials.

Physical rehabilitation interventions for adult intensive care patients across the continuum of recovery (i.e. within the intensive care unit (ICU) and following ICU and hospital discharge): an overview of systematic reviews

Background
Patients admitted to the intensive care unit with critical illness often experience significant physical impairments, which typically persist for many years following resolution of the original illness. Physical rehabilitation interventions that enhance restoration of physical function have been evaluated across the continuum of recovery following critical illness including within the intensive care unit, following discharge to the ward and beyond hospital discharge. Multiple systematic reviews have been published appraising the expanding evidence investigating these physical rehabilitation interventions, although there appears to be variability in review methodology and quality. We aim to conduct an overview of existing systematic reviews of physical rehabilitation interventions for adult intensive care patients across the continuum of recovery.

Methods/design
This protocol has been developed according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses Protocol (PRISMA-P) guidelines. We will search the Cochrane Systematic Review Database, Database of Abstracts of Reviews of Effectiveness, Cochrane Central Register of Controlled Trials, MEDLINE, Excerpta Medica Database and Cumulative Index to Nursing and Allied Health Literature databases. We will include systematic reviews of randomised controlled trials of adult patients, admitted to the intensive care unit and who have received physical rehabilitation interventions at any time point during their recovery. Data extraction will include systematic review aims and rationale, study types, populations, interventions, comparators, outcomes and quality appraisal method. Primary outcomes of interest will focus on findings reflecting recovery of physical function. Quality of reporting and methodological quality will be appraised using the PRISMA checklist and the Assessment of Multiple Systematic Reviews tool.

Discussion
We anticipate the findings from this novel overview of systematic reviews will contribute to the synthesis and interpretation of existing evidence regarding physical rehabilitation interventions and physical recovery in post-critical illness patients across the continuum of recovery.

Methodologic rigor of clinical trials on surgical management of eyes with coexisting cataract and glaucoma.

OBJECTIVE:

To assess the methodologic quality of published studies of the surgical management of coexisting cataract and glaucoma.

DESIGN:

Literature review and analysis.

METHOD:

We performed a systematic search of the literature to identify all English language articles pertaining to the surgical management of coexisting cataract and glaucoma in adults. Quality assessment was performed on all randomized controlled trials, nonrandomized controlled trials, and cohort studies. Overall quality scores and scores for individual methodologic domains were based on the evaluations of two experienced investigators who independently reviewed articles using an objective quality assessment form.

MAIN OUTCOME MEASURES:

Quality in each of five domains (representativeness, bias and confounding, intervention description, outcomes and follow-up, and statistical quality and interpretation) measured as the percentage of methodologic criteria met by each study.

RESULTS:

Thirty-six randomized controlled trials and 45 other studies were evaluated. The mean quality score for the randomized, controlled clinical trials was 63% (range, 11%-88%), and for the other studies the score was 45% (range, 3%-83%). The mean domain scores were 65% for description of therapy (range, 0%-100%), 62% for statistical analysis (range, 0%-100%), 58% for representativeness (range, 0%-94%), 49% for outcomes assessment (range, 0%-83%), and 30% for bias and confounding (range, 0%-83%). Twenty-five of the studies (31%) received a score of 0% in the bias and confounding domain for not randomizing patients, not masking the observers to treatment group, and not having equivalent groups at baseline.

CONCLUSIONS:

Greater methodologic rigor and more detailed reporting of study results, particularly in the area of bias and confounding, could improve the quality of published clinical studies assessing the surgical management of coexisting cataract and glaucoma.

Searching for the IRA 'disappeared': Ground-penetrating radar investigation of a churchyard burial site, Northern Ireland

A search for the body of a victim of terrorist abduction and murder was made in a graveyard on the periphery of a major conurbation in Northern Ireland. The area is politically sensitive and the case of high profile. This required non-invasive, completely non-destructive and rapid assessment of the scene. A MALA RAMAC ground-penetrating radar system was used to achieve these objectives. Unprocessed and processed 400MHz data shows the presence of a collapse feature above and around a known 1970s burial with no similar collapse above the suspect location. In the saturated, clay-rich sediments of the site, 200MHz data offered no advantage over 400MHz data. Unprocessed 100MHz data shows a series of multiples in the known burial with no similar features in the suspect location. Processed 100MHz lines defined the shape of the collapse around the known burial to 2m depth, together with the geometry of the platform (1m depth) the gravedigger used in the 1970s to construct the site. In addition, processed 100MHz data showed both the dielectric contrast in and internal reflection geometry of the soil imported above the known grave. Thus the sequence, geometry, difference in infill and infill direction of the grave was reconstructed 30 years after burial. The suspect site showed no evidence of shallow or deep inhumation. Subsequently, the missing person������¢���¯���¿���½���¯���¿���½s body was found some distance from this site, vindicating the results and interpretation from ground-penetrating radar. The acquisition, processing, collapse feature and sequence stratigraphic interpretation of the known burial and empty (suspect) burial site may be useful proxies for other, similar investigations. GPR was used to evaluate this site within 3 hours of the survey commencing, using unprocessed data. An additional day of processing established that the suspect body did not reside here, which was counter to police and community intelligence.

Uniplanar left-handed artificial metamaterials

Planar periodic arrays of metallic elements printed on grounded dielectric substrates are presented to exhibit left-handed properties for surface wave propagation. The proposed structures dispense with the need for grounding vias and ease the implementation of uniplanar left-handed metamaterials at higher frequencies. A transmission line description is used for the initial design and interpretation of the left-handed property. A thorough study based on full wave simulations is carried out with regards to the effect of the element geometrical characteristics and the array periodicity to the properties of the artificial material. Dispersion curves are presented and studied. The distribution of the modal fields in the unit cell is also studied in order to provide an explanation of the material properties. The scalability of the proposed structures to infrared frequencies is demonstrated.

So mechanical or routine: The not original in Feist

The United States Supreme Court case of 1991, Feist Publications, Inc. v. Rural Tel. Service Co., continues to be highly significant for property in data and databases, but remains poorly understood. The approach taken in this article contrasts with previous studies. It focuses upon the “not original” rather than the original. The delineation of the absence of a modicum of creativity in selection, coordination, and arrangement of data as a component of the not original forms a pivotal point in the Supreme Court decision. The author also aims at elucidation rather than critique, using close textual exegesis of the Supreme Court decision. The results of the exegesis are translated into a more formal logical form to enhance clarity and rigor.


The insufficiently creative is initially characterized as “so mechanical or routine.” Mechanical and routine are understood in their ordinary discourse senses, as a conjunction or as connected by AND, and as the central clause. Subsequent clauses amplify the senses of mechanical and routine without disturbing their conjunction.


The delineation of the absence of a modicum of creativity can be correlated with classic conceptions of computability. The insufficiently creative can then be understood as a routine selection, coordination, or arrangement produced by an automatic mechanical procedure or algorithm. An understanding of a modicum of creativity and of copyright law is also indicated.


The value of the exegesis and interpretation is identified as its final simplicity, clarity, comprehensiveness, and potential practical utility.