DotMapper: an open source tool for creating interactive disease point maps

BACKGROUND: Molecular strain typing of tuberculosis isolates has led to increased understanding of the epidemiological characteristics of the disease and improvements in its control, diagnosis and treatment. However, molecular cluster investigations, which aim to detect previously unidentified cases, remain challenging. Interactive dot mapping is a simple approach which could aid investigations by highlighting cases likely to share epidemiological links. Current tools generally require technical expertise or lack interactivity. RESULTS: We designed a flexible application for producing disease dot maps using Shiny, a web application framework for the statistical software, R. The application displays locations of cases on an interactive map colour coded according to levels of categorical variables such as demographics and risk factors. Cases can be filtered by selecting combinations of these characteristics and by notification date. It can be used to rapidly identify geographic patterns amongst cases in molecular clusters of tuberculosis in space and time; generate hypotheses about disease transmission; identify outliers, and guide targeted control measures. CONCLUSIONS: DotMapper is a user-friendly application which enables rapid production of maps displaying locations of cases and their epidemiological characteristics without the need for specialist training in geographic information systems. Enhanced understanding of tuberculosis transmission using this application could facilitate improved detection of cases with epidemiological links and therefore lessen the public health impacts of the disease. It is a flexible system and also has broad international potential application to other investigations using geo-coded health information

A comparative analysis of single cell small RNA sequencing data reveals heterogeneous isomiR expression and regulation.

MicroRNAs (miRNAs) are non-coding small RNAs which play a critical role in the regulation of gene expression in cells. It is known that miRNAs are often expressed as multiple isoforms, called isomiRs, which may have alternative regulatory functions. Despite the recent development of several single cell small RNA sequencing protocols, these methods have not been leveraged to investigate isomiR expression and regulation to better understand their role on a single cell level. Here we integrate sequencing data from three independent studies and find substantial differences in isomiR composition that suggest that cell autonomous mechanisms may drive isomiR processing. We also find evidence of altered regulatory functions of different classes of isomiRs, when compared to their respective wild-type miRNA, which supports a biological role for many of the isomiRs that are expressed

Experimental techniques for ductile damage characterisation

Ductile damage in metallic materials is caused by the nucleation, growth and coalesce of voids and micro-cracks in the metal matrix when it is subjected to plastic strain. A considerable number of models have been proposed to represent ductile failure focusing on the ultimate failure conditions; however, only some of them study in detail the whole damage accumulation process. The aim of this work is to review experimental techniques developed by various authors to measure the accumulation of ductile damage under tensile loads. The measurement methods reviewed include: stiffness degradation, indentation, microstructure analysis, ultrasonic waves propagation, X-ray tomography and electrical potential drop. Stiffness degradation and indentation techniques have been tested on stainless steel 304L hourglass-shaped samples. A special interest is placed in the Continuum Damage Mechanics approach (CDM) as its equations incorporate macroscopic parameters that can represent directly the damage accumulation measured in the experiments. The other main objective lies in identifying the strengths and weaknesses of each technique for the assessment of materials subjected to different strain-rate and temperature conditions

Demonstration of astrocytes in cultured amniotic fluid cells of three cases with neural-tube defect

We have investigated the origin of rapidly adhering (RA) cells in three cases of neural tube defects (two anencephali, one encephalocele). We were able to demonstrate the presence of glial fibrillary acidic (GFA) protein in variable percentages (4–80%) of RA cells cultured for 4–6 days by use of indirect immunofluorescence with GFA antiserum. Cells cultured from amniotic fluids of normal pregnancies and fetal fibroblasts were completely GFA protein negative. GFA protein is well established as a highly specific marker for astrocytes. Demonstration of astrocytes may prove to be a criterion of high diagnostic value for neural tube defects. The percentage of astrocytes decreased with increasing culture time, while the percentage of fibronectin positive cells increased both in amniotic fluid cell cultures from neural tube defects and normal pregnancies

Kronian Magnetospheric Reconnection Statistics Across Cassini's Lifetime

Magnetic reconnection is a fundamental physical process in planetary magnetospheres, in which plasma can be exchanged between the solar wind and a planetary magnetosphere, and material can be disconnected and ultimately lost from a magnetosphere. Magnetic reconnection in a planetary magnetotail can result in the release of plasmoids downtail and dipolarizations planetward of an x-line. The signatures of these products include characteristic deflections in the north-south component of the magnetic field which can be detected by in-situ spacecraft. These signatures have been identified by eye, semi-automated algorithms, and recently machine learning methods. Here, we apply statistical analysis to the most thorough catalogue of Kronian magnetospheric reconnection signatures created through machine learning methods to improve understanding of magnetospheric evolution. This research concludes that no quasi-steady position of the magnetotail x-line exists within 70 RS. This research introduces prediction equations to estimate the distribution of duration of plasmoid passage over the spacecraft (N = 300∆t −1.3 , bin width = 1 min) and north-south field deflection (N = 52∆B −2.1 θ , bin width = 0.25 nT) expected to be identified by an orbiting spacecraft across a year of observations. Furthermore, this research finds a local time asymmetry for reconnection identifications, with a preference for dusk-side over dawn-side. This may indicate a preference for Vasyliunas style reconnection over Dungey style for Saturn. Finally, through these distributions, the reconnection rate of Saturn’s magnetotail can be estimated as 3.22 reconnection events per day, with a resulting maximum mass loss from plasmoids of 44.87 kg s−1 on average, which is comparable with the magnetospheric mass loading from Enceladus (8-250 kg s−1 )

Hierarchical regression for epidemiologic analyses of multiple exposures.

Many epidemiologic investigations are designed to study the effects of multiple exposures. Most of these studies are analyzed either by fitting a risk-regression model with all exposures forced in the model, or by using a preliminary-testing algorithm, such as stepwise regression, to produce a smaller model. Research indicates that hierarchical modeling methods can outperform these conventional approaches. These methods are reviewed and compared to two hierarchical methods, empirical-Bayes regression and a variant here called "semi-Bayes" regression, to full-model maximum likelihood and to model reduction by preliminary testing. The performance of the methods in a problem of predicting neonatal-mortality rates are compared. Based on the literature to date, it is suggested that hierarchical methods should become part of the standard approaches to multiple-exposure studies

Nomadic ecology shaped the highland geography of Asia's Silk Roads

There are many unanswered questions about the evolution of the ancient 'Silk Roads' across Asia. This is especially the case in their mountainous stretches, where harsh terrain is seen as an impediment to travel. Considering the ecology and mobility of inner Asian mountain pastoralists, we use ‘flow accumulation’ modelling to calculate the annual routes of nomadic societies (from 750 m to 4,000 m elevation). Aggregating 500 iterations of the model reveals a high-resolution flow network that simulates how centuries of seasonal nomadic herding could shape discrete routes of connectivity across the mountains of Asia. We then compare the locations of known high-elevation Silk Road sites with the geography of these optimized herding flows, and find a significant correspondence in mountainous regions. Thus, we argue that highland Silk Road networks (from 750 m to 4,000 m) emerged slowly in relation to long-established mobility patterns of nomadic herders in the mountains of inner Asia

Latest climate models confirm need for urgent mitigation

Many recently updated climate models show greater future warming than previously. Separate lines of evidence suggest that their warming rates may be unrealistically high, but the risk of such eventualities only emphasizes the need for rapid and deep reductions in emissions