MNE software for processing MEG and EEG data

Magnetoencephalography and electroencephalography (M/EEG) measure the weak electromagnetic signals generated by neuronal activity in the brain. Using these signals to characterize and locate neural activation in the brain is a challenge that requires expertise in physics, signal processing, statistics, and numerical methods. As part of the MNE software suite, MNE-Python is an open-source software package that addresses this challenge by providing state-of-the-art algorithms implemented in Python that cover multiple methods of data preprocessing, source localization, statistical analysis, and estimation of functional connectivity between distributed brain regions. All algorithms and utility functions are implemented in a consistent manner with well-documented interfaces, enabling users to create M/EEG data analysis pipelines by writing Python scripts. Moreover, MNE-Python is tightly integrated with the core Python libraries for scientific comptutation (NumPy, SciPy) and visualization (matplotlib and Mayavi), as well as the greater neuroimaging ecosystem in Python via the Nibabel package. The code is provided under the new BSD license allowing code reuse, even in commercial products. Although MNE-Python has only been under heavy development for a couple of years, it has rapidly evolved with expanded analysis capabilities and pedagogical tutorials because multiple labs have collaborated during code development to help share best practices. MNE-Python also gives easy access to preprocessed datasets, helping users to get started quickly and facilitating reproducibility of methods by other researchers. Full documentation, including dozens of examples, is available at http://martinos.org/mne.

MEG and EEG data analysis with MNE-Python

Bloodstream infections by Salmonella enterica serovar Typhimurium constitute a major health burden in sub-Saharan Africa (SSA). These invasive non-typhoidal (iNTS) infections are dominated by isolates of the antibiotic resistance-associated sequence type (ST) 313. Here, we report emergence of ST313 sublineage II.1 in the Democratic Republic of the Congo. Sublineage II.1 exhibits extensive drug resistance, involving a combination of multidrug resistance, extended spectrum β-lactamase production and azithromycin resistance. ST313 lineage II.1 isolates harbour an IncHI2 plasmid we name pSTm-ST313-II.1, with one isolate also exhibiting decreased ciprofloxacin susceptibility. Whole genome sequencing reveals that ST313 II.1 isolates have accumulated genetic signatures potentially associated with altered pathogenicity and host adaptation, related to changes observed in biofilm formation and metabolic capacity. Sublineage II.1 emerged at the beginning of the 21st century and is involved in on-going outbreaks. Our data provide evidence of further evolution within the ST313 clade associated with iNTS in SSA.

/pdf/an-african-salmonella-typhimurium-st313-sublineage-with-3mr9u57h81.pdf

An African Salmonella Typhimurium ST313 sublineage with extensive drug-resistance and signatures of host adaptation.

Recent data on conventional bike and/or electric bike (e-bike) sharing systems reveal that more than 2900 systems are operating in cities worldwide, indicating the increased adoption of this alternative mode of transportation. Addressing the existing gap in the literature regarding the deployment of e-bike sharing systems (e-BSSs) in particular, this paper reviews their spatio-temporal characteristics, and attempts to (a) map the worldwide distribution of e-BSSs, (b) identify temporal trends in terms of annual growth/expansion of e-BSS deployment worldwide and (c) explore the spatial characteristics of the recorded growth, in terms of adoption on a country scale, population coverage and type of system/initial fleet sizes. To that end, it examines the patterns identified from the global to the country level, based on data collected from an online source of BSS information worldwide. A comparative analysis is performed with a focus on Europe, North America and Asia, providing insights on the growth rate of the specific bikesharing market segment. Although the dockless e-BSS has been only within three years of competition with station-based implementations, it shows a rapid integration to the overall technology diffusion trend, while it is more established in Asia and North America in comparison with Europe and launches with larger fleet sizes.

/pdf/spatio-temporal-trends-of-e-bike-sharing-system-deployment-a-8w764msqvr.pdf

Spatio-Temporal Trends of E-Bike Sharing System Deployment: A Review in Europe, North America and Asia

Software for complex problem solving can dazzle people with advanced features and alluring visuals, but when actually put to use it often disappoints and even frustrates users. This software rarely follows the user's own work methods, nor does it give people the degree of control and choice that they truly need.

This book presents a groundbreaking approach to interaction design for complex problem solving applications. The author uses her vast field experience to present a new way of looking at the whole process, and treats complex problem solving software and web applications as a distinct class with its own set of usefulness demands and design criteria. This approach highlights integrated interactions rather than discrete actions, clearly defines what makes problem solving complex, and explores strategies for analyzing, modeling, and designing for exploratory inquiries.

?In depth case studies ranging from IT troubleshooting to marketing analysis to risk assessments in healthcare show exactly where and what goes wrong in real world activities and how to improve them.

?Presents a system and framework for analyzing complex work and takes the mystery out of eliciting patterns of work and their meanings.

?Offers new perspectives for support and new design strategies for building the right models into programs so that they effectively address users' dynamic work. 

?Allows designers to turn findings into useful designs for problems that require users to create new knowledge but with no one right answer and with many methods of reaching solutions.

Table of Contents

Preface
Introduction
Part One - Understanding the Work
1 What Makes Complex Problem Solving Complex?
2 Usefulness: Focusing on Inquiry Patterns, Task Landscapes, and Core Activities
3 Filling in the Gaps: Integrating Usefulness Into User-Centered Design
Part Two - Solving Problems in Technical, Social, and Co-emergent Systems
4 Keeping the System Up and Running
5 Getting IT Right
6 Criteria, Constraints, and Choices for Optimizing the Mix
7 Examining Design Strategies and Choices for Optimizing the Mix
8 Decision-Making in Complex Socio-Technical Systems of Patient Care
9 Designing for Usefulness Across Cases
Part Three - Thinking Strategically
10 Next Steps: Politics and Positioning of Usefulness
Appendix A

Interaction Design for Complex Problem Solving: Developing Useful and Usable Software

The map() function in S permits a wide range of line and filled area maps to be drawn for use with map-oriented data analysis. The data underlying these maps is stored in a geographical database. This report describes the format of the geographical database and the steps involved in constructing one. The process is illustrated by our experience in creating a database for the coastlines and national political boundaries of the world. The world database allows data to be displayed on a map of the entire world or on smaller subsets such as Europe or individual countries. The data comes from the World Data Bank II (US Dept. of Commerce) but we have performed edits to correct digitizing errors and have added accurate descriptions of the polygonal regions that make up each country. Because the database contains polygonal information, choropleth maps can be drawn that use data values to control the color of regions, and because it is so detailed, maps can be made in a wide range of scales.

/pdf/constructing-a-geographical-database-30c2ibss9h.pdf

Constructing a Geographical Database

/pdf/a-tour-of-trellis-graphics-3jqs8svs0v.pdf

A Tour of Trellis Graphics

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Constructing a Geographical Database

A Tour of Trellis Graphics