Open-source deep-learning software for bioimage segmentation

Microscopy images are rich in information about the dynamic relationships among biological structures. However, extracting this complex information can be challenging, especially when biological structures are closely packed, distinguished by texture rather than intensity, and/or low intensity relative to the background. By learning from large amounts of annotated data, deep learning can accomplish several previously intractable bioimage analysis tasks. Until the past few years, however, most deep-learning workflows required significant computational expertise to be applied. Here, we survey several new open-source software tools that aim to make deep-learning–based image segmentation accessible to biologists with limited computational experience. These tools take many different forms, such as web apps, plug-ins for existing imaging analysis software, and preconfigured interactive notebooks and pipelines. In addition to surveying these tools, we overview several challenges that remain in the field. We hope to expand awareness of the powerful deep-learning tools available to biologists for image analysis.     

Ecological Infrastructure as a framework for mapping ecosystem services for place-based conservation and management

Ecosystem services are an important nexus between people and nature. Nevertheless, their inclusion in place-based conservation and management is limited also because they are often intangible. The Ecological Infrastructure (EI) concept is a promising framework to address this, but a clear definition and mapping approach is still missing. We aim to analyse the uses of EI and to distil a definition and recommendations for using EI as a framework for mapping ecosystem services. A semi-systematic review of peer-reviewed and grey literature was conducted to examine: (1) perceptions of what constitutes EI (n = 117), and (2) EI mapping approaches (n = 51). The main interpretations of EI indicated that it should be natural or naturally functioning (56%); deliver multiple services (75%); and benefit humans (64%) and biodiversity (36%). EI was thus defined as ‘natural and naturally functioning ecological systems or networks of ecological systems that deliver multiple services to humans and enable biodiversity persistence’. Studies have used simple proxies, e.g., land cover, to identify EI, sometimes combined with service-specific variables. To evaluate EI performance (26% of studies), modelling all three ecosystem service aspects (capacity, flow, and demand) was considered appropriate. EI prioritisation (50% of studies) as part of a systematic spatial prioritisation process was recommended. Sixteen recommendations for mapping EI for inclusion in place-based conservation and management were developed. We illustrate how EI can be used to integrate ecosystem services into conservation and management in three real-world applications. The EI-based framework is a promising approach and supports the new ‘people and nature’ era in conservation.     

pyActigraphy: Open-source python package for actigraphy data visualization and analysis

Over the past 40 years, actigraphy has been used to study rest-activity patterns in circadian rhythm and sleep research. Furthermore, considering its simplicity of use, there is a growing interest in the analysis of large population-based samples, using actigraphy. Here, we introduce pyActigraphy, a comprehensive toolbox for data visualization and analysis including multiple sleep detection algorithms and rest-activity rhythm variables. This open-source python package implements methods to read multiple data formats, quantify various properties of rest-activity rhythms, visualize sleep agendas, automatically detect rest periods and perform more advanced signal processing analyses. The development of this package aims to pave the way towards the establishment of a comprehensive open-source software suite, supported by a community of both developers and researchers, that would provide all the necessary tools for in-depth and large scale actigraphy data analyses.     

Introducing accessibility analysis in mapping cultural ecosystem services

In recent years, there has been an increasing interest in the study of the spatial link between service providing areas (SPA) and service benefiting areas (SBA). Understanding the spatial link between SPAs and SBAs is essential when studying the ecosystem service delivery and the fulfilment of ecosystem service demand. However, far too little attention has been paid to the user movement related ecosystem services and where people should be geographically situated in order to benefit from these services. In the movement related services, benefiting areas are equal to providing areas and the spatial link from residential area to SPA is important. The spatial link is addressed through the concept of accessibility which determines the opportunity to move from the area where beneficiaries are located to areas where ecosystem services are produced.This study presents an accessibility approach to the ecosystem services research. Accessibility analyses offer an opportunity to identify the gap between the ecosystems’ potential to produce services and the actual usage possibilities of such services. We demonstrate the suitability of the method by using outdoor recreation and cultural heritage as examples of cultural ecosystem services that people actively want to reach. Accessibility was calculated using a geographical information system-based least-cost path analysis, which measures travel time by car between residential location and the nearest SPA via road network.The examples highlight that accessibility varies according to the ecosystem service and depends mostly on population distribution and travel possibilities. Our results demonstrate that the density of the analysed ecosystem service opportunities is higher near urban areas than elsewhere. The accessibility of different ecosystem services also depends on how much time people are willing to spend for reaching these services. Our study emphasised that, from a population perspective, accessibility analyses provide a powerful tool for illustrating the utilisation possibilities of spatially distributed ecosystem services. The accessibility approach offers great potential to assess the potential use of SPAs and respond to the need to develop a practical tool for ecosystem service research. It effectively shows, for example, the areas where the risk of overuse of ecosystem services is increased. Knowing about the regional differences in ecosystem service usage also gives background information for the decision-makers for drawing conclusions about how much and where it is sensible to invest in the maintenance of ecosystem services.     

China electrical manufacturing services industry value stream mapping collaboration

The paper analyzes the Electrical Manufacturing Services (EMS) industry’s current status in China, introduces a value stream mapping (VSM) collaboration tool which brings solid working process with agile information flow, and builds a theoretical foundation with a new management concept for China EMS to promote its integrated core competencies and to increase the market returns. VSM collaboration tools can be used across the electronics industry and other industries; it provides EMS the strategic advantages of a flexible, reactive system that agilely adapts to customers’ real-time needs, and builds EMS high profile with core competencies of being a strategic world-class performer.     

Single nucleotide polymorphisms in Cryptomeria japonica: their discovery and validation for genome mapping and diversity studies

In order to develop a large set of single-nucleotide polymorphisms (SNPs) in Cryptomeria japonica, for a wide range of applications, we adopted a systematic EST (expressed sequence tags) re-sequencing approach. We examined a group of four genotypes comprising parents of a mapping population as well as representatives of two main lines from natural populations. We sequenced 5,170 gene fragments, representing analysis of over 1.3?Mb of DNA sequences in C. japonica. This analysis leads to the discovery of 13,413 SNPs in 3,744 amplicons, with an average of one SNP for every 101.0?bp (one SNP for every 78.3?bp in introns and for every 106.7?bp in exon regions). Nucleotide diversity in C. japonica (???=?0.0045) was found to be similar to values recorded in highly polymorphic forest tree species such as pine. We also validated the use of the SNPs as molecular markers for genetic diversity studies using the high throughput SNP genotyping platform GoldenGate. From 1,536 candidate SNP sites tested, 1,164 (75.8?%) were confirmed to be polymorphic. We anticipate that the genome-wide SNP markers reported here will be useful for evaluating the species?? range-wide genetic structure and in marker-assisted selection used as part of the C. japonica tree improvement program.     

Challenges for mental health services raised by disaster preparedness: mapping the ethical and therapeutic terrain

Identifying vulnerable groups and ensuring that their needs are met during disasters--whether naturally occurring or manmade--are vital aspects of preparedness planning. Developing preparedness strategies that are responsive to those at greatest risk is a moral mandate, justified by the principles of beneficence, justice, and respect for autonomy. Individuals with preexisting mental disorders and newly emergent psychological symptoms are particularly vulnerable to adverse outcomes during and after disasters. Without advance planning, these individuals might not benefit from necessary mental health services and treatments during and after disasters. In this commentary, we discuss ethical issues that arise in emergency preparedness planning for vulnerable individuals with psychological and psychiatric conditions and disorders.     

Community mapping of ecosystem services in tropical rainforest of Ecuador

Tropical forests provide a wide range of ecosystem services (ES), and their continuous supply depends on efficient and effective management against deforestation and forest degradation. In Ecuador, indigenous communities are highly dependent on the forest and therefore on forest ES. However, there is a lack of knowledge about their demands concerning ES. In order to better understand how local and indigenous people use the forest and to facilitate its management, this study completed a spatially explicit assessment of ES using participatory mapping in the Sumaco Biosphere Reserve (Napo province, Central-Northern Ecuador). The Biosphere Reserve is suitable as a case study because it is a protected area with high land-use and population pressure and therefore requires the development and monitoring of management plans.First, semi-structured interviews were conducted with experts (n = 15) in order to identify the most important ES used by the communities in the study area. In a second step, members (n = 208) of 24 communities were asked to indicate on a 3-D map where they utilize the different ES (food, wood, water, tourism, hunting). The highlighted localities were digitized and then analyzed with statistical and GIS techniques. The results showed that the ES locations were not randomly distributed, but were most abundant four kilometers or less from roads. Spatial pattern analysis identified hotspots of ES provision, and the evaluation according to administrative units allowed us to identify five municipalities where demand for all assessed ES was high. In conclusion, the combination of participatory mapping of ES and GIS-based analysis can facilitate the identification of priority protection areas, provide guidance for developing specific forest management strategies, and also support monitoring systems to detect forest degradation.     

Characterization of 155 EST-derived microsatellites from Atlantic cod (Gadus morhua) and validation for linkage mapping

Microsatellite markers for Atlantic cod (Gadus morhua) were identified from a collection of 30 630 expressed sequence tags. Primers were designed for 395 microsatellites and 155 were successfully amplified. Allele number varied from 1 to 26 (average 6.34). Average observed and expected heterozygosities were 0.50 and 0.54, respectively. A subset of 105 microsatellites tested for Mendelian segregation showed no significant distortion of segregation when correcting for multiple tests. Null alleles were detected at four loci. Significant blastx matches were found for 23 loci. These microsatellites will be used to create a linkage map to enhance genetic selection in commercial cod breeding.     

Molecular mapping of the wheat powdery mildew resistance gene Pm24 and marker validation for molecular breeding

Molecular markers were identified in common wheat for the Pm24 locus conferring resistance to different isolates of the powdery mildew pathogen, Erysiphe graminis DM f. sp. tritici (Em. Marchal). Bulked segregant analysis was used to identify amplified fragment length polymorphism (AFLP) markers and microsatellite markers linked to the gene Pm24 in an F₂ progeny from the cross Chinese Spring (susceptible)× Chiyacao (resistant). Two AFLP markers XACA/CTA-407 and XACA/CCG-420, and three microsatellite markers Xgwm106, Xgwm337 and Xgwm458, were mapped in coupling phase to the Pm24 locus. The AFLP marker locus XACA/CTA-407 co-segregated with the Pm24 gene, and XACA/CCG-420 mapped 4.5 cM from this gene. Another AFLP marker locus XAAT/CCA-346 co- segregated in repulsion phase with the Pm24 locus. Pm24 was mapped close to the centromere on the short arm of chromosome 1D, contrary to the previously reported location on chromosome 6D. Pm24 segregated independently of gene Pm22, also located on chromosome 1D. An allele of microsatellite locus Xgwm337 located 2.4±1.2 cM from Pm24 was shown to be diagnostic and therefore potentially useful for pyramiding two or more genes for powdery mildew resistance in a single genotype. Received: 25 August 1999 / Accepted: 16 December 1999     

Identification of scapular kinematics using surface mapping: a validation study

The immediate goal of this study was to develop and validate a noninvasive, computational surface mapping approach for measuring scapular kinematics by using available motion capture technology in an innovative manner. The long-term goal is to facilitate clinical determination of the role of the scapula in children with brachial plexus birth palsy (BPBP). The population for this study consisted of fourteen healthy adults with prominent scapulae. Subject-specific scapular templates were created using the coordinates of five scapular landmarks obtained from palpation with subjects seated and arms relaxed in a neutral position. The scapular landmarks were re-palpated and their locations recorded in the six arm positions of the modified Mallet classification. The six Mallet positions were repeated with approximately 300 markers covering the scapula. The markers formed a surface map covering the tissue over the scapula. The scapular template created in the neutral position was iteratively fit to the surface map of each trial, providing an estimate of the orientation of the scapula. These estimates of scapular orientation were compared to the known scapular orientation determined from the scapular landmarks palpated in each Mallet position. The magnitude of the largest mean difference about an anatomical axis between the two measures of scapular orientation was 3.8° with an RMS error of 5.9°. This technique is practical for populations with visibly prominent scapulae (e.g., BPBP patients), for which it is a viable alternative to existing clinical methods with comparable accuracy.     

A new land-cover map of Africa for the year 2000

Aim In the framework of the Global Land Cover 2000 (GLC 2000), a land‐cover map of Africa has been produced at a spatial resolution of 1 km using data from four sensors on‐board four different Earth observing satellites. Location The map documents the location and distribution of major vegetation types and non‐vegetated land surface formations for the entire African continent plus Madagascar and the other surrounding islands. Methods The bulk of these data were acquired on a daily basis throughout the year 2000 by the VEGETATION sensor on‐board the SPOT‐4 satellite. The map of vegetation cover has been produced based upon the spectral response and the temporal profile of the vegetation cover. Digital image processing and geographical information systems techniques were employed, together with local knowledge, high resolution imagery and expert consultation, to compile a cartographic map product. Radar data and thermal sensors were also used for specific land‐cover classes. Results A total of 27 land cover categories are documented, which has more thematic classes than previously published land cover maps of Africa contain. Systematic comparison with existing land cover data and 30‐m resolution imagery from Landsat are presented, and the map is also compared with other pan‐continental land cover maps. The map and digital data base are freely available for non‐commercial uses from http://www.gvm.jrc.it/tem/africa/products.htm Main conclusions The map improves our state of knowledge of the land‐cover of Africa and presents the most spatially detailed view yet published at this scale. This first version of the map should provide an important input for regional stratification and planning purposes for natural resources, biodiversity and climate studies.     

A multi-indicator framework for mapping cultural ecosystem services: The case of freshwater recreational fishing

Despite recent interest, ecosystem services are not yet fully incorporated into private and public decisions about natural resource management. Cultural ecosystem services (CES) are among the most challenging of services to include because they comprise complex ecological and social properties and processes that make them difficult to measure, map or monetize. Like others, CES are vulnerable to landscape changes and unsustainable use. To date, the sustainability of services has not been adequately addressed and few studies have considered measures of service capacity and demand simultaneously. To facilitate sustainability assessments and management of CES, our study objectives were to (1) develop a spatially explicit framework for mapping the capacity of ecosystems to provide freshwater recreational fishing, an important cultural service, (2) map societal demand for freshwater recreational fishing based on license data and identify areas of potential overuse, and (3) demonstrate how maps of relative capacity and relative demand could be interfaced to estimate sustainability of a CES. We mapped freshwater recreational fishing capacity at the 12-digit hydrologic unit-scale in North Carolina and Virginia using a multi-indicator service framework incorporating biophysical and social landscape metrics and mapped demand based on fishing license data. Mapping of capacity revealed a gradual decrease in capacity eastward from the mountains to the coastal plain and that fishing demand was greatest in urban areas. When comparing standardized relative measures of capacity and demand for freshwater recreational fishing, we found that ranks of capacity exceeded ranks of demand in most hydrologic units, except in 17% of North Carolina and 5% of Virginia. Our GIS-based approach to view freshwater recreational fishing through an ecosystem service lens will enable scientists and managers to examine (1) biophysical and social factors that foster or diminish cultural ecosystem services delivery, (2) demand for cultural ecosystem services relative to their capacity, and (3) ecological pressures like potential overuse that affect service sustainability. Ultimately, we expect such analyses to inform decision-making for freshwater recreational fisheries and other cultural ecosystem services.     

ATGme: Open-source web application for rare codon identification and custom DNA sequence optimization

Background

Codon usage plays a crucial role when recombinant proteins are expressed in different organisms. This is especially the case if the codon usage frequency of the organism of origin and the target host organism differ significantly, for example when a human gene is expressed in E. coli. Therefore, to enable or enhance efficient gene expression it is of great importance to identify rare codons in any given DNA sequence and subsequently mutate these to codons which are more frequently used in the expression host.

Results

We describe an open-source web-based application, ATGme, which can in a first step identify rare and highly rare codons from most organisms, and secondly gives the user the possibility to optimize the sequence.

Conclusions

This application provides a simple user-friendly interface utilizing three optimization strategies: 1. one-click optimization, 2. bulk optimization (by codon-type), 3. individualized custom (codon-by-codon) optimization. ATGme is an open-source application which is freely available at: http://atgme.org     

Testing the applicability of ecosystem services mapping methods for peri-urban contexts: A case study for Paris

Through their semi-natural and agricultural areas, peri-urban regions are pivotal in providing ecosystem services (ES) to city dwellers. To quantify the ES provided by these areas, it is possible to use ES mapping methods: many ES mapping methods rely on land cover maps, but most maps are coarse compared to the peri-urban scale. Nevertheless, readily-available land use data and methods are often used to map ES at such scales, without contextualisation. As a result, such methods may not be able to capture the diversity that is present in the peri-urban vegetation, which could have consequences for their accuracy and furthermore for urban planning policies.To increase our understanding of the applicability of ES mapping methods in peri-urban regions, we assessed to what degree sites with similar plant composition in the green belt of Paris, France, were also projected to have similar ES bundles. We considered two commonly used ES model types: proxy-based models (here: look-up tables) and phenomenological models. We used 252 sites for which botanical survey data were available and applied the ES models to seven ES relevant in the peri-urban context. A cluster analysis was used to group sites, hence facilitating analyse of the spatial congruence between types of vegetation and bundles of ES.Clustering sites based on plant composition revealed six distinct clusters. Clustering sites based on ES bundles as estimated by phenomenological models and proxy-based models, resulted in four and two clusters, respectively. The proxy-based clustering only highlighted broad-leaved forests as an important ES supply source. The phenomenological model estimates of ES allowed a more nuanced clustering of sites into four different groups. The level of congruence between the different sets of clusters based on plant composition and estimated ES bundles was low. Except for forests, the commonly used ES models tested here were not able to represent the same level of heterogeneity in the peri-urban landscape as was found in the vegetation. Our results demonstrate the need to integrate finer scale approaches and primary data in ES assessments of peri-urban areas.     

OpenPIP: An Open-source Platform for Hosting,Visualizing and Analyzing Protein Interaction Data

Knowing which proteins interact with each other is essential information for understanding how most biological processes at the cellular and organismal level operate and how their perturbation can cause disease. Continuous technical and methodological advances over the last two decades have led to many genome-wide systematically-generated protein–protein interaction (PPI) maps. To help store, visualize, analyze and disseminate these specialized experimental datasets via the web, we developed the freely-available Open-source Protein Interaction Platform (openPIP) as a customizable web portal designed to host experimental PPI maps. Such a portal is often required to accompany a paper describing the experimental data set, in addition to depositing the data in a standard repository. No coding skills are required to set up and customize the database and web portal. OpenPIP has been used to build the databases and web portals of two major protein interactome maps, the Human and Yeast Reference Protein Interactome maps (HuRI and YeRI, respectively). OpenPIP is freely available as a ready-to-use Docker container for hosting and sharing PPI data with the scientific community at http://openpip.baderlab.org/ and the source code can be downloaded from https://github.com/BaderLab/openPIP/.     

Covalent perturbation as a tool for validation of identifications and PTM mapping applied to bovine alpha‐crystallin

Proteomic identifications hinge on the measurement of both parent and fragment masses and matching these to amino acid sequences via database search engines. The correctness of the identifications is assessed by statistical means. Here we present an experimental approach to test identifications. Chemical modification of all peptides in a sample leads to shifts in masses depending on the chemical properties of each peptide. The identification of a native peptide sequence and its perturbed version with a different parent mass and fragment ion masses provides valuable information. Labeling all peptides using reductive alkylation with formaldehyde is one such perturbation where the ensemble of peptides shifts mass depending on the number of reactive amine groups. Matching covalently perturbed fragmentation patterns from the same underlying peptide sequence increases confidence in the assignments and can salvage low scoring post‐translationally modified peptides. Applying this strategy to bovine alpha‐crystallin, we identify 9 lysine acetylation sites, 4 O‐GlcNAc sites and 13 phosphorylation sites.