Unlocking the key role of bentonite fungal isolates in tellurium and selenium bioremediation and biorecovery: Implications in the safety of radioactive waste disposal

Research on eco-friendly bioremediation strategies for mitigating the environmental impact of toxic metals has gained attention in the last years. Among all promising solutions, bentonite clays, to be used as artificial barriers to isolate radioactive wastes within the deep geological repository (DGR) concept, have emerged as effective reservoir of microorganisms with remarkable bioremediation potential. The present study aims to investigate the impact of bentonite fungi in the speciation and mobility of selenium (Se) and tellurium (Te), as natural analogues 79Se and 132Te present in radioactive waste, to screen for those strains with bioremediation potential within the context of DGR. For this purpose, a multidisciplinary approach combining microbiology, biochemistry, and microscopy was performed. Notably, Aspergillus sp. 3A demonstrated a high tolerance to Te(IV) and Se(IV), as evidenced by minimal inhibitory concentrations of >16 and >32 mM, respectively, along with high tolerance indexes. The high metalloid tolerance of Aspergillus sp. 3A is mediated by its capability to reduce these mobile and toxic elements to their elemental less soluble forms [Te(0) and Se(0)], forming nanostructures of various morphologies. Advanced electron microscopy techniques revealed intracellular Te(0) manifesting as amorphous needle-like nanoparticles and extracellular Te(0) forming substantial microspheres and irregular accumulations, characterized by a trigonal crystalline phase. Similarly, Se(0) exhibited a diverse array of morphologies, including hexagonal, irregular, and needle-shaped structures, accompanied by a monoclinic crystalline phase. The formation of less mobile Te(0) and Se(0) nanostructures through novel and environmentally friendly processes by Aspergillus sp. 3A suggests it would be an excellent candidate for bioremediation in contaminated environments, such as the vicinity of deep geological repositories. It moreover holds immense potential for the recovery and synthesis of Te and Se nanostructures for use in numerous biotechnological and biomedical applications.

Modeling of cryopreservation pathway operation at an aquatic biomedical stock center for zebrafish

Aquatic biomedical model organisms play a substantial role in advancing our understanding of human health, however, comparably little work has been directed towards developing dependable, high-throughput storage programs for valuable genetic resources. The Zebrafish International Resource Center (ZIRC) has developed a standardized cryopreservation pathway and stored thousands of genetic lines in their repository for use by the biomedical research community. This has yet to be replicated in other facilities, and an overall repository-level pathway has never been analyzed for aquatic species. To encourage repository development for other biomedical models and to improve the ZIRC storage process and system, this study used discrete-event simulation modeling to systematically analyze the cryopreservation pathway for efficiency, and to identify improvements. The models reflected "real-world" working conditions and were used to simulate key outputs, such as production capacity over time (throughput) and steps in the process that limit production (bottlenecks). With these models, recommendations were identified to eliminate waiting times and increase efficiency. These included following proper husbandry protocols because male quality significantly affected production time, and the use of part-time operators to assist with steps that had longer Waiting Times (i.e., time samples spent in a queue) to increase production capacity. Simulation process modeling is a powerful tool that can improve the operations of existing repositories. It can also support repository development at other biomedical stock centers, and at other facilities devoted to aquatic species such as research, conservation, and aquaculture production hatcheries.

Maintenance of dental records and awareness of forensic odontology among pakistani dentists: a mixed-method study with implications for dental data repository

OBJECTIVE

Dental records and forensic odontology play an important role in both healthcare and the legal system, aiding in personalized patient care, human identification, and legal proceedings. This study aims to investigate dental record-keeping practices and assess the awareness of forensic odontology among Pakistani dentists over 12 months. This study aims to collect data from 500 dentists, identify areas for enhancement, and develop a strategic action plan to improve record-keeping quality and forensic odontology application, culminating in a comprehensive dental data repository to support legal and criminal investigations in Pakistan.

METHODOLOGY

This study employed a mixed-method approach conducted at Hamdard Dental College from January to March 2023. The quantitative phase involved distributing questionnaires to 463 dentists, chosen through stratified random sampling. Out of these, 413 responded, yielding an 86% response rate. These questionnaires focused on dental record-keeping practices and dentists' awareness of forensic odontology. Subsequently, based on the questionnaire results, face-to-face interviews were conducted with 20 purposively selected dentists to gain deeper insight into the challenges and potential solutions. Data from both phases were integrated and analyzed accordingly.

RESULTS

The study included 413 participants, mainly females (79%), with ages ranging from 27 to 65 years and an average age of 46.4 years. Most dentists had 5-20 years of work experience (53%), and most (87.4%) were practicing in private clinical settings. All the dentists generated medical and dental records, but the duration of their record-keeping varied, with some maintaining them for up to a year and others for two years or longer. Five themes were generated from the qualitative content analysis. These themes were dentists' perceptions, barriers and challenges, knowledge and awareness, and improvement strategies.

CONCLUSION

Our study revealed that local practitioners in Pakistan exhibit subpar practices in dental record-keeping and maintenance of patient history, irrespective of whether they use a digital or traditional file-based system. Even though dentists are cognizant of the importance of record-keeping, they do not actively maintain comprehensive records. This suggests the need for improved training and system improvements to address the gaps in record-keeping practices.

Leveraging electronic medical records for HIV testing, care, and treatment programming in Kenya-the national data warehouse project

BACKGROUND

Aggregate electronic data repositories and population-level cross-sectional surveys play a critical role in HIV programme monitoring and surveillance for data-driven decision-making. However, these data sources have inherent limitations including inability to respond to public health priorities in real-time and to longitudinally follow up clients for ascertainment of long-term outcomes. Electronic medical records (EMRs) have tremendous potential to bridge these gaps when harnessed into a centralised data repository. We describe the evolution of EMRs and the development of a centralised national data warehouse (NDW) repository. Further, we describe the distribution and representativeness of data from the NDW and explore its potential for population-level surveillance of HIV testing, care and treatment in Kenya.

MAIN BODY

Health information systems in Kenya have evolved from simple paper records to web-based EMRs with features that support data transmission to the NDW. The NDW design includes four layers: data warehouse application programming interface (DWAPI), central staging, integration service, and data visualization application. The number of health facilities uploading individual-level data to the NDW increased from 666 in 2016 to 1,516 in 2020, covering 41 of 47 counties in Kenya. By the end of 2020, the NDW hosted longitudinal data from 1,928,458 individuals ever started on antiretroviral therapy (ART). In 2020, there were 936,869 individuals who were active on ART in the NDW, compared to 1,219,276 individuals on ART reported in the aggregate-level Kenya Health Information System (KHIS), suggesting 77% coverage. The proportional distribution of individuals on ART by counties in the NDW was consistent with that from KHIS, suggesting representativeness and generalizability at the population level.

CONCLUSION

The NDW presents opportunities for individual-level HIV programme monitoring and surveillance because of its longitudinal design and its ability to respond to public health priorities in real-time. A comparison with estimates from KHIS demonstrates that the NDW has high coverage and that the data maybe representative and generalizable at the population-level. The NDW is therefore a unique and complementary resource for HIV programme monitoring and surveillance with potential to strengthen timely data driven decision-making towards HIV epidemic control in Kenya. DATABASE LINK: ( https://dwh.nascop.org/ ).

The MARS PETCARE BIOBANK protocol: establishing a longitudinal study of health and disease in dogs and cats

BACKGROUND

The veterinary care of cats and dogs is increasingly embracing innovations first applied to human health, including an increased emphasis on preventative care and precision medicine. Large scale human population biobanks have advanced research in these areas; however, few have been established in veterinary medicine. The MARS PETCARE BIOBANK™ (MPB) is a prospective study that aims to build a longitudinal bank of biological samples, with paired medical and lifestyle data, from 20,000 initially healthy cats and dogs (10,000 / species), recruited through veterinary hospitals over a ten-year period. Here, we describe the MPB protocol and discuss its potential as a platform to increase understanding of why and how diseases develop and how to advance personalised veterinary healthcare.

METHODS

At regular intervals, extensive diet, health and lifestyle information, electronic medical records, clinicopathology and activity data are collected, genotypes, whole genome sequences and faecal metagenomes analysed, and blood, plasma, serum, and faecal samples stored for future research.

DISCUSSION

Proposed areas for research include the early detection and progression of age-related disease, risk factors for common conditions, the influence of the microbiome on health and disease and, through genome wide association studies, the identification of candidate loci for disease associated genetic variants. Genomic data will be open access and research proposals for access to data and samples will be considered. Over the coming years, the MPB will provide the longitudinal data and systematically collected biological samples required to generate important insights into companion animal health, identifying biomarkers of disease, supporting earlier identification of risk, and enabling individually tailored interventions to manage disease.

pandasGWAS: a Python package for easy retrieval of GWAS catalog data

BACKGROUND

Since the NHGRI-EBI Catalog of human genome-wide association studies was established by NHGRI in 2008, research on it has attracted more and more researchers as the amount of data has grown rapidly. Easy-to-use, open-source, general-purpose programs for accessing the NHGRI-EBI Catalog of human genome-wide association studies are in great demand for current Python data analysis pipeline.

RESULTS

In this work we present pandasGWAS, a Python package that provides programmatic access to the NHGRI-EBI Catalog of human genome-wide association studies. Instead of downloading all data locally, pandasGWAS queries data based on input criteria and handles paginated data gracefully. The data is then transformed into multiple associated pandas.DataFrame objects according to its hierarchical relationships, which makes it easy to integrate into current Python-based data analysis toolkits.

CONCLUSIONS

pandasGWAS is an open-source Python package that provides the first Python client interface to the GWAS Catalog REST API. Compared with existing tools, the data structure of pandasGWAS is more consistent with the design specification of GWAS Catalog REST API, and provides many easy-to-use mathematical symbol operations.

dbGaPCheckup: pre-submission checks of dbGaP-formatted subject phenotype files

BACKGROUND

Data archiving and distribution are essential to scientific rigor and reproducibility of research. The National Center for Biotechnology Information's Database of Genotypes and Phenotypes (dbGaP) is a public repository for scientific data sharing. To support curation of thousands of complex data sets, dbGaP has detailed submission instructions that investigators must follow when archiving their data.

RESULTS

We developed dbGaPCheckup, an R package which implements a series of check, awareness, reporting, and utility functions to support data integrity and proper formatting of the subject phenotype data set and data dictionary prior to dbGaP submission. For example, as a tool, dbGaPCheckup ensures that the data dictionary contains all fields required by dbGaP, and additional fields required by dbGaPCheckup; the number and names of variables match between the data set and data dictionary; there are no duplicated variable names or descriptions; observed data values are not more extreme than the logical minimum and maximum values stated in the data dictionary; and more. The package also includes functions that implement a series of minor/scalable fixes when errors are detected (e.g., a function to reorder the variables in the data dictionary to match the order listed in the data set). Finally, we also include reporting functions that produce graphical and textual descriptives of the data to further reduce the likelihood of data integrity issues. The dbGaPCheckup R package is available on CRAN ( https://CRAN.R-project.org/package=dbGaPCheckup ) and developed on GitHub ( https://github.com/lwheinsberg/dbGaPCheckup ).

CONCLUSION

dbGaPCheckup is an innovative assistive and timesaving tool that fills an important gap for researchers by making dbGaP submission of large and complex data sets less error prone.

Quality control of fighting fish nucleotide sequences in public repositories reveals a dark matter of systematic taxonomic implication

BACKGROUND

The number of nucleotide sequences in public repositories has exploded recently. However, the data contain errors, leading to incorrect species identification. Several fighting fish (Betta spp.) are poorly described, with unresolved cryptic species complexes masking undescribed species. Here, DNA barcoding was used to detect erroneous sequences in public repositories.

OBJECTIVE

This study reflects the current quantitative and qualitative status of DNA barcoding in fighting fish and provides a rapid and reliable identification tool.

METHODS

A total of 1034 barcode sequences were analyzed from mitochondrial cytochrome c oxidase I (COI) and cytochrome b (Cytb) genes from 71 fighting fish species.

RESULTS

The nearest neighbor test showed the highest percentage of intraspecific nearest neighbors at 93.41% for COI and 91.67% for Cytb, which can be used as reference barcodes for certain taxa. Intraspecific variation was usually less than 13%, while most species differed by more than 54%. The barcoding gap, calculated from the difference between inter- and intraspecific sequence divergences, was negative in the COI data set indicating overlapping intra- and interspecific sequence divergence. Sequence saturation was observed in the Cytb data set but not in the COI data set.

CONCLUSION

The COI gene should thus be used as the main barcoding marker for fighting fish.

Online Resources Useful for Plant Cytogenetics and Cytogenomics Research

The advancements in research in the field of plant cytogenetics and genomics in recent decades have led to a significant increase in publications. To simplify access to the widely dispersed data, there has been a rise in the number of online databases, repositories, and analytical tools. This chapter presents a comprehensive overview of these resources, which can be beneficial to researchers in these areas. It includes, among others, databases on chromosome numbers, special chromosomes (such as B chromosomes or sex chromosomes), some of which are taxon-specific; genome sizes, cytogenetics; and online applications and tools for genomic analysis and visualization.

The World Health Organization COVID-19 surveillance database

In January 2020, SARS-CoV-2 virus was identified as a cause of an outbreak in China. The disease quickly spread worldwide, and the World Health Organization (WHO) declared the pandemic in March 2020.From the first notifications of spread of the disease, the WHO's Emergency Programme implemented a global COVID-19 surveillance system in coordination with all WHO regional offices. The system aimed to monitor the spread of the epidemic over countries and across population groups, severity of the disease and risk factors, and the impact of control measures. COVID-19 surveillance data reported to WHO is a combination of case-based data and weekly aggregated data, focusing on a minimum global dataset for cases and deaths including disaggregation by age, sex, occupation as a Health Care Worker, as well as number of cases tested, and number of cases newly admitted for hospitalization. These disaggregations aim to monitor inequities in COVID-19 distribution and risk factors among population groups.SARS-CoV-2 epidemic waves continue to sweep the world; as of March 2022, over 445 million cases and 6 million deaths have been reported worldwide. Of these, over 327 million cases (74%) have been reported in the WHO surveillance database, of which 255 million cases (57%) are disaggregated by age and sex. A public dashboard has been made available to visualize trends, age distributions, sex ratios, along with testing and hospitalization rates. It includes a feature to download the underlying dataset.This paper will describe the data flows, database, and frontend public dashboard, as well as the challenges experienced in data acquisition, curation and compilation and the lessons learnt in overcoming these. Two years after the pandemic was declared, COVID-19 continues to spread and is still considered a Public Health Emergency of International Concern (PHEIC). While WHO regional and country offices have demonstrated tremendous adaptability and commitment to process COVID-19 surveillance data, lessons learnt from this major event will serve to enhance capacity and preparedness at every level, as well as institutional empowerment that may lead to greater sharing of public health evidence during a PHEIC, with a focus on equity.

getSequenceInfo: a suite of tools allowing to get genome sequence information from public repositories

Background

Biological sequences are increasing rapidly and exponentially worldwide. Nucleotide sequence databases play an important role in providing meaningful genomic information on a variety of biological organisms.

Results

The getSequenceInfo software tool allows to access sequence information from various public repositories (GenBank, RefSeq, and the European Nucleotide Archive), and is compatible with different operating systems (Linux, MacOS, and Microsoft Windows) in a programmatic way (command line) or as a graphical user interface. getSequenceInfo or gSeqI v1.0 should help users to get some information on queried sequences that could be useful for specific studies (e.g. the country of origin/isolation or the release date of queried sequences). Queries can be made to retrieve sequence data based on a given kingdom and species, or from a given date. This program allows the separation between chromosomes and plasmids (or other genetic elements/components) by arranging each component in a given folder. Some basic statistics are also performed by the program (such as the calculation of GC content for queried assemblies). An empirically designed nucleotide ratio is calculated using nucleotide information in order to tentatively provide a “NucleScore” for studied genome assemblies. Besides the main gSeqI tool, other additional tools have been developed to perform various tasks related to sequence analysis.

Conclusion

The aim of this study is to democratize the use of public repositories in programmatic ways, and to facilitate sequence data analysis in a pedagogical perspective. Output results are available in FASTA, FASTQ, Excel/TSV or HTML formats. The program is freely available at: https://github.com/karubiotools/getSequenceInfo. getSequenceInfo and supplementary tools are partly available through the recently released Galaxy KaruBioNet platform (http://calamar.univ-ag.fr/c3i/galaxy_karubionet.html).

Supplementary Information

The online version contains supplementary material available at 10.1186/s12859-022-04809-5.

Reflections on Data Sharing Practices in Spinal Cord Injury Research

There are few pharmacological therapeutics available for spinal cord injury despite years of preclinical and clinical research. This brief editorial discusses some of the shortcomings of translational research efforts. In addition, we comment on our previous experiences with data curation and highlight evolving efforts by the spinal cord injury research community to improve prospects for future therapeutic development, especially pertaining to preclinical data sharing through the Open Data Commons for Spinal Cord Injury (ODC-SCI).

MicroRNA Databases and Tools

In this era of big data, sets of methodologies and strategies are designed to extract knowledge from huge volumes of data. However, the cost of where and how to get this information accurately and quickly is extremely important, given the diversity of genomes and the different ways of representing that information. Among the huge set of information and relationships that the genome carries, there are sequences called miRNAs (microRNAs). These sequences were described in the 1990s and are mainly involved in mechanisms of regulation and gene expression. Having this in mind, this chapter focuses on exploring the available literature and providing useful and practical guidance on the miRNA database and tools topic. For that, we organized and present this text in two ways: (a) the update reviews and articles, which best summarize and discuss the theme; and (b) our update investigation on miRNA literature and portals about databases and tools. Finally, we present the main challenge and a possible solution to improve resources and tools.

On the Periodicity of Cardiovascular Fluid Dynamics Simulations

Three-dimensional cardiovascular fluid dynamics simulations typically require computation of several cardiac cycles before they reach a periodic solution, rendering them computationally expensive. Furthermore, there is currently no standardized method to determine whether a simulation has yet reached that periodic state. In this work, we propose the use of an asymptotic error measurement to quantify the difference between simulation results and their ideal periodic state using open-loop lumped-parameter modeling. We further show that initial conditions are crucial in reducing computational time and develop an automated framework to generate appropriate initial conditions from a one-dimensional model of blood flow. We demonstrate the performance of our initialization method using six patient-specific models from the Vascular Model Repository. In our examples, our initialization protocol achieves periodic convergence within one or two cardiac cycles, leading to a significant reduction in computational cost compared to standard methods. All computational tools used in this work are implemented in the open-source software platform SimVascular. Automatically generated initial conditions have the potential to significantly reduce computation time in cardiovascular fluid dynamics simulations.

Developing a topic-based repository of clinical trial individual patient data: experiences and lessons learned from a pilot project

BACKGROUND

Building a dataset of individual participant data (IPD) for meta-analysis represents considerable research investment as well as collaboration across multiple institutions and researchers. Making arrangements to curate and share the dataset beyond the IPD meta-analysis project for which it was established, for reuse in future research projects, would maximise the value of this investment.

METHODS

Our aim was to establish the Cochrane repository for individual patient data from clinical trials in pregnancy and childbirth (CRIB) as an example of how an IPD repository could become part of Cochrane infrastructure. We believed that establishing CRIB under Cochrane auspices would engender trust and encourage trial investigators to share data, and at the same time position Cochrane to take steps towards expanding the number of reviews with IPD synthesis.

RESULTS

CRIB was designed as a web-based platform to receive, host and facilitate onward sharing of de-identified data. Development was not straightforward and we did not fully achieve our aim as intended. We describe the challenges encountered and suggest ways that future repositories might overcome these. In particular, securing the legal agreements required to facilitate data sharing proved to be the main barrier, being time-consuming and more complex than anticipated.

CONCLUSIONS

We would recommend that researchers conducting IPD meta-analysis should consider discussing the option to transfer the curated IPD datasets to a repository at the end of the initial meta-analysis and this should be recognised within the data sharing agreements made with the original data contributors.

The sharing of research data facing the COVID-19 pandemic

During the previous Ebola and Zika outbreaks, researchers shared their data, allowing many published epidemiological studies to be produced only from open research data, to speed up investigations and control of these infections. This study aims to evaluate the dissemination of the COVID-19 research data underlying scientific publications. Analysis of COVID-19 publications from December 1, 2019, to April 30, 2020, was conducted through the PubMed Central repository to evaluate the research data available through its publication as supplementary material or deposited in repositories. The PubMed Central search generated 5,905 records, of which 804 papers included complementary research data, especially as supplementary material (77.4%). The most productive journals were The New England Journal of Medicine, The Lancet and The Lancet Infectious Diseases, the most frequent keyword was pneumonia, and the most used repositories were GitHub and GenBank. An expected growth in the number of published articles following the course of the pandemics is confirmed in this work, while the underlying research data are only 13.6%. It can be deduced that data sharing is not a common practice, even in health emergencies, such as the present one. High-impact generalist journals have accounted for a large share of global publishing. The topics most often covered are related to epidemiological and public health concepts, genetics, virology and respiratory diseases, such as pneumonia. However, it is essential to interpret these data with caution following the evolution of publications and their funding in the coming months.

The jPOST Repository as a Public Data Repository for Shotgun Proteomics

In recent years, mass spectrometry-based proteomics approach has made significant progress and the number of datasets related to various proteomics projects has increased worldwide. To promote the sharing and reuse of promising datasets, it is important to build an appropriate, high-quality public data repository. For this purpose, several repositories have already been created. The jPOST repository that we developed in 2016 has successfully implemented several unique features, such as fast file upload, flexible file management, and an easy-to-use interface. In addition, this repository is an official member of the ProteomeXchange Consortium established to facilitate standard data submission and global dissemination of mass spectrometry proteomics data. Our repository contributes to the global partnership for sharing and storing all the datasets related to various proteomics experiments.

Iodine effective diffusion coefficients through volcanic rock: Influence of iodine speciation and rock geochemistry

Accurate prediction of the subsurface transport of iodine species is important for the assessment of long-term nuclear waste repository performance, as well as monitoring compliance with the Comprehensive Nuclear-Test-Ban Treaty, given that radioiodine decays into radioxenon. However, the transport of iodine through intact geologic media is not well understood, compromising our ability to assess risk associated with radioiodine migration. The current study's goal is to quantify the matrix diffusion of iodine species through saturated volcanic rock, with particular attention paid to the redox environment and potential speciation changes. Diffusion experiments were run for iodide through lithophysae-rich lava, lithophysae-poor lava, and welded tuff, whereas iodate diffusion was studied through welded tuff. Iodine transport was compared with a conservative tracer, HDO, and effective diffusion coefficients were calculated. Likely due to a combination of size and anion exclusion effects, iodine species diffused more slowly than the conservative tracer through all rock types tested. Furthermore, oxidation of iodide to iodate was observed in the lithophysae-poor lava, affecting transport. Results provide much needed data for subsurface transport models that predict radioiodine migration from underground sources, and indicate the pressing need for geochemical and redox interactions to be incorporated into these models.

A Comprehensive Framework to Capture the Arcana of Neuroimaging Analysis

Mastering the "arcana of neuroimaging analysis", the obscure knowledge required to apply an appropriate combination of software tools and parameters to analyse a given neuroimaging dataset, is a time consuming process. Therefore, it is not typically feasible to invest the additional effort required generalise workflow implementations to accommodate for the various acquisition parameters, data storage conventions and computing environments in use at different research sites, limiting the reusability of published workflows. We present a novel software framework, Abstraction of Repository-Centric ANAlysis (Arcana), which enables the development of complex, "end-to-end" workflows that are adaptable to new analyses and portable to a wide range of computing infrastructures. Analysis templates for specific image types (e.g. MRI contrast) are implemented as Python classes, which define a range of potential derivatives and analysis methods. Arcana retrieves data from imaging repositories, which can be BIDS datasets, XNAT instances or plain directories, and stores selected derivatives and associated provenance back into a repository for reuse by subsequent analyses. Workflows are constructed using Nipype and can be executed on local workstations or in high performance computing environments. Generic analysis methods can be consolidated within common base classes to facilitate code-reuse and collaborative development, which can be specialised for study-specific requirements via class inheritance. Arcana provides a framework in which to develop unified neuroimaging workflows that can be reused across a wide range of research studies and sites.

Rapid establishment of a COVID-19 perinatal biorepository: early lessons from the first 100 women enrolled

BACKGROUND

Collection of biospecimens is a critical first step to understanding the impact of COVID-19 on pregnant women and newborns - vulnerable populations that are challenging to enroll and at risk of exclusion from research. We describe the establishment of a COVID-19 perinatal biorepository, the unique challenges imposed by the COVID-19 pandemic, and strategies used to overcome them.

METHODS

A transdisciplinary approach was developed to maximize the enrollment of pregnant women and their newborns into a COVID-19 prospective cohort and tissue biorepository, established on March 19, 2020 at Massachusetts General Hospital (MGH). The first SARS-CoV-2 positive pregnant woman was enrolled on April 2, and enrollment was expanded to SARS-CoV-2 negative controls on April 20. A unified enrollment strategy with a single consent process for pregnant women and newborns was implemented on May 4. SARS-CoV-2 status was determined by viral detection on RT-PCR of a nasopharyngeal swab. Wide-ranging and pregnancy-specific samples were collected from maternal participants during pregnancy and postpartum. Newborn samples were collected during the initial hospitalization.

RESULTS

Between April 2 and June 9, 100 women and 78 newborns were enrolled in the MGH COVID-19 biorepository. The rate of dyad enrollment and number of samples collected per woman significantly increased after changes to enrollment strategy (from 5 to over 8 dyads/week, P < 0.0001, and from 7 to 9 samples, P < 0.01). The number of samples collected per woman was higher in SARS-CoV-2 negative than positive women (9 vs 7 samples, P = 0.0007). The highest sample yield was for placenta (96%), umbilical cord blood (93%), urine (99%), and maternal blood (91%). The lowest-yield sample types were maternal stool (30%) and breastmilk (22%). Of the 61 delivered women who also enrolled their newborns, fewer women agreed to neonatal blood compared to cord blood (39 vs 58, P < 0.0001).

CONCLUSIONS

Establishing a COVID-19 perinatal biorepository required patient advocacy, transdisciplinary collaboration and creative solutions to unique challenges. This biorepository is unique in its comprehensive sample collection and the inclusion of a control population. It serves as an important resource for research into the impact of COVID-19 on pregnant women and newborns and provides lessons for future biorepository efforts.

Assessment of a demonstrator repository for individual clinical trial data built upon DSpace

Background: Given the increasing number and heterogeneity of data repositories, an improvement and harmonisation of practice within repositories for clinical trial data is urgently needed. The objective of the study was to develop and evaluate a demonstrator repository, using a widely used repository system (DSpace), and then explore its suitability for providing access to individual participant data (IPD) from clinical research.

Methods: After a study of the available options, DSpace (version 6.3) was selected as the software for developing a demonstrator implementation of a repository for clinical trial data. In total, 19 quality criteria were defined, using previous work assessing clinical data repositories as a guide, and the demonstrator implementation was then assessed with respect to those criteria.

Results: Generally, the performance of the DSpace demonstrator repository in supporting sensitive personal data such as that from clinical trials was strong, with 14 requirements demonstrated (74%), including the necessary support for metadata and identifiers. Two requirements could not be demonstrated (the ability to include de-identification tools and the availabiltiy of a self-attestation system) and three requirements were only partially demonstrated (ability to provide links to de-identification tools and requirements, incorporation of a data transfer agreement in system workflow, and capability to offer managed access through application on a case by case basis).

Conclusions: Technically, the system was able to support most of the pre-defined requirements, though there are areas where support could be improved. Of course, in a productive repository, appropriate policies and procedures would be needed to direct the use of the available technical features. A technical evaluation should therefore be seen as indicating a system’s potential, rather than being a definite assessment of its suitability. DSpace clearly has considerable potential in this context and appears a suitable base for further exploration of the issues around storing sensitive data.

Open Access publishing practice in geochemistry: overview of current state and look to the future

Open Access (OA) describes the free, unrestricted access to and re-use of research articles. Recently, a new wave of interest, debate, and practice surrounding OA publishing has emerged. In this paper, we provide a simple overview of the trends in OA practice in the broad field of geochemistry. Characteristics of the approach such as whether or not an article processing charge (APC) exists, what embargo periods or restrictions on self-archiving' policies are in place, and whether or not the sharing of preprints is permitted are described. The majority of journals have self-archiving policies that allow authors to share their peer reviewed work via green OA without charge. There is no clear relationship between journal impact and APC. The journals with the highest APC are typically those of the major commercial publishers, rather than the geochemistry community themselves. The rise in OA publishing has potential impacts on the profiles of researchers and tends to devolve costs from organizations to individuals. Until the geochemistry community makes the decision to move away from journal-based evaluation criteria, it is likely that such high costs will continue to impose financial inequities upon research community. However, geochemists could more widely choose legal self-archiving as an equitable and sustainable way to disseminate their research.

Data Storage

While research data has become integral to the scholarly endeavour, a number of challenges hinder its development, management and dissemination. This chapter follows the life cycle of research data, by considering aspects ranging from storage and preservation to sharing and legal factors. While it provides a wide overview of the current ecosystem, it also pinpoints the elements comprising the modern research sharing practices such as metadata creation, the FAIR principles, identifiers, Creative Commons licencing and the various repository options. Furthermore, the chapter discusses the mandates and regulations that influence data sharing and the possible technological means of overcoming their complexity, such as blockchain systems.

Increasing the accessibility and impact of justice-related student and practitioner research

Much good quality research by pre-doctoral students and case-work focused practitioners remains unpublished. However, their findings could contribute to the evidence base underpinning science and practice within international justice system contexts. There are two main challenges to making findings accessible: reaching all criminal justice stakeholders, and encouraging collaborative efforts in research addressing 'real world' problems. This article presents the rationale for a new, open access repository. The aim is to share good quality pre-doctoral and practitioner criminal justice research across traditional disciplinary and international borders. Such a repository should be easy to use, well maintained and sustainable. Its reach, value and impact also need to be measurable. We present the major considerations relating to the operation and workflow of such a repository, and outline the potential value, benefits and limitations. Our research suggests that the proposed repository could foster interdisciplinary and collaborative work to benefit global justice systems and societies.

Collection and Analyses of Cerebrospinal Fluid for Pediatric Translational Research

Cerebrospinal fluid sample collection and analysis is imperative to better elucidate central nervous system injury and disease in children. Sample collection methods are varied and carry with them certain ethical and biologic considerations, complications, and contraindications. Establishing best practices for sample collection, processing, storage, and transport will ensure optimal sample quality. Cerebrospinal fluid samples can be affected by a number of factors including subject age, sampling method, sampling location, volume extracted, fraction, blood contamination, storage methods, and freeze-thaw cycles. Indicators of sample quality can be assessed by matrix-associated laser desorption/ionization time-of-flight mass spectrometry and include cystatin C fragments, oxidized proteins, prostaglandin D synthase, and evidence of blood contamination. Precise documentation of sample collection processes and the establishment of meticulous handling procedures are essential for the creation of clinically relevant biospecimen repositories. In this review we discuss the ethical considerations and best practices for cerebrospinal fluid collection, as well as the influence of preanalytical factors on cerebrospinal fluid analyses. Cerebrospinal fluid biomarkers in highly researched pediatric diseases or disorders are discussed.

PyCellBase, an efficient python package for easy retrieval of biological data from heterogeneous sources

BACKGROUND

Biological databases and repositories are incrementing in diversity and complexity over the years. This rapid expansion of current and new sources of biological knowledge raises serious problems of data accessibility and integration. To handle the growing necessity of unification, CellBase was created as an integrative solution. CellBase provides a centralized NoSQL database containing biological information from different and heterogeneous sources. Access to this information is done through a RESTful web service API, which provides an efficient interface to the data.

RESULTS

In this work we present PyCellBase, a Python package that provides programmatic access to the rich RESTful web service API offered by CellBase. This package offers a fast and user-friendly access to biological information without the need of installing any local database. In addition, a series of command-line tools are provided to perform common bioinformatic tasks, such as variant annotation. CellBase data is always available by a high-availability cluster and queries have been tuned to ensure a real-time performance.

CONCLUSION

PyCellBase is an open-source Python package that provides an efficient access to heterogeneous biological information. It allows to perform tasks that require a comprehensive set of knowledge resources, as for example variant annotation. Queries can be easily fine-tuned to retrieve the desired information of particular biological features. PyCellBase offers the convenience of an object-oriented scripting language and provides the ability to integrate the obtained results into other Python applications and pipelines.

The end user sensor tree: An end-user friendly sensor database

Detailed knowledge regarding sensor based technologies for the detection of food contamination often remains concealed within scientific journals or divided between numerous commercial kits which prevents optimal connectivity between companies and end-users. To overcome this barrier The End user Sensor Tree (TEST) has been developed. TEST is a comprehensive, interactive platform including over 900 sensor based methods, retrieved from the scientific literature and commercial market, for aquatic-toxins, mycotoxins, pesticides and microorganism detection. Key analytical parameters are recorded in excel files while a novel classification system is used which provides, tailor-made, experts' feedback using an online decision tree and database introduced here. Additionally, a critical comparison of reviewed sensors is presented alongside a global perspective on research pioneers and commercially available products. The lack of commercial uptake of the academically popular electrochemical and nanomaterial based sensors, as well as multiplexing platforms became very apparent and reasons for this anomaly are discussed.

Investigation of 3H, 99Tc, and 90Sr transport in fractured rock and the effects of fracture-filling/coating material at LILW disposal facility

Batch adsorption, batch diffusion, and flow-through column experiments were conducted using groundwater and fractured rock collected in unsaturated zone to increase our understanding of sorption and transport behavior of radionuclides. Increasing K_d values were observed in the sequence ⁹⁰Sr, ⁹⁹Tc, and ³H regardless of the geological media tested. For all sorbing radionuclides, K_d values for the fracture-filling/coating material were observed to be higher than those for without fracture-filling/coating material regardless of the groundwater. These higher K_d values are the result of zeolite mineral in filling/coating material of fractured rock. The batch diffusion and flow-through column experiments were also conducted using the same fractured rock sample, and the results of diffusion and column experiments showed similar trend of radionuclide sorption and transport to sorption experiment. In this study, sorption K_d of radionuclide was determined and used to increase our understanding of radionuclide retardation through fracture-filling/coating materials.

A Walkthrough to the Use of GreeNC: The Plant lncRNA Database

Experimentally validated plant lncRNAs have been shown to regulate important agronomic traits such as phosphate starvation response, flowering time, and interaction with symbiotic organisms, making them of great interest in plant biology and in breeding. We developed a pipeline to annotate lncRNAs and applied it to 37 plant species and 6 algae, resulting in the annotation of more than 120,000 lncRNAs. To facilitate the study of lncRNAs for the plant research community, the information gathered is organized in the Green Non-Coding Database (GreeNC, http://greenc.sciencedesigners.com/) . This chapter contains a detailed explanation of the content of GreeNC and how to access both programmatically and with a web browser.

Automated Metadata Suggestion During Repository Submission

Knowledge discovery via an informatics resource is constrained by the completeness of the resource, both in terms of the amount of data it contains and in terms of the metadata that exists to describe the data. Increasing completeness in one of these categories risks reducing completeness in the other because manually curating metadata is time consuming and is restricted by familiarity with both the data and the metadata annotation scheme. The diverse interests of a research community may drive a resource to have hundreds of metadata tags with few examples for each making it challenging for humans or machine learning algorithms to learn how to assign metadata tags properly. We demonstrate with ModelDB, a computational neuroscience model discovery resource, that using manually-curated regular-expression based rules can overcome this challenge by parsing existing texts from data providers during user data entry to suggest metadata annotations and prompt them to suggest other related metadata annotations rather than leaving the task to a curator. In the ModelDB implementation, analyzing the abstract identified 6.4 metadata tags per abstract at 79% precision. Using the full-text produced higher recall with low precision (41%), and the title alone produced few (1.3) metadata annotations per entry; we thus recommend data providers use their abstract during upload. Grouping the possible metadata annotations into categories (e.g. cell type, biological topic) revealed that precision and recall for the different text sources varies by category. Given this proof-of-concept, other bioinformatics resources can likewise improve the quality of their metadata by adopting our approach of prompting data uploaders with relevant metadata at the minimal cost of formalizing rules for each potential metadata annotation.

Microplastics in seawater and zooplankton from the Yellow Sea

Marine plastic pollution is a worldwide problem. Microplastics (MPs) are the predominant form of marine plastic debris, a form small enough to be ingested by and potentially harm marine organisms. It is urgent to develop ecologically relevant metrics for the risk assessment of MPs based on in situ data, especially for coastal areas. For the first time, we performed a comprehensive study of the characteristics of MPs in seawater and zooplankton in the Yellow Sea. For MPs in seawater, the average concentration is 0.13 ± 0.20 pieces/m³, dominated by fragments (42%). The average size is 3.72 ± 4.70 mm, with the most frequent size appearing at 1200 μm. The major polymer types are polypropylene and polyethylene, accounting for 88.13% in total. The distribution of MPs in seawater is patchy, with high MP concentrations close to the coastal cities. The average concentration of MPs in 11 total zooplankton groups is 12.24 ± 25.70 pieces/m³. The average size is 154.62 ± 152.90 μm, with 90% being <500 μm. Fiber is the dominant shape of MPs found in zooplankton, accounting for 46%, but the composition of the polymer type is diverse. The retention of MPs in zooplankton depends on the taxa and their abundance in the Yellow Sea. Siphonophorea, Copepoda, Euphausiacea and Amphipoda are the main repositories compared to other groups, achieving 3.57, 2.44, 1.41 and 1.36 pieces/m³, respectively. The high concentration area of MPs in zooplankton appeared near the adjacent waters of the Yangtze estuary. These results prove that zooplankton act as a repository for MPs in coastal waters. The retention of MPs in zooplankton is recommended as a key index for further ecological risk assessment of MPs.

The Role of the Mizar Mathematical Library for Interactive Proof Development in Mizar

The Mizar system is one of the pioneering systems aimed at supporting mathematical proof development on a computer that have laid the groundwork for and eventually have evolved into modern interactive proof assistants. We claim that an important milestone in the development of these systems was the creation of organized libraries accumulating all previously available formalized knowledge in such a way that new works could effectively re-use all previously collected notions. In the case of Mizar, the turning point of its development was the decision to start building the Mizar Mathematical Library as a centrally-managed knowledge base maintained together with the formalization language and the verification system. In this paper we show the process of forming this library, the evolution of its design principles, and also present some data showing its current use with the modern version of the Mizar proof checker, but also as a rich corpus of semantically linked mathematical data in various areas including web-based and natural language proof presentation, maths education, and machine learning based automated theorem proving.

A method for independent modelling in support of regulatory review of dose assessments

Several countries consider geological disposal facilities as the preferred option for spent nuclear fuel due to their potential to provide isolation from the surface environment on very long timescales. In 2011 the Swedish Nuclear Fuel & Waste Management Co. (SKB) submitted a license application for construction of a spent nuclear fuel repository. The disposal method involves disposing spent fuel in copper canisters with a cast iron insert at about 500 m depth in crystalline basement rock, and each canister is surrounded by a buffer of swelling bentonite clay. SKB's license application is supported by a post-closure safety assessment, SR-Site. SR-Site has been reviewed by the Swedish Radiation Safety Authority (SSM) for five years. The main method for review of SKB's license application is document review, which is carried out by SSM's staff and supported by SSM's external experts. The review has proven a challenging task due to its broad scope, complexity and multidisciplinary nature. SSM and its predecessors have, for several decades, been developing independent models to support regulatory reviews of post-closure safety assessments for geological repositories. For the review of SR-Site, SSM has developed a modelling approach with a structured application of independent modelling activities, including replication modelling, use of alternative conceptual models and bounding calculations, to complement the traditional document review. This paper describes this scheme and its application to biosphere and dose assessment modelling. SSM's independent modelling has provided important insights regarding quality and reasonableness of SKB's rather complex biosphere modelling and has helped quantifying conservatisms and highlighting conceptual uncertainty.

Concrete and cement composites used for radioactive waste deposition

This review article presents the current state-of-knowledge of the use of cementitious materials for radioactive waste disposal. An overview of radwaste management processes with respect to the classification of the waste type is given. The application of cementitious materials for waste disposal is divided into two main lines: i) as a matrix for direct immobilization of treated waste form; and ii) as an engineered barrier of secondary protection in the form of concrete or grout. In the first part the immobilization mechanisms of the waste by cement hydration products is briefly described and an up-to date knowledge about the performance of different cementitious materials is given, including both traditional cements and alternative binder systems. The advantages, disadvantages as well as gaps in the base of information in relation to individual materials are stated. The following part of the article is aimed at description of multi-barrier systems for intermediate level waste repositories. It provides examples of proposed concepts by countries with advanced waste management programmes. In the paper summary, the good knowledge of the material durability due to its vast experience from civil engineering is highlighted however with the urge for specific approach during design and construction of a repository in terms of stringent safety requirements.

The Swedish radiological environmental protection regulations applied in a review of a license application for a geological repository for spent nuclear fuel

For the first time, a system for specific consideration of radiological environmental protection has been applied in a major license application in Sweden. In 2011 the Swedish Nuclear Fuel & Waste Management Co. (SKB) submitted a license application for construction of a geological repository for spent nuclear fuel at the Forsmark site. The license application is supported by a post-closure safety assessment, which in accordance with regulatory requirements includes an assessment of environmental consequences. SKB's environmental risk assessment uses the freely available ERICA Tool. Environmental media activity concentrations needed as input to the tool are calculated by means of complex biosphere modelling based on site-specific information gathered from site investigations, as well as from supporting modelling studies and projections of future biosphere conditions in response to climate change and land rise due to glacial rebound. SKB's application is currently being reviewed by the Swedish Radiation Safety Authority (SSM). In addition to a traditional document review with an aim to determine whether SKB's models are relevant, correctly implemented and adequately parametrized, SSM has performed independent modelling in order to gain confidence in the robustness of SKB's assessment. Thus, SSM has used alternative stylized reference biosphere models to calculate environmental activity concentrations for use in subsequent exposure calculations. Secondly, an alternative dose model (RESRAD-BIOTA) is used to calculate doses to biota that are compared with SKB's calculations with the ERICA tool. SSM's experience from this review is that existing tools for environmental dose assessment are possible to use in order to show compliance with Swedish legislation. However, care is needed when site representative species are assessed with the aim to contrast them to generic reference organism. The alternative modelling of environmental concentrations resulted in much lower concentrations compared to SKB's results. However, SSM judges that SKB's in this part conservative approach is relevant for a screening assessment. SSM also concludes that there are big differences in dose rates calculated to different organisms depending on which tool that is used, although not systematically higher for either of them. Finally, independent regulatory modelling has proven valuable for SSM's review in gaining understanding and confidence in SKB's assessment presented in the license application.

Impact of alkaline alterations to a Brazilian soil on cesium retention under low temperature conditions

To be used as backfilling materials in radioactive waste disposal facilities, a natural material must have a suitable permeability, mechanical properties and a high sorption capacity for radionuclides. Also important when considering a material as a backfill is the effect of its interaction with the alkaline solution generated from concrete degradation. This solution promotes mineralogical alterations that result in significant changes in the material key properties influencing its performance as a safety component of the repository. This paper presents results of an investigation on the effect of alkaline interaction under a low temperature on cesium retention properties of a local soil being considered suitable as a backfill for the Brazilian near surface disposal facility. A sample of the Brazilian soil was mixed with an alkaline solution, simulating the pore water leached in the first stage of cement degradation, during 1, 7, 14 and 28 days. The experiments were conducted under low temperature (25 °C) aiming to evaluate similar conditions found on a low and intermediate level radioactive waste disposal installation. A non-classical isotherm sorption model was fitted to sorption data obtained from batch experiments, for unaltered and altered samples, providing parameters that allowed us to assess the effect of the interaction on material quality as Cs sorbent. The sorption parameters obtained from the data-fitted isotherm were used then to estimate the corresponding retardation factor (R). Alkaline interaction significantly modified the soil sorption properties for Cs. The parameter Q, related to the maximum sorption capacity, as well as the affinity parameter (K) and the retardation coefficients became significantly smaller (about 1000 times for the R coefficient) after pretreatment with the simulated alkaline solutions. Moreover, the increase in n-values, which is related with the energy distribution width and heterogeneity of surface site energies, demonstrated that the adsorbent surface became more homogenous as a consequence of the alkaline alteration. Together these results suggest that cementitious leachate has a profound effect on Cs retention and should be accounted for estimating radionuclide retention in radioactive waste disposal systems containing cementitious materials.

Assessing metal mobilization from industrial lead-contaminated soils in an urban site

A series of leaching and partitioning tests (Toxicity Characteristic Leaching Procedure (TCLP), Synthetic Precipitation Leaching Procedure (SPLP), Controlled Acidity Leaching Protocol (CALP), Acid Neutralization Capacity (ANC), and sequential extraction) were applied to three different soils to study the potential mobility of metals into groundwater. Two of these soils were lead (Pb)-contaminated soils (Hotspot 1 and Hotspot 2) collected from an urban site associated with lead smelting and other industrial operations. The third sample (Stockpile) was soil affected by previous contamination in the area, removed from residential properties, stockpiled, and selected to be used as fill material in the studied site. The TCLP and CALP showed that Pb could be released from both hotspots, but were not released in the acidic rainfall extraction fluid of the SPLP. The sequential extraction showed that Pb in the hotspot soils was associated with the carbonate fraction, while As was associated with the Fe and Mn oxides. The stockpile released traces of Pb or As in the TCLP and CALP, but the ANC only released Pb under acidic conditions and the SPLP did not release Pb or As. Overall, the projected repository with Stockpile would not pose imminent danger to groundwater because, under the expected environmental conditions, Pb and As tend to remain in the solid phase.

Databases, Repositories, and Other Data Resources in Structural Biology

Structural biology, like many other areas of modern science, produces an enormous amount of primary, derived, and "meta" data with a high demand on data storage and manipulations. Primary data come from various steps of sample preparation, diffraction experiments, and functional studies. These data are not only used to obtain tangible results, like macromolecular structural models, but also to enrich and guide our analysis and interpretation of various biomedical problems. Herein we define several categories of data resources, (a) Archives, (b) Repositories, (c) Databases, and (d) Advanced Information Systems, that can accommodate primary, derived, or reference data. Data resources may be used either as web portals or internally by structural biology software. To be useful, each resource must be maintained, curated, as well as integrated with other resources. Ideally, the system of interconnected resources should evolve toward comprehensive "hubs", or Advanced Information Systems. Such systems, encompassing the PDB and UniProt, are indispensable not only for structural biology, but for many related fields of science. The categories of data resources described herein are applicable well beyond our usual scientific endeavors.

Mortality and oral anticoagulants in the Food and Drug Administration Adverse Event Reporting System

OBJECTIVE

The comparative crude death rates (CDR) among non-vitamin K antagonist oral anticoagulants (NOACs) are unknown. Further, whether NOACs improve survival when compared with warfarin is also unclear. We compared CDR co-reported for four NOACs combined or separately versus warfarin within the US Food and Drug Administration (FDA) Adverse Event Reporting System (FAERS) database.

METHODS

We selected CDR from the FAERS database linked to four NOACs and warfarin. The primary endpoints were differences in proportional reporting ratios (PRRs), and Chi-Square (χ2)for dabigatran, rivaroxaban, apixaban and edoxaban when compared with warfarin.

RESULTS

The FAERS database contains significantly less death reports associated with all NOACs combined (14 917 out of 128 267 reports (11.63%); PRR=1.089; χ2=70.0; p=6.05e-17) than for warfarin (19 493 out of 153 911 reports (12.67%)). The numbers for rivaroxaban (6318 out of 64 512 reports or (9.79%); PRR=1.293; χ2=359.4; p=3.72e-80), apixaban (1693 out of 17 789 reports (9.52%); PRR=1.331; χ2=145.8; p=1.43e-33) and edoxaban (53 out of 755 reports (7.02%); PRR=1.804; χ2=21.18; p=4.18e-06) were favourable as compared with warfarin, while the numbers of fatalities co-reported with dabigatran (6989 out of 46 250 reports (15.11%); PRR=0.838; χ2=185.2; p=3.61e-42) were higher than for warfarin.

CONCLUSION

Overall, based on these CDR, NOACs appear to be associated with a mortality benefit over warfarin. Among NOACs, we observed remarkably similar for factor Xa inhibitors (rivaroxiban, apixaban and edoxaban) but unfavourable signal for the direct thrombin inhibitor (dabigatran). However, these data are clearly not sufficient to change the prescription patterns.

The JRC Nanomaterials Repository: A unique facility providing representative test materials for nanoEHS research

The European Commission has established a Nanomaterials Repository that hosts industrially manufactured nanomaterials that are distributed world-wide for safety testing of nanomaterials. In a first instance these materials were tested in the OECD Testing Programme. They have then also been tested in several EU funded research projects. The JRC Repository of Nanomaterials has thus developed into serving the global scientific community active in the nanoEHS (regulatory) research. The unique Repository facility is a state-of-the-art installation that allows customised sub-sampling under the safest possible conditions, with traceable final sample vials distributed world-wide for research purposes. This paper describes the design of the Repository to perform a semi-automated subsampling procedure, offering high degree of flexibility and precision in the preparation of NM vials for customers, while guaranteeing the safety of the operators, and environmental protection. The JRC nanomaterials are representative for part of the world NMs market. Their wide use world-wide facilitates the generation of comparable and reliable experimental results and datasets in (regulatory) research by the scientific community, ultimately supporting the further development of the OECD regulatory test guidelines.

ModelView for ModelDB: Online Presentation of Model Structure

ModelDB ( modeldb.yale.edu ), a searchable repository of source code of more than 950 published computational neuroscience models, seeks to promote model reuse and reproducibility. Code sharing is a first step; however, model source code is often large and not easily understood. To aid users, we have developed ModelView, a web application for ModelDB that presents a graphical view of model structure augmented with contextual information for NEURON and NEURON-runnable (e.g. NeuroML, PyNN) models. Web presentation provides a rich, simulator-independent environment for interacting with graphs. The necessary data is generated by combining manual curation, text-mining the source code, querying ModelDB, and simulator introspection. Key features of the user interface along with the data analysis, storage, and visualization algorithms are explained. With this tool, researchers can examine and assess the structure of hundreds of models in ModelDB in a standardized presentation without installing any software, downloading the model, or reading model source code.

The BioHub Knowledge Base: Ontology and Repository for Sustainable Biosourcing

Background

The motivation for the BioHub project is to create an Integrated Knowledge Management System (IKMS) that will enable chemists to source ingredients from bio-renewables, rather than from non-sustainable sources such as fossil oil and its derivatives.

Method

The BioHubKB is the data repository of the IKMS; it employs Semantic Web technologies, especially OWL, to host data about chemical transformations, bio-renewable feedstocks, co-product streams and their chemical components. Access to this knowledge base is provided to other modules within the IKMS through a set of RESTful web services, driven by SPARQL queries to a Sesame back-end. The BioHubKB re-uses several bio-ontologies and bespoke extensions, primarily for chemical feedstocks and products, to form its knowledge organisation schema.

Results

Parts of plants form feedstocks, while various processes generate co-product streams that contain certain chemicals. Both chemicals and transformations are associated with certain qualities, which the BioHubKB also attempts to capture. Of immediate commercial and industrial importance is to estimate the cost of particular sets of chemical transformations (leading to candidate surfactants) performed in sequence, and these costs too are captured. Data are sourced from companies’ internal knowledge and document stores, and from the publicly available literature. Both text analytics and manual curation play their part in populating the ontology. We describe the prototype IKMS, the BioHubKB and the services that it supports for the IKMS.

Availability

The BioHubKB can be found via http://biohub.cs.manchester.ac.uk/ontology/biohub-kb.owl.

High-performance web services for querying gene and variant annotation

Efficient tools for data management and integration are essential for many aspects of high-throughput biology. In particular, annotations of genes and human genetic variants are commonly used but highly fragmented across many resources. Here, we describe MyGene.info and MyVariant.info, high-performance web services for querying gene and variant annotation information. These web services are currently accessed more than three million times permonth. They also demonstrate a generalizable cloud-based model for organizing and querying biological annotation information. MyGene.info and MyVariant.info are provided as high-performance web services, accessible at http://mygene.info and http://myvariant.info . Both are offered free of charge to the research community.

A Young Scientists' Perspective on DBS: A Plea for an International DBS Organization

Our think tank tasked by the Dutch Health Council, consisting of Radboud University Nijmegen Honours Academy students with various backgrounds, investigated the implications of Deep Brain Stimulation (DBS) for psychiatric patients. During this investigation, a number of methodological, ethical and societal difficulties were identified. We consider these difficulties to be a reflection of a still fragmented field of research that can be overcome with improved organization and communication. To this effect, we suggest that it would be useful to found a centralized DBS organization. Such an organization makes it possible to 1) set up and maintain a repository, 2) facilitate DBS studies with a larger sample size, 3) improve communication amongst researchers, clinicians and ethical committees, and 4) improve communication between DBS experts and the public at large.

Why sharing matters for electrophysiological data analysis

We present the case for the sharing of electrophysiological datasets and tools for their analysis. Some of the problems, both sociological and technical, associated with improving the sharing of data and analysis tools are discussed. The work that has been done to try to improve data and code sharing in the electrophysiology area is reviewed. The sharing aspects of the current large projects in brain research are considered.

YPED: an integrated bioinformatics suite and database for mass spectrometry-based proteomics research

We report a significantly-enhanced bioinformatics suite and database for proteomics research called Yale Protein Expression Database (YPED) that is used by investigators at more than 300 institutions worldwide. YPED meets the data management, archival, and analysis needs of a high-throughput mass spectrometry-based proteomics research ranging from a single laboratory, group of laboratories within and beyond an institution, to the entire proteomics community. The current version is a significant improvement over the first version in that it contains new modules for liquid chromatography-tandem mass spectrometry (LC-MS/MS) database search results, label and label-free quantitative proteomic analysis, and several scoring outputs for phosphopeptide site localization. In addition, we have added both peptide and protein comparative analysis tools to enable pairwise analysis of distinct peptides/proteins in each sample and of overlapping peptides/proteins between all samples in multiple datasets. We have also implemented a targeted proteomics module for automated multiple reaction monitoring (MRM)/selective reaction monitoring (SRM) assay development. We have linked YPED's database search results and both label-based and label-free fold-change analysis to the Skyline Panorama repository for online spectra visualization. In addition, we have built enhanced functionality to curate peptide identifications into an MS/MS peptide spectral library for all of our protein database search identification results.

A dataset comprising 141 magnetic resonance imaging scans of 98 extant sea urchin species

BACKGROUND

Apart from its application in human diagnostics, magnetic resonance imaging (MRI) can also be used to study the internal anatomy of zoological specimens. As a non-invasive imaging technique, MRI has several advantages, such as rapid data acquisition, output of true three-dimensional imagery, and provision of digital data right from the onset of a study. Of particular importance for comparative zoological studies is the capacity of MRI to conduct high-throughput analyses of multiple specimens. In this study, MRI was applied to systematically document the internal anatomy of 98 representative species of sea urchins (Echinodermata: Echinoidea).

FINDINGS

The dataset includes raw and derived image data from 141 MRI scans. Most of the whole sea urchin specimens analyzed were obtained from museum collections. The attained scan resolutions permit differentiation of various internal organs, including the digestive tract, reproductive system, coelomic compartments, and lantern musculature. All data deposited in the GigaDB repository can be accessed using open source software. Potential uses of the dataset include interactive exploration of sea urchin anatomy, morphometric and volumetric analyses of internal organs observed in their natural context, as well as correlation of hard and soft tissue structures.

CONCLUSIONS

The dataset covers a broad taxonomical and morphological spectrum of the Echinoidea, focusing on 'regular' sea urchin taxa. The deposited files significantly expand the amount of morphological data on echinoids that are electronically available. The approach chosen here can be extended to various other vertebrate and invertebrate taxa. We argue that publicly available digital anatomical and morphological data gathered during experiments involving non-invasive imaging techniques constitute one of the prerequisites for future large-scale genotype-phenotype correlations.

A dataset comprising four micro-computed tomography scans of freshly fixed and museum earthworm specimens

Background

Although molecular tools are increasingly employed to decipher invertebrate systematics, earthworm (Annelida: Clitellata: ‘Oligochaeta’) taxonomy is still largely based on conventional dissection, resulting in data that are mostly unsuitable for dissemination through online databases. In order to evaluate if micro-computed tomography (μCT) in combination with soft tissue staining techniques could be used to expand the existing set of tools available for studying internal and external structures of earthworms, μCT scans of freshly fixed and museum specimens were gathered.

Findings

Scout images revealed full penetration of tissues by the staining agent. The attained isotropic voxel resolutions permit identification of internal and external structures conventionally used in earthworm taxonomy. The μCT projection and reconstruction images have been deposited in the online data repository GigaDB and are publicly available for download.

Conclusions

The dataset presented here shows that earthworms constitute suitable candidates for μCT scanning in combination with soft tissue staining. Not only are the data comparable to results derived from traditional dissection techniques, but due to their digital nature the data also permit computer-based interactive exploration of earthworm morphology and anatomy. The approach pursued here can be applied to freshly fixed as well as museum specimens, which is of particular importance when considering the use of rare or valuable material. Finally, a number of aspects related to the deposition of digital morphological data are briefly discussed.

Establishment and maintenance of a PBMC repository for functional cellular studies in support of clinical vaccine trials

A large repository of cryopreserved peripheral blood mononuclear cells (PBMCs) samples was created to provide laboratories testing the specimens from human immunodeficiency virus-1 (HIV-1) vaccine clinical trials the material for assay development, optimization, and validation. One hundred thirty-one PBMC samples were collected using leukapheresis procedure between 2007 and 2013 by the Comprehensive T cell Vaccine Immune Monitoring Consortium core repository. The donors included 83 human immunodeficiency virus-1 (HIV-1) seronegative and 32 HIV-1 seropositive subjects. The samples were extensively characterized for the ability of T cell subsets to respond to recall viral antigens including cytomegalovirus, Epstein-Barr virus, influenza virus, and HIV-1 using Interferon-gamma (IFN-γ) enzyme linked immunospot (ELISpot) and IFN-γ/interleukin 2 (IL-2) intracellular cytokine staining (ICS) assays. A subset of samples was evaluated over time to determine the integrity of the cryopreserved samples in relation to recovery, viability, and functionality. The principal results of our study demonstrate that viable and functional cells were consistently recovered from the cryopreserved samples. Therefore, we determined that this repository of large size cryopreserved cellular samples constitutes a unique resource for laboratories that are involved in optimization and validation of assays to evaluate T, B, and NK cellular functions in the context of clinical trials.

Childhood vesicoureteral reflux studies: registries and repositories sources and nosology

Despite several recent studies, the advisability of antimicrobial prophylaxis and certain imaging studies for urinary tract infections (UTIs) remains controversial. The role of vesicoureteral reflux (VUR) on the severity and re-infection rates for UTIs is also difficult to assess. Registries and repositories of data and biomaterials from clinical studies in children with VUR are valuable. Disease registries are collections of secondary data related to patients with a specific diagnosis, condition or procedure. Registries differ from indices in that they contain more extensive data. A research repository is an entity that receives, stores, processes and/or disseminates specimens (or other materials) as needed. It encompasses the physical location as well as the full range of activities associated with its operation. It may also be referred to as a biorepository. This report provides information about some current registries and repositories that include data and samples from children with VUR. It also describes the heterogeneous nature of the subjects, as some registries and repositories include only data or samples from patients with primary reflux while others also include those from patients with syndromic or secondary reflux.